PaperBLAST

PaperBLAST Hits for SwissProt::O07002 Aspartate-proton symporter; L-aspartate transporter (Bacillus subtilis (strain 168)) (520 a.a., MSKQGNFQKS...)

Show query sequence

>SwissProt::O07002 Aspartate-proton symporter; L-aspartate transporter (Bacillus subtilis (strain 168))
MSKQGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGL
VYAELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYWFPG
LTIKGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPITIIIVLIFH
FQPENLSVQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALIICI
IVSTIIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILDAIL
SPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLPFPS
WNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIVYWS
GWKTVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIGSFG
HGLGIISNPVDLILVAIGSLAIYYWAKYTGLPKAAIDYDK

Running BLASTp...

Found 250 similar proteins in the literature:

ASPP_BACSU / O07002 Aspartate-proton symporter; L-aspartate transporter from Bacillus subtilis (strain 168) (see paper)
TC 2.A.3.11.1 / O07002 The aspartate uptake permease, YveA from Bacillus subtilis (see 3 papers)
100% identity, 100% coverage

• function: Uptake of L-aspartate with the concomitant import of a proton. Can also transport aspartate hydroxamate and L-glutamate with lower affinity and efficiency
• substrates: L-aspartate hydroxamate, aspartate, glutamate

PFLU3323 putative amino-acid permease membrane protein from Pseudomonas fluorescens SBW25
58% identity, 96% coverage

• Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment
  Gómez, Biology letters 2022
  • “...dehydrogenases resource utilization 0 0 0 0 0 0 0 0 1 0 0 0 PFLU3323 putative amino acid permease membrane protein cytoplasmic membrane amino acid transporters resource utilization 0 0 0 0 0 0 0 0 1 0 0 0 PFLU3510 putative transmembrane protein cytoplasmic...”

PP1259 amino acid transporter, putative from Pseudomonas putida KT2440
59% identity, 96% coverage

• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

BPSS0330 putative amino-acid permease membrane protein from Burkholderia pseudomallei K96243
57% identity, 96% coverage

• Characterization and analysis of the Burkholderia pseudomallei BsaN virulence regulon
  Chen, BMC microbiology 2014
  • “...PKS biosynthesis locus 3.0 - (6.1) BPSS0328 Malate/L-lactate dehydrogenase 7.8 BPSS0329 Fatty aldehyde dehydrogenase 9.6 BPSS0330 Amino acid transporter 19.7 BPSS0331 Dihydrodipicolinate synthase 19.0 BPSS0332 Hydroxyproline-2-epimerase 21.7 BPSS0333 Deaminating oxidase subunit 18.8 BPSS0334 Deaminating oxidase subunit 24.7 BPSS0335 Deaminating oxidase subunit 20.1 BPSS0337 3.0 BPSS0338 Transposase...”

BCAM1265 putative amino acid permease from Burkholderia cenocepacia J2315
59% identity, 96% coverage

• Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
  O'Grady, Frontiers in cellular and infection microbiology 2011
  • “...Putative ironsulfur cluster protein 1.60 BCAM1213 Putative membrane protein 2.19 BCAM1255 Putative exported protein 1.88 BCAM1265 Putative amino acid permease 1.80 BCAM1316a Conserved hypothetical protein 2.00 BCAM1316b Conserved hypothetical protein 1.54 BCAM1335 Glycosyltransferase 1.52 BCAM1358 Gluconate 2-dehydrogenase cytochrome c subunit 1.52 BCAM1411 Putative short-chain dehydrogenase 1.53...”

ACX60_11495 APC family permease from Acinetobacter baumannii
56% identity, 98% coverage

• Genetic synergy between Acinetobacter baumannii undecaprenyl phosphate biosynthesis and the Mla system impacts cell envelope and antimicrobial resistance
  Noel, mBio 2024
  • “...variants were more common for ObgE (99%), UppS (99%), ActP (99%), the amino acid symporter ACX60_11495 (79%), and DUF817 (89%) ( Fig. 1 ). Thus, both 17978VU and 17978UN contain alleles representing the majority of published A. baumannii genomes. Next, the mlaF ::Kn ( mlaF )...”

EAM_RS12130 APC family permease from Erwinia amylovora ATCC 49946
55% identity, 96% coverage

• A complete twelve-gene deletion null mutant reveals that cyclic di-GMP is a global regulator of phase-transition and host colonization in Erwinia amylovora
  Kharadi, PLoS pathogens 2022
  • “...protein -5.30482975 0 EAM_RS05285 leucine-rich repeat domain-containing protein CDS leucine-rich repeat domain-containing protein -4.983851837 0 EAM_RS12130 APC family permease CDS APC family permease -4.936317974 1.0207E-268 EAM_RS00070 rbsD CDS D-ribose pyranase -4.850327937 0 EAM_RS09500 htpX CDS protease HtpX -4.366262025 1.1091E-160 EAM_RS10695 mglB CDS galactose/glucose ABC transporter substrate-binding...”

BPHYT_RS17540 L-aspartate/L-glutamate/L-glutamine:H+ symporter from Burkholderia phytofirmans PsJN
38% identity, 97% coverage

• mutant phenotype: Specifically important for utilization of glutamine, glutamate, or asparagine.

AIMA_BACSU / Q45577 Glutamate/serine transporter AimA; Amino acid importer A from Bacillus subtilis (strain 168) (see 2 papers)
NP_388094 putative H+/amino acid transporter from Bacillus subtilis subsp. subtilis str. 168
37% identity, 94% coverage

• function: Major glutamate and serine transporter (PubMed:32743959, PubMed:33481774). Cannot transport threonine (PubMed:32743959). AimA is the major glutamate transporter under standard growth conditions when glutamate is not limiting in the medium (PubMed:33481774).
  disruption phenotype: Loss of the gene confers resistance to both serine and its toxic analog serine hydroxamate (PubMed:32743959). Deletion mutant is still able to transport serine, but the deletion of the three permease-encoding genes aimA (ybeC), ybxG and bcaP results in an unprecedented resistance to serine up to 100 mM (PubMed:32743959).
• Resistance to serine in Bacillus subtilis: identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism.
  Klewing, Environmental microbiology 2020
  • GeneRIF: Resistance to serine in Bacillus subtilis: identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism.

LSA1424 Putative L-aspartate transport protein from Lactobacillus sakei subsp. sakei 23K
34% identity, 94% coverage

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...cationic amino acid transport protein 0.7 LSA1415 lsa1415 Putative amino acid/polyamine transport protein 1.1 0.7 LSA1424 lsa1424 Putative L-aspartate transport protein -1.4 -0.9 -1.2 LSA1435 lsa1435 Putative amino acid:H(+) symporter 1.0 0.8 LSA1496 lsa1496 Putative glutamine/glutamate ABC transporter, ATP-binding subunit 1.2 LSA1497 lsa1497 Putative glutamine/glutamate ABC...”

SE2021 amino acid transporter from Staphylococcus epidermidis ATCC 12228
SERP2034 amino acid permease family protein from Staphylococcus epidermidis RP62A
33% identity, 88% coverage

• Evolution of antibiotic cross-resistance and collateral sensitivity in Staphylococcus epidermidis using the mutant prevention concentration and the mutant selection window
  Lozano-Huntelman, Evolutionary applications 2020
  • “...of resistance that may be due to novel or nontarget mutations (SE_p103, SE0706, SE608, SE1860, SE2021) and are shared between both strains (Table 2 ). Table 2 Resistance conferring mutations Resistance Associated gene or plasmid Strains Type of mutation References Chromosomal position Nucleotide substitution Amino acid...”
  • “...n/a n/a n/a SE0075 TET R1 TET R2 Stop gained * 74230 C T p.Gln281* SE2021 TET R1 TET R2 Missense * 2059908 G C p.Met201Ile Doxycycline SE_p103 DOX R1 DOX R2 Upstream gene variant * 3147 T C n/a SE0706 DOX R1 DOX R2 Missense...”
• A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation
  Balasubramanian, Frontiers in microbiology 2018
  • “...dehydrogenase 2.6290 7.14E-09 glyA Serine hydroxymethyltransferase -2.3637 4.36E-33 secY Preprotein translocase SecY subunit 2.5474 1.38E-20 SERP2034 Amino acid permease family protein 3.3899 3.46E-17 SERP2043 Peptidase M42 family -3.4218 1.54E-47 cysJ Sulfite reductase (NADPH) flavoprotein alpha-component -2.1931 2.60E-23 cysH Phosophoadenylyl-sulfate reductase -2.5134 3.48E-28 arcA Arginine deiminase -2.3875...”

SAR2540 putative amino acid permease from Staphylococcus aureus subsp. aureus MRSA252
32% identity, 92% coverage

• Dysregulation of Cell Envelope Homeostasis in Staphylococcus aureus Exposed to Solvated Lignin
  Grossman, Applied and environmental microbiology 2022 (secret)

SAMSHR1132_RS12095 APC family permease from Staphylococcus argenteus
32% identity, 92% coverage

• Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus
  Zhang, BMC genomics 2017
  • “...+ 3141 SAOUHSC_00355 Uncharacterized protein YxeA + + 2176 SAOUHSC_00867 Unknown + + -# 2198 SAMSHR1132_RS12095 Probable amino acid-proton symporter YbeC +* + S.simiae , S. caprae (20) 2192 SAMSHR1132_RS03980 Uncharacterized protein YwqG +* + S. lugdunensis 2211 SAMSHR1132_RS02265 Unknown +* + -# 2234 a, *,present...”

SAFDA_2310 APC family permease from Staphylococcus aureus
NWMN_2349 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
32% identity, 92% coverage

• Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations
  Ruparel, Drug target insights 2023
  • “...2.47 0.001 73 drm Phosphopentomutase 2.45 0 74 SAFDA_0392 Cobalamin synthesis protein 2.45 0.01 75 SAFDA_2310 Amino acid transporter 2.43 0.008 76 SAFDA_2453 2-dehydropantoate 2-reductase 2.43 0.002 77 sarA Transcriptional regulator SarA 2.43 2.11E-07 78 SAFDA_1135 Hypothetical protein 2.43 0.003 79 nreA NreA protein; GAF domain...”
• Inactivation of the Ecs ABC transporter of Staphylococcus aureus attenuates virulence by altering composition and function of bacterial wall
  Jonsson, PloS one 2010
  • “...IIBC component 2.4 NWMN_2311 amino acid ABC transporter ATP-binding protein 2.0 NWMN_2343 drug transporter 0.5 NWMN_2349 amino acid permease 0.6 NWMN_2370 transporter 0.5 0.5 NWMN_2412 ABC transporter ATP-binding protein 1.9 NWMN_2413 ABC transporter permease 4.5 NWMN_2458 cation transporter E1-E2 family ATPase 1.8 2.6 NWMN_2521 permease domain-containing...”

SAEMRSA15_RS12955 APC family permease from Staphylococcus aureus subsp. aureus HO 5096 0412
32% identity, 92% coverage

• A functional menadione biosynthesis pathway is required for capsule production by Staphylococcus aureus
  Altwiley, Microbiology (Reading, England) 2021
  • “...ligase 0.00139006 SAEMRSA15_RS12840 glycerate kinase 0.00280998 SAEMRSA15_RS11120 ATP synthase subunit I 0.0030996 SAEMRSA15_RS02630 amidohydrolase 0.00366703 SAEMRSA15_RS12955 APC family permease 0.00386528 SAEMRSA15_RS13455 LrgB family protein 0.00400753 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase 0.00507518 SAEMRSA15_RS09800 metal-dependent hydrolase 0.00516556 graR response regulator transcription factor GraR/ApsR 0.00546077 rsmG 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG 0.00895798...”

MW2374 ORFID:MW2374~hypothetical protein, similar to amino acid transporter from Staphylococcus aureus subsp. aureus MW2
32% identity, 92% coverage

• Rsp inhibits attachment and biofilm formation by repressing fnbA in Staphylococcus aureus MW2
  Lei, Journal of bacteriology 2011
  • “...MW0114 MW0115 MW0147 MW0148 MW0253 MW2370 MW2261 MW0218 MW0958 MW2374 2.4 3.7 2.6 2.2 4.1 3.5 4.3 2.0 3.9 2.1 2.2 2.3 opuD proP Osmoprotectant transporter, BCCT...”

SA2239 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV2450 amino acid transporter from Staphylococcus aureus subsp. aureus Mu50
32% identity, 92% coverage

• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...3.4 15 stable rplB SA2236 50S ribosomal protein L2 sa_c4888s4195_a_at * 3.1 5 stable rplC SA2239 50S ribosomal protein L3 sa_c4880s4187_at 4.0 5 30 rplD SA2238 50S ribosomal protein L4 sa_c4848s4156_at * 2.8 15 stable rplE SA2227 50S ribosomal protein L5 sa_c9951s8647_at * 2.8 15 stable...”
  • “...5.8 15 15 rplB SA2236 50S ribosomal protein L2 sa_c4888s4195_a_at * 4.8 5 5 rplC SA2239 50S ribosomal protein L3 sa_c4848s4156_at * 4.9 15 15 rplE SA2227 50S ribosomal protein L5 sa_c9951s8647_at * 5.3 15 15 rplF SA2224 50S ribosomal protein L6 sa_c7621s6634_a_at * 4.6 5...”
• Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus
  Seidl, BMC microbiology 2009
  • “...part) OpuCB 1.9 1.1 *SA2237 NWMN_2347 opuCA glycine betaine/carnitine/choline ABC transporter (ATP-binding) OpuCA 2.6 1.0 SA2239 NWNM_2349 similar to amino acid transporter 2.2 1.1 SA2443 NWMN_2549 similar to accessory secretory protein Asp3 2.0 1.2 SA2444 NWMN_2550 similar to accessory secretory protein Asp2 2.3 1.3 Partially controlled...”
• An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus
  Campbell, Antimicrobial agents and chemotherapy 2012
  • “...2.1 2.0 2.7 7.3 6.2 4.6 4.3 4.1 4.1 SAV2450 SAR2537 NA opuCB SAV2446 opuCC SACOL2449 SAV1866 SAS2251 SAV2359 NA NA hrtB hrtA Energy metabolism SAV0523 SAV2536...”
  • “...iron availability (3, 29). Genes SAS0283, SAV0838, and SAV2450, encoding several putative amino acid transporters, are also upregulated. The genes opuCB and...”

EQ812_06165 APC family permease from Staphylococcus lugdunensis
32% identity, 92% coverage

• Comparative proteomics analysis of biofilms and planktonic cells of Enterococcus faecalis and Staphylococcus lugdunensis with contrasting biofilm-forming ability
  Cho, PloS one 2024
  • “...proteins were annotated, including YycI domain-containing protein ( EQ_ EQ812_05590 ), APC family permease ( EQ812_06165 ), NupC/NupG family nucleoside CNT transporter ( EQ812_06755 ), etc., to membrane, transmembrane or transmembrane helix. The resulting pathway networks were analyzed as depicted in Fig 3a and 3b ....”
  • “...EQ812_05230, ARJ28872.1 = EQ812_01650, ARJ30410.1 = EQ812_09225, ARJ29784.1 = EQ812_07770, ARJ28661.1 = HMPREF3225_02342, ARJ28536.1 = EQ812_06165, ARJ30089.1 = rihC, ARJ30169.1 = HMPREF3225_00709, ARJ30675.1 = yabA, ARJ29954.1 = HMPREF3225_00598, ARJ28686.1 = HMPREF3225_02322, ARJ29222.1 = HMPREF3225_00188. e and f . Gene ontology (GO) classification. The differentially expressed proteins...”

KAR41_04250 APC family permease from Periweissella fabalis
33% identity, 95% coverage

• Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
  Fanelli, Microbiology spectrum 2023
  • “...diphosphokinase folK NA NA KAR41_07600 KAR50_07300 KAR53_10105 KAR63_02150 Riboflavin biosynthetic cluster ribABCDEFHU NA NA KAR41_01765-01780, KAR41_04250, KAR41_06605 KAR50_01690-01705, KAR50_01585, KAR50_06090 KAR53_07575-07590, KAR53_04320, KAR53_02345 NA Starch metabolism Oligo-1,6-glucosidase/-glucosidase malL / agl NA NA KAR41_06265 KAR50_01875 KAR53_01435 KAR63_01965 a T , type strain; NA, not annotated; CLA, conjugated...”

Saci_2189 conserved Archaeal membrane protein from Sulfolobus acidocaldarius DSM 639
32% identity, 84% coverage

• Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius
  Chauhan, Frontiers in microbiology 2021
  • “...Finally, the LysM iModulon consists of three poorly characterized genes: Saci_1028 , Saci_2071 , and Saci_2189 . Saci_1028 putatively codes for an acetyl-ornithine aminotransferase family protein and Saci_2189 putatively codes for an APC family permease (potentially an aspartate-proton symporter), while Saci_2071 is completely uncharacterized, encoding a...”

PSLF89_180 APC family permease from Piscirickettsia salmonis LF-89 = ATCC VR-1361
32% identity, 97% coverage

• Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis
  Ortiz-Severín, Frontiers in microbiology 2021
  • “...an aromatic amino acid transport family protein (PSLF89_3306), and various amino acid permeases (PSLF89_3168, PSLF89_2573, PSLF89_180 and PSLF89_817). This correlates with an underrepresentation of GO terms related to transmembrane transport (C/S comparison), and amino acid metabolic processes (C/S and A/S comparisons), which was indicative of a...”

SiRe_1024 APC family permease from Saccharolobus islandicus REY15A
34% identity, 80% coverage

• Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A
  Huang, Frontiers in microbiology 2020
  • “...factor type A SiRe_1011 S304, T314, T327 0.641, 0.677, 0.736 von Willebrand factor type A SiRe_1024 T6 0.368 Amino acid permease-associated region SiRe_1033 T257 0.651 Biotin/lipoate A/B protein ligase SiRe_1169 S35 0.679 Uncharacterized protein SiRe_1186 S385 1.310 Valyl-tRNA synthetase SiRe_1199 S483 1.662, 1.537 Phosphoenolpyruvate synthase SiRe_1202...”

lpg0228 amino acid permease family protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
34% identity, 98% coverage

• Mammalian Solute Carrier (SLC)-like transporters of Legionella pneumophila
  Best, Scientific reports 2018
  • “...SLC7a1 (0.953) LstD (Lpg0049) 25% 44% Cationic amino acids (arginine, lysine, ornithine) SLC7a5 (0.954) LstE (Lpg0228) 25% 42% Cationic amino acids (arginine, lysine, ornithine) SLC7a1 (0.848) LstF (Lpg0281) 25% 53% Cationic amino acids (arginine, lysine, ornithine) SLC7a1 (0.985) LstG (Lpg0970) 25% 44% Cationic amino acids (arginine,...”
• Transcriptomic changes of Legionella pneumophila in water
  Li, BMC genomics 2015
  • “...2.51 4.11 4.80 Amino acid permeases lpg0970 1.91 3.42 5.45 Amino acid permease family protein lpg0228 2.77 5.41 6.13 Amino acid transporter lpg0049 3.27 Ferrous iron transporter lpg2658 feoA 2.56 2.80 4.47 Ferrous iron transporter lpg2657 feoB 3.10 5.23 DotA lpg2686 dotA 1.35 DotC lpg2675 dotC...”
• Small Regulatory RNA and Legionella pneumophila
  Faucher, Frontiers in microbiology 2011
  • “...lpr0006 74969 74729 240 lpg0066 Weissenmayer et al. ( 2011 ) lpr0008 262101 262297 196 lpg0228 Weissenmayer et al. ( 2011 ) lpr0009 291705 291852 147 lpg0245 Weissenmayer et al. ( 2011 ) lpr0012 369510 369457 53 lpg0320 Weissenmayer et al. ( 2011 ) lpr0015 425773...”

SSO1906 Amino acid transporter related protein from Sulfolobus solfataricus P2
35% identity, 69% coverage

• Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus
  Song, Nucleic acids research 2013
  • “...CG TA C ++ 1.7 Sso0977 G TT CG TATGT CG AA C ++ 6 Sso1906 G TA CG ATTACA G TAT + 9 Sso0157 G TT C TAAAAT CG TA C ++ 11 Sso0684 G TT CG GAAAT C AAA C ++ 42 Sso2336 ATA...”
  • “...ChIP-enriched regions: Sso0571 ( A ), gltB ( B ), leuA -2 ( C ), Sso1906 ( D ), Sso2043 ( E ), Sso2336 ( F ), Sso2497 ( G ) and Sso2824 ( H ). Zoomed profiles are plotted as the log 2 of enrichment...”

SSO2043 Amino acid transporter related protein from Sulfolobus solfataricus P2
35% identity, 69% coverage

• Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus
  Song, Nucleic acids research 2013
  • “...assays Predicted K D (nM) Closest ORF Predicted binding motif Observed in vitro binding 0.3 Sso2043 G TA CG ATTAG CG TA C ++ 1.7 Sso0977 G TT CG TATGT CG AA C ++ 6 Sso1906 G TA CG ATTACA G TAT + 9 Sso0157 G...”
  • “...A ), gltB ( B ), leuA -2 ( C ), Sso1906 ( D ), Sso2043 ( E ), Sso2336 ( F ), Sso2497 ( G ) and Sso2824 ( H ). Zoomed profiles are plotted as the log 2 of enrichment fold (y-axis) versus genomic...”
• The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation
  Nguyen-Duc, BMC genomics 2013
  • “...Sso1463 1321798 1323084 overlap (98%) - -* III Sso1890 1705187 1705830 Inside - -* III Sso2043 1859092 1860291 overlap (75%) - + II Sso2159 1985046 1985784 Inside - -* III Sso2233 2050931 2052374 Including + -* I Sso2289 2099312 2099902 Inside - -* III Sso2309 2111358...”

PSLF89_3168 APC family permease from Piscirickettsia salmonis LF-89 = ATCC VR-1361
32% identity, 98% coverage

• Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis
  Ortiz-Severín, Frontiers in microbiology 2021
  • “...and PSLF89_725), an aromatic amino acid transport family protein (PSLF89_3306), and various amino acid permeases (PSLF89_3168, PSLF89_2573, PSLF89_180 and PSLF89_817). This correlates with an underrepresentation of GO terms related to transmembrane transport (C/S comparison), and amino acid metabolic processes (C/S and A/S comparisons), which was indicative...”

Saci_1127 amino acid permease from Sulfolobus acidocaldarius DSM 639
34% identity, 72% coverage

• Impact of nutrient excess on physiology and metabolism of <i>Sulfolobus acidocaldarius</i>
  Sedlmayr, Frontiers in microbiology 2024
  • “...saci_1859 1.6 NA saci_1860 2.1 NA saci_1861 1.9 NA saci_1862 1.8 NA EAmino acid transport saci_1127 Na+/proline symporter 2.3 1.2 saci_1745 Amino acid transporter 2.7 NA saci_1760 ABC-type transport system 2.1 1.2 saci_1835 Amino acid transporter 2.4 1.5 saci_2181 Amino acid transporter 2.1 NA GCarbohydrate transport...”
  • “...on amino acids and glucose ( Vetter, 2020 ). Among these, the differential expression of saci_1127 with increasing nutrient availability and of saci_1835 when comparing Overfeed against High and Low was observed. Glutamate enters the TCA cycle via oxidative deamination by glutamate dehydrogenase ( saci_0155 )...”
• Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements
  Anderson, Genome biology and evolution 2017
  • “...0 Phosphate transport regulator (distant homolog of PhoU) Saci_0783 0 3 0 NAD (FAD)-dependent dehydrogenase Saci_1127 0 0 0 Amino acid permease Variation within YNP 2012 Population Saci_1274 0 2 0 Uncharacterized membrane protein, required for N-linked glycosylation Both variable within the NG population Saci_1320 0...”

SSO1069 Amino acid transporter from Sulfolobus solfataricus P2
36% identity, 65% coverage

• Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus
  Tachdjian, Journal of bacteriology 2006
  • “...SSO1893 SSO1894 SSO0489 SSO0490 SSO2469 SSO0786 SSO1009 SSO1069 SSO1173 SSO2726 SSO2728 SSO3047 SSO3048 SSO1274 SSO1275 SSO1276 oppD SSO1277 oppF SSO1281...”

FTN_0004 aspartate/glutamate transporter from Francisella tularensis subsp. novicida U112
29% identity, 90% coverage

• Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance
  Felix, Scientific reports 2021
  • “...putP FTN_0299 Proline/Na+symporter 1.206589507 0.001401361 FTN_0452 Hypothetical protein 1.274923951 4.08167E08 FTN_0006 Hypothetical protein 1.345660313 1.02878E06 FTN_0004 Aspartate/glutamate transporter 1.352713527 0.003023321 FTN_0829 Hypothetical protein 1.454738617 6.98601E07 FTN_1388 Oxidoreductase 1.515433578 0.000565317 FTN_1267 ABC transporter ATP-binding protein 1.74578111 3.84443E09 lptC FTN_0904 Lipopolysaccharide export ABC transporter periplasmic protein 1.999604273 1.63282E05...”

Syncc9902_2241 amino acid permease family protein from Synechococcus sp. CC9902
29% identity, 98% coverage

• Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes
  Tai, PloS one 2011
  • “...0.108 Syncc9902_2149 hypothetical Inf Inf 8/2.0 A nh Syncc9902_2225 hypothetical Inf Inf 4/1.2 A nh Syncc9902_2241 amino acid permease family Inf Inf 15/2.0 A nh Syncc9902_0591 hypothetical 0.465 0.466 89/12.4 C 2.850 Syncc9902_0952 Conserved hypothetical 0.216 0.218 100/26.4 C 2.075 Syncc9902_1111 Peptidase S13, D-Ala- D-Ala carboxypeptidase...”

PSLF89_2573 APC family permease from Piscirickettsia salmonis LF-89 = ATCC VR-1361
33% identity, 78% coverage

• Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis
  Ortiz-Severín, Frontiers in microbiology 2021
  • “...PSLF89_725), an aromatic amino acid transport family protein (PSLF89_3306), and various amino acid permeases (PSLF89_3168, PSLF89_2573, PSLF89_180 and PSLF89_817). This correlates with an underrepresentation of GO terms related to transmembrane transport (C/S comparison), and amino acid metabolic processes (C/S and A/S comparisons), which was indicative of...”

FTN_0319 amino acid-polyamine-organocation family protein from Francisella tularensis subsp. novicida U112
31% identity, 73% coverage

• Exploitation of host cell biology and evasion of immunity by francisella tularensis
  Asare, Frontiers in microbiology 2010
  • “...synthetase FTN_0199 cyoE Heme O synthase FTN_0211 pcp Pyrrolidone carboxylate peptidase FTN_0218 nfnB Dihydropteridine reductase FTN_0319 Amino acidpolyamineorganocation family protein FTN_0343 Aminotransferase FTN_0358 tRNA-methylthiotransferase MiaB protein FTN_0420 SAICAR synthetase/phosphoribosylamine-glycine ligase FTN_0483 Bifunctional NMN adenylyltransferase/nudix hydrolase FTN_0496 Slt Soluble lytic murein transglycosylase FTN_0504 Lysine decarboxylase FTN_0507 gcvP1...”
• Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
  Asare, Environmental microbiology 2010
  • “...carboxylylate peptidase 1 1 # tnfn1_pw060418p03q177 FTN_0211 pcp pyrrolidone carboxylylate peptidase 3 4 # tnfn1_pw060418p01q187 FTN_0319 amino acid-polyamine-organocation family protein 6 7 tnfn1_pw060323p06q113 FTN_0420 SAICAR synthetase/phosphoribosylamine-glycine ligase 7 5 tnfn1_pw060323p05q182 FTN_0504 lysine decarboxylase 4 4 tnfn1_pw060510p01q124 FTN_0507 gcvP1 glycine cleavage system P protein, subunit 1 5...”
• Molecular bases of proliferation of Francisella tularensis in arthropod vectors
  Asare, Environmental microbiology 2010
  • “...carboxylylate peptidase 1 1 # tnfn1_pw060418p03q177 FTN_0211 pcp pyrrolidone carboxylylate peptidase 3 4 # tnfn1_pw060418p01q187 FTN_0319 amino acid-polyamine-organocation family protein 6 7 tnfn1_pw060323p06q113 FTN_0420 SAICAR synthetase/phosphoribosylamine-glycine ligase 7 5 tnfn1_pw060323p05q182 FTN_0504 lysine decarboxylase 4 4 tnfn1_pw060510p01q124 FTN_0507 gcvP1 glycine cleavage system P protein, subunit 1 5...”

FTN_0898 amino acid permease from Francisella tularensis subsp. novicida U112
28% identity, 95% coverage

• Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance
  Felix, Scientific reports 2021
  • “...infection bacteriophage resistance protein 1.909345488 0.006797082 FTN_0655 N6-adenine-specific methylase 1.645819843 0.009836595 FTN_1348 Acetyltransferase 1.493386099 3.68028E07 FTN_0898 Amino acid permease 1.424644622 3.5435E06 panD FTN_1354 Aspartate 1-decarboxylase 1.405501066 0.006567341 FTN_0862 Hypothetical protein 1.276557703 0.000969217 ung FTN_1486 Uracil-DNA glycosylase 1.261354286 4.40904E07 FTN_0308 Membrane protein of unknown function 1.255628185 0.000806353...”
• Francisella-arthropod vector interaction and its role in patho-adaptation to infect mammals
  Akimana, Frontiers in microbiology 2011
  • “...Hypothetical membrane protein FTN_0889 Helix-turn-helix family protein FTN_0891 Holliday junction DNA helicase, subunit B ruvB FTN_0898 Amino acid permease FTN_0900 Protein of unknown function with predicted hydrolase and phosphorylase activity FTN_0921 FKBP-type peptidyl-prolyl cis -trans isomerase FTN_0928 Sulfate adenylyltransferase subunit 2 cysD FTN_0949 50S ribosomal protein...”

FTH_0800 APC family amino acid-polyamine-organocation transporter from Francisella tularensis subsp. holarctica OSU18
31% identity, 73% coverage

• Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
  Horák, Soft matter 2012
  • “...cyt FTH_0719 Ribonuclease E 95.95/7.12 cyt cyt FTH_0799 Bifunctional 1-pyrroline-5-carboxylate dehydrogenase/proline dehydrogenase 150.39/7.97 cyt cyt FTH_0800 APC family amino acidpolyamine-organocation transporter 55.00/9.27 CM TMH FTH_0836 Preprotein translocase subunit 12.87/10.55 CM SPI FTH_0837 RND superfamily resistance-nodulation-cell division antiporter 69.67/9.52 CM TMH/SPI FTH_0886 Probable membrane protease subunit HflK...”
  • “...IV pilus assembly protein 23.00/9.58 ? SPI FTH_0799 Bifunctional 1-pyrroline-5-carboxylate dehydrogenase/proline dehydrogenase 150.39/7.97 cyt cyt FTH_0800 APC family amino acid-polyamine-organocation transporter 55.00/9.27 CM TMH FTH_0837 RND superfamily resistance-nodulation-cell division antiporter 69.67/9.52 CM TMH/SPI FTH_0881 Conserved hypothetical protein 54.87/8.16 CM TMH FTH_0886 Probable membrane protease subunit HflK...”

GBAA0593 amino acid permease family protein from Bacillus anthracis str. 'Ames Ancestor'
27% identity, 76% coverage

• The global transcriptional responses of Bacillus anthracis Sterne (34F2) and a Delta sodA1 mutant to paraquat reveal metal ion homeostasis imbalances during endogenous superoxide stress
  Passalacqua, Journal of bacteriology 2007
  • “...GBAA0350 GBAA0351 GBAA0378 GBAA0528 GBAA0532 GBAA0534 GBAA0535 GBAA0593 GBAA0615 GBAA0616 GBAA0617 GBAA0618 GBAA0739 Sterne with LB plus paraquat vs LB alone...”

EP10_000138 amino acid permease from Geobacillus icigianus
27% identity, 82% coverage

• The Transcriptomic Response of Cells of the Thermophilic Bacterium <i>Geobacillus icigianus</i> to Terahertz Irradiation
  Peltek, International journal of molecular sciences 2024
  • “...carboxylic acid transporter gene (EP10_002156) and genes encoding transporters of glutamine and other amino acids (EP10_000138, EP10_001536, EP10_002622, EP10_00263, EP10_002624, and EP10_002625). These data indicate the beginning of a recovery of systems responsible for the utilization of amino acids and of other carbon sources from the...”
  • “...0.1) 10 min after THz irradiation of G. icigianus cells. Locus ID log2FoldChange padj Protein/Enzyme EP10_000138 1.355826 0.000163 Putative amino acid permease YhdG EP10_000693 0.863538 0.084168 5-oxoprolinase subunit A EP10_001536 0.875392 0.066384 Glutamine-binding periplasmic protein EP10_002112 0.894702 0.098217 Threonine synthase EP10_002113 1.012461 0.041217 Homoserine kinase EP10_002156...”

6f34A / Q5L1G5 Crystal structure of a bacterial cationic amino acid transporter (cat) homologue bound to arginine. (see paper)
28% identity, 84% coverage

• Ligands: peptide; arginine; cholesterol (6f34A)

Q5L1G5 Amino acid transporter from Geobacillus kaustophilus (strain HTA426)
28% identity, 84% coverage

• They all rock: A systematic comparison of conformational movements in LeuT-fold transporters.
  Licht, bioRxiv : the preprint server for biology 2024
  • “...alanine X-ray 3.24 Mj ApcT Q58026 3GIA (A) I op n/a X-ray 2.32 Gk ApcT Q5L1G5 5OQT (A) I op alanine X-ray 2.86 C _BasC A8UCQ5 6F2G (A) I op n/a X-ray 2.92 Hs BAT1 P82251 6LI9 (B) I op arginine cryo-EM 2.3 Ec GadC P63235...”
• Potent Inhibition of Macropinocytosis by Niclosamide in Cancer Cells: A Novel Mechanism for the Anticancer Efficacy for the Antihelminthic
  Sennoune, Cancers 2023
  • “...Aquifex aeolicus VF5 leucine transporter LeuT (O67854) (PDB: 6NLE), Geobacillus kaustophilus cationic amino acid transporter (Q5L1G5) (PDB: 6F34, 5OQT), and Carnobacterium sp. AT7 amino acid transporter asc (A8UCQ5) (PDB: 6F2W). This theoretically deduced SLC38A5 structure was docked with niclosamide, pyrvinium and glutamine molecules using AutoDock/Vina with...”
• Structural basis for amino acid transport by the CAT family of SLC7 transporters
  Jungnickel, Nature communications 2018
  • “...gradient within the APC superfamily. Methods Protein expression and purification The gene encoding GkApcT (Uniprot Q5L1G5) was amplified from Geobacillus kaustophilus genomic DNA and cloned into the pWaldo-GFP vector using primers detailed in Supplementary Table 1 49 . Variant forms of GkApcT were made through site...”

lmo0645 similar to amino acid transporter from Listeria monocytogenes EGD-e
25% identity, 82% coverage

• Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling
  Schauer, BMC genomics 2010
  • “...protein, putative permease no 7.2 3.0 lmo2770 -glutamylcysteine synthetase and cyanophycin synthetase no 5.8 2.3 lmo0645 amino acid transporter no 4.9 1.5 6 serC (lmo2825) phosphoserine aminotransferase possible 5.7 3.5 5 lmo0650 conserved membrane protein possible 2.8 2.0 metabolism of nucleotides and nucleic acids lmo0787 amino...”
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...lmo0286 lmo0519b lmo0537 lmo0560b hisD hisZ lmo0611 lmo0645 lmo0787 lmo0798 lmo0802 lmo0837 lmo0841 lmo0847 lmo0897 lmo0912a lmo0945 lmo0947 lmo0960 lmo0981...”

lp_0861 amino acid transport protein (putative) from Lactobacillus plantarum WCFS1
26% identity, 75% coverage

• Identification and functional characterization of the Lactococcus lactis CodY-regulated branched-chain amino acid permease BcaP (CtrA)
  den, Journal of bacteriology 2006
  • “...Streptococcus thermophilus CNRZ1066 BcaP (CtrA) CtrA YP_187408 ZP_00384379 Lp_0861 Lin0648 NP_814667 ZP_00238192 YhdG YfnA Str1361 465 469 482 464 465 463 463...”

lin0648 similar to amino acid transporter from Listeria innocua Clip11262
26% identity, 82% coverage

• Identification and functional characterization of the Lactococcus lactis CodY-regulated branched-chain amino acid permease BcaP (CtrA)
  den, Journal of bacteriology 2006
  • “...thermophilus CNRZ1066 BcaP (CtrA) CtrA YP_187408 ZP_00384379 Lp_0861 Lin0648 NP_814667 ZP_00238192 YhdG YfnA Str1361 465 469 482 464 465 463 463 471 465 467...”

EF0929 amino acid permease family protein from Enterococcus faecalis V583
26% identity, 74% coverage

• Comparative genomic analysis of pathogenic and probiotic Enterococcus faecalis isolates, and their transcriptional responses to growth in human urine
  Vebø, PloS one 2010
  • “...enhanced at t 30 , while the transcription of three amino acid permease genes (EF0635, EF0929 and EF2377) and two operons encoding amino acid transporters (EF0247-46 and EF0761-60) was reduced in all three strains at the same time point ( Table S1 ). These observations indicate...”

T1E_3208 amino acid permease from Pseudomonas putida DOT-T1E
27% identity, 88% coverage

• Insights into the susceptibility of Pseudomonas putida to industrially relevant aromatic hydrocarbons that it can synthesize from sugars
  García-Franco, Microbial cell factories 2023
  • “...these were found in operons related to the transport of amino acids (i.e., T1E_2666, T1E_2667, T1E_3208, T1E_0341, T1E_3315) and potassium (T1E_2369) (Additional file 7 : Table S4). While some transporters were downregulated in the presence of trans- cinnamic acid (i.e., T1E_1254, T1E_3944, T1E_0320, T1E_0710, etc.), this...”

BCAP_BACSU / O07576 Branched-chain amino acid permease BcaP; BCAA permease from Bacillus subtilis (strain 168) (see 4 papers)
BSU09460 branched-chain amino acid transporter from Bacillus subtilis subsp. subtilis str. 168
25% identity, 86% coverage

• function: Branched-chain amino acid transport system which is involved in the uptake of isoleucine, valine and probably leucine (PubMed:25645558). Can also transport threonine, and is active as a minor serine permease (PubMed:25645558, PubMed:32743959). May be an amino acid permease of rather broad specificity, because several amino acids, albeit at 100-fold excess, are able to prevent isoleucine uptake (PubMed:25645558). Probably does not transport methionine (PubMed:25645558). Together with BraB and BrnQ, plays an important role in the activation of CodY, a branched-chain amino acid-responsive transcriptional regulator that controls the expression of several dozen transcription units in B.subtilis (PubMed:25645558).
  disruption phenotype: Mutant is still able to take up isoleucine, leucine and valine (PubMed:25645558). Deletion of the gene confers a weak resistance to growth inhibition by serine (PubMed:32743959). The deletion of the three permease-encoding genes aimA (ybeC), ybxG and bcaP results in an unprecedented resistance to serine up to 100 mM (PubMed:32743959).
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...coli BSU39390 No BSU09130 No Yes BSU36900 Yes Yes BSU09460 No BSU33330 No Yes Yes Yes 3.6.3.14 3.6.3.14 Yes S protein of tryptophan ECF transporter Methionine...”

BA3141 amino acid permease family protein from Bacillus anthracis str. Ames
27% identity, 82% coverage

• Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis
  Han, Journal of bacteriology 2006
  • “...(BA3139), UvrC-like protein (BA3140), and amino acid permease (BA3141). B. Flanking region of insertion boundary. The orthologs of genes are shown as arrows of...”

SCO5977 amino acid permease from Streptomyces coelicolor A3(2)
26% identity, 88% coverage

• A Second Gamma-Glutamylpolyamine Synthetase, GlnA2, Is Involved in Polyamine Catabolism in Streptomyces coelicolor
  Krysenko, International journal of molecular sciences 2022
  • “...was also tested with promoters of other genes of the polyamine utilization pathway: sco5676 , sco5977 , sco6960 . These potential targets were identified based on their localization in the genome closely to genes that are involved in the utilization of polyamines as reported by [...”
  • “...regulated by EpuRII: sco5676 , coding for a putative homologue of the 4-amino-butyrate aminotransferase GabT, sco5977 encoding a putative polyamine antiporter, and sco6960 with unknown function ( Figure 8 B). The interacting promoter regions also involved those of all four regulators epuRI , epuRII , epuRIII...”
• Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity
  Krysenko, Medical sciences (Basel, Switzerland) 2022
  • “...EMSA analysis, EpuRII revealed control of several polyamine-associated genes, including glnA3 , sco5676 , and sco5977 ( Table 1 ). Another regulator of polyamine utilization genes is the global regulator of the nitrogen metabolism GlnR. This has been demonstrated to control the transcription of the second...”
  • “...SCO5676 Succinate-semialdehyde dehydrogenase gabD-like GabD (b2661) GabD (PA0265) SCO5679 Amino acids/polyamine permease PuuP (b1296) PA5510/PAO322 SCO5977 Hydrolase - - SCO6960 Amidohydrolase - - SCO6961 -glutamyl-polyamine synthetase PuuA (b1297) PauA7 (PA5508)/SpuI (PA0296) SCO6962 medsci-10-00040-t002_Table 2 Table 2 Combined list of enzymes involved in ethanolamine utilization in C....”
• Initial Metabolic Step of a Novel Ethanolamine Utilization Pathway and Its Regulation in Streptomyces coelicolor M145
  Krysenko, mBio 2019
  • “...coelicolor M145 allowed in silico identification of two putative ethanolamine/amino acid permease genes, SCO6014 and SCO5977 , with rather low similarity to the putative ethanolamine permease target from other Streptomycetes spp. (43% to 45%). To verify whether the expression of SCO6014 and SCO5977 might be influenced...”
  • “...of ethanolamine and ammonium (control) as the sole N source. Transcriptional analysis of SCO6014 and SCO5977 revealed strong expression of these genes in the presence of ammonium, whereas no expression was observed in the presence of ethanolamine under the tested conditions (see Fig.S1 in the supplemental...”
• Gamma-Glutamylpolyamine Synthetase GlnA3 Is Involved in the First Step of Polyamine Degradation Pathway in Streptomyces coelicolor M145
  Krysenko, Frontiers in microbiology 2017
  • “...). In contrast, the expression of the genes encoding the putative polyamine permeases SCO5057 and SCO5977 was strongly induced in the presence of all polyamines or only putrescine, respectively ( Figure 5 ). The expression of SCO5658 (encoding predicted polyamine binding protein) was strongly induced in...”

MTRTR_BACSU / Q797A7 Methylthioribose transporter from Bacillus subtilis (strain 168) (see paper)
28% identity, 67% coverage

• function: Involved in import of methylthioribose (MTR) into the cell.
  disruption phenotype: Disruption of the gene leads to almost full resistance to trifluoromethylthioribose (3FMTR), a toxic analog of MTR.

GBAA_0818 amino acid permease from Bacillus anthracis str. 'Ames Ancestor'
BAS0779 amino acid permease family protein from Bacillus anthracis str. Sterne
23% identity, 87% coverage

• BrnQ-Type Branched-Chain Amino Acid Transporters Influence Bacillus anthracis Growth and Virulence
  Dutta, mBio 2022
  • “...GBAA_1935, and GBAA_1936, predicted to be ABC transporters for BCAAs as well as another gene, GBAA_0818, that is similar to bcaP , an amino acid permease gene that is found in many Gram-positive bacteria ( 16 , 29 , 31 , 49 ). In contrast, the...”
• Identification of CodY targets in Bacillus anthracis by genome-wide in vitro binding analysis
  Château, Journal of bacteriology 2013
  • “...(nprB) BAS0580 BAS0610 BAS0638 (inhA2) BAS0660 BAS0669 BAS0779 BAS0809 BAS0841 (sap) BAS0842 (eag) BAS0842 (eag) BAS0847 BAS0848* IMP dehydrogenase Transition...”

B1745_03815 APC family permease from Lactobacillus amylolyticus
25% identity, 79% coverage

• Adaptive mechanism of Lactobacillus amylolyticus L6 in soymilk environment based on metabolism of nutrients and related gene-expression profiles
  Fei, Food science & nutrition 2022
  • “...ligase 1.22 B1745_01405 secY preprotein translocase subunit SecY 1.38 B1745_02435 cth aluminum resistance protein 1.74 B1745_03815 amino acid permease 2.08 John Wiley & Sons, Ltd TABLE 3 Genes differentially expressed in the stationary phase compared to logarithmic phase Function group and ORF Gene Description Expression ratio...”
  • “...(B1745_03105, B1745_06875, B1745_06870, and B1745_06860) were upregulated, while two amino acid permease genes (B1745_04680 and B1745_03815) were downregulated in the logarithmic and stationary phase. Interestingly, two genes livB and brnQ coding for branchedchain amino acid transport system II carrier protein and branchedchain amino acid ABC transporter...”

O28661 Cationic amino acid transporter (Cat-1) from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
25% identity, 54% coverage

• Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
  Paparoditis, Biochimica et biophysica acta 2014
  • “...12 2.A.3 Amino Acid-Polyamine- Organocation (APC) Superfamily 2.A.3.3.17 Q9F2U9 10 unknown unknown Q7UY13 12 2.A.3.6.1 O28661 13 amino acids cationic amino acid Q7UFY5 12 2.A.3.8.12 O34739 12 amino acids Ser/Thr, aromatic amino acids Q7ULF6 12 2.A.4 Cation Diffusion Facilitator (CDF) Family 2.A.4.1.3 O07084 5 cations Cd...”

OTBS_1417 Cationic amino acid transporter-1 from Orientia tsutsugamushi Boryong
26% identity, 80% coverage

• Genome-based construction of the metabolic pathways of Orientia tsutsugamushi and comparative analysis within the Rickettsiales order
  Min, Comparative and functional genomics 2008
  • “...transporter tlc : OTBS_0312, OTBS_0313, ATP/ADP antiporter OTBS_0547, OTBS_1035, OTBS_1636 OTBS_1312, OTBS_0017? Malate atrC1 : OTBS_1417 Cationic aminio acid potE : OTBS_1403 Arginine/orinithine p34 : OTBS_1715 Cation kefB : OTBS_1539 Potassium gltP : OTBS_0443 Proton/glutamate rarD : OTBS_0203, OTBS_0407? S-adenosylmethionine proP : OTBS_0158, OTBS_0204, Proline/betaine OTBS_0844,...”

lpp0026 hypothetical protein from Legionella pneumophila str. Paris
25% identity, 85% coverage

• Isotopologue profiling of Legionella pneumophila: role of serine and glucose as carbon substrates
  Eylert, The Journal of biological chemistry 2010
  • “...protein (Lpp2269) and the putative amino acid transporters Lpp0026 and Lpp0357 are predicted. Indeed, using [U-13C3]Ser as a supplement to AYE medium at a...”

lp_1120 amino acid transport protein from Lactobacillus plantarum WCFS1
24% identity, 80% coverage

• Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis
  Rud, Microbial biotechnology 2011
  • “...0.6 lp_0749 pstB Phosphate ABC transporter, ATPbinding protein 2.1 a lp_0770 Multidrug transport protein 0.7 lp_1120 Amino acid transport protein 2.0 lp_1945 ABC transporter, ATPbinding protein 2.8 lp_2509 Transport protein 2.2 lp_2780 pts20A Cellobiose PTS, EIIA 2.9 0.6 0.6 lp_3008 pts23A Cellobiose PTS, EIIA 2.1 lp_3278...”

PP1059, PP_1059 amino acid permease from Pseudomonas putida KT2440
28% identity, 65% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria
  Browne, BMC microbiology 2010
  • “...sugar transporter 2.3 4.9 oprB-1 PP_1019 PP_1019 Glucose/carbohydrate outer membrane porin OprB precursor 3.5 2.9 PP_1059 PP_1059 probable amino acid permease 6.4 nd aatJ PP_1071 PP_1071 probable binding protein component of ABC transporter 3.3 7.7 NM PP_1400 dicarboxylate MFS transporter 2.5 nd tctC PP_1418 PP_1418 hypothetical...”

lpg0026 amino acid permease from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Q5ZZI4 Amino acid permease from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
25% identity, 85% coverage

• Mammalian Solute Carrier (SLC)-like transporters of Legionella pneumophila
  Best, Scientific reports 2018
  • “...other monosaccharides SLC2a1 (0.903) LstB (Lpg1653) 30% 48% Glucose and other monosaccharides SLC2a1 (0.922) LstC (Lpg0026) 37% 56% Cationic amino acids (arginine, lysine, ornithine) SLC7a1 (0.953) LstD (Lpg0049) 25% 44% Cationic amino acids (arginine, lysine, ornithine) SLC7a5 (0.954) LstE (Lpg0228) 25% 42% Cationic amino acids (arginine,...”
• bdhA-patD operon as a virulence determinant, revealed by a novel large-scale approach for identification of Legionella pneumophila mutants defective for amoeba infection
  Aurass, Applied and environmental microbiology 2009
  • “...scatter screena Closest homolog (organism) E value lpg0026 lpg0072 lpg0129 lpg0166 lpg0200 lpg0230 lpg0233 lpg0237 lpg0243 lpg0265 lpg0277 lpg0493 lpg0515...”
• Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach
  Khan, Microbiology spectrum 2022
  • “...cefoperazone, cefazolin, amdinocillin, cefonicid, cefepime, ceftibuten, mezlocillin, ceftazidime, ertapenem, and doripenem 486.493 612 7 tr| Q5ZZI4 Amino acid permease DB00123, DB00125, and DB00129 l -Lysine, l -arginine, and ornithine 155.606 424 a Drug names correspond respectively to the DrugBank ID numbers listed in Table 3, column...”

CAC3285 Predicted amino acid transporter from Clostridium acetobutylicum ATCC 824
24% identity, 80% coverage

• A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing
  Borden, Metabolic engineering 2010
  • “...Although no such decarboxylase/antiporter system has yet been characterized in C. acetobutylicum , the gene CAC3285 shows 44% sequence identity with the E. coli gene gadC , while several C. acetobutylicum genes show some homology to adiA (CAC0297 [18% identity] and CAC2338 [19% identity]) and adiC...”
  • “...E. coli acid decarboxylation/transport system of acid tolerance were consistently upregulated, including CAC1984,CAP0128, CAC0297 and CAC3285 ( Fig. 8 and Supplementary Fig. 6 ). As discussed earlier, CAC3285 has high similarity to gadC , which codes for a cognate glutamate/GABA antiporter in E. coli , and...”

PS417_05405 L-alanine and D-alanine permease from Pseudomonas simiae WCS417
27% identity, 66% coverage

• mutant phenotype: Important for utilizing both isomers of alanine, and no other transporter is apparent. Both phenotypes are conserved.

MSMEG_1412 amino acid permease from Mycobacterium smegmatis str. MC2 155
25% identity, 83% coverage

• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...11.6 0.00 100% Scavenging Pathways MSMEG_1411 universal stress protein family protein 1.3 10.3 0.00 85% MSMEG_1412 amino acid permease 1.3 11.0 0.00 91% MSMEG_1413 ornithine--oxo-acid transaminase rocD 2.3 10.9 0.00 94% MSMEG_1414 Amidinotransferase 2.0 11.3 0.00 97% MSMEG_1417 glyoxalase family protein 1.0 9.9 0.00 65% MSMEG_1418...”

lmo2469 similar to amino acid transporter from Listeria monocytogenes EGD-e
26% identity, 80% coverage

• A bacterial virulence factor interacts with the splicing factor RBM5 and stimulates formation of nuclear RBM5 granules
  Pourpre, Scientific reports 2022
  • “...L.monocytogenes strain EGDe genome, the inlP gene (also known as lmo2470 ) is located between lmo2469 and lmo2471 , two divergently transcribed genes encoding an amino acid transporter and a NADPH dehydrogenase, respectively (Fig. 1 A). Using previous RNA-sequencing (RNA-seq) transcriptomic data from the EGDe strain...”
• Listeria monocytogenes MDR transporters are involved in LTA synthesis and triggering of innate immunity during infection
  Tadmor, Frontiers in cellular and infection microbiology 2014
  • “...Similar to O-acetylhomoserine sulfhydrylase Amino acids metabolism LMRG_00310.2 lmo0644 Membrane sulfatase family protein LTA LMRG_00332.2 lmo2469 Similar to amino acid transporter/amino acid permease family protein Transporters LMRG_00541.6 lmo1079 Similar to YfhO Unknown LMRG_00672.6 lmo1226 Similar to transporter ( B. subtilis YdgH); lmo1225 is a transcriptional regulator...”
• Polyphasic characterization and genetic relatedness of low-virulence and virulent Listeria monocytogenes isolates
  Roche, BMC microbiology 2012
  • “...previously [ 7 , 8 ]. The clpP gene and its flanking regions (lmo2467 and lmo2469) were amplified from total isolated DNA using PCR. Primers and temperature annealing are listed in the Additional file 2 . The prfA and inlA virulence genes were fully sequenced, whereas...”
• The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production
  Stasiewicz, Applied and environmental microbiology 2011
  • “...enzyme; lmo0689 (cheV), encoding a chemotaxis protein; lmo2469, encoding an amino acid permease; and lmo0714 (fliG), encoding a flagellar motor switch...”
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...lmo2175 fruA lmo2341 lmo2389 lmo2434 lmo2463 lmo2469 lmo2569 lmo2573b lmo2580 lmo2584a,b lmo2586a,b lmo2592 lmo2650b lmo2651a,b lmo2659a lmo2660a lmo2663a...”
  • “...inlCc ilvB ilvN ilvCb ilvA lmo2114 lmo2115 arpJ lmo2390 lmo2469 glyA lmo2580 lmo2650b lmo2651 lmo2684 lmo2685 cydD cydC serS GC-B 5424 JOSEPH ET AL. J....”
• Identification of genes induced in Listeria monocytogenes during growth and attachment to cut cabbage, using differential display
  Palumbo, Applied and environmental microbiology 2005
  • “...catabolism Oligopeptide ABC transporter (permease) lmo2381 lmo2469 Na/pH homeostasis Amino acid transporter Transporters lmo2678 lmo2677, lmo2678 tcsA lmo1999,...”

lp_3278 amino acid permease from Lactiplantibacillus plantarum WCFS1
F9UTG8 Amino acid transport protein from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_3278 amino acid transport protein from Lactobacillus plantarum WCFS1
25% identity, 81% coverage

• Transcriptional analysis of the molecular mechanism underlying the response of Lactiplantibacillus plantarum to lactic acid stress conditions
  Jang, Heliyon 2023
  • “...both acidic conditions. Membrane proteins (lp_1684, lp_3080, lp_2949, lp_3178, lp_3177, lp_0309, lp_1946), amino acid transporter (lp_3278), and manganese ABC transporter (lp_2992) were up-regulated, and cold shock protein (lp_1160, lp_0997), carbohydrate proton transporter (lp_1792), and ammonium transporter (lp_0349) were down-regulated under both acidic conditions ( Supplementary Table...”
• Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments.
  Jung, Scientific reports 2020
  • “...GMP reductase lp_3271 F9UTG4 COG0516 K00364 lp_3278 1.47 0.000514 0.002559 Amino acid transport protein lp_3278 F9UTG8 COG0531 K03294 dapA2 1.59 6.43E19 1.18E17 hydroxy-tetrahydrodipicolinate synthase lp_2685 F9URH0 COG0329 K01714 Fold change in gene expression of group exposed to acidic conditions was calculated by edgeR R package. The...”
• Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments
  Jung, Scientific reports 2020
  • “...synthetase lp_3270 F9UTG3 COG0104 K01939 guaC 1.88 1.04E41 4.67E40 GMP reductase lp_3271 F9UTG4 COG0516 K00364 lp_3278 1.47 0.000514 0.002559 Amino acid transport protein lp_3278 F9UTG8 COG0531 K03294 dapA2 1.59 6.43E19 1.18E17 hydroxy-tetrahydrodipicolinate synthase lp_2685 F9URH0 COG0329 K01714 Fold change in gene expression of group exposed to...”
• Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis
  Rud, Microbial biotechnology 2011
  • “...2.2 lp_2780 pts20A Cellobiose PTS, EIIA 2.9 0.6 0.6 lp_3008 pts23A Cellobiose PTS, EIIA 2.1 lp_3278 Amino acid transport protein 2.1 lp_3279 kup2 Potassium uptake protein 0.6 0.5 lp_3303 Multidrug transport protein 0.6 lp_3540 Transport protein 6.5 a 0.6 a lp_3541 pts34B PTS, EIIB 6.5 lp_3547...”
• Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1
  Serrano, Microbial cell factories 2007
  • “...catalytic subunit lp_0761 23,5 trxB1 thioredoxin reductase (NADPH) lp_1230 1,6 transcription regulator Regulatory function (4%) lp_3278 1,8 amino acid transport protein Transport and binding proteins (11%) lp_1087 1,8 cation transport protein lp_2992 2,6 mntH2 manganese transport protein antilp_3469 1,6 lp_RNA02 2,6 plasmids (15%) lp_p2_01 3,1 lp_p2_02...”

BMB171_C0217 amino acid permease from Bacillus thuringiensis BMB171
24% identity, 80% coverage

• Single Amino Acid Substitution in Homogentisate Dioxygenase Affects Melanin Production in Bacillus thuringiensis
  Yang, Frontiers in microbiology 2018
  • “...HAD superfamily hydrolase; BMB171_C0214, HppD, 4-hydroxyphenylpyruvate dioxygenase; BMB171_C0215, FahA, fumarylacetoacetate hydrolase; BMB171_C0216, HmgA, homogentisate 1,2-dioxygenase; BMB171_C0217, amino acid permease; BMB171_C0218, MFS transporter. The vector pBMB3141, a derivative of pBMBL, contained the hmgA gene (1,173 bp) amplified from the genomic DNA of BMB171 by using primers hmgA1...”

AO356_17670 L-alanine and D-alanine permease from Pseudomonas fluorescens FW300-N2C3
27% identity, 65% coverage

• mutant phenotype: Specific phenotype on D-alanine and L-alanine

NP_461145 APC family lysine-specific permease from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM2200 APC family, lysine-specific permease from Salmonella typhimurium LT2
28% identity, 77% coverage

• A L-lysine transporter of high stereoselectivity of the amino acid-polyamine-organocation (APC) superfamily: production, functional characterization, and structure modeling.
  Kaur, The Journal of biological chemistry 2014
  • GeneRIF: a proton-dependent amino acid transporter of the APC superfamily, a homology model of STM2200 was created.
• Pseudomonas stutzeri as an alternative host for membrane proteins
  Sommer, Microbial cell factories 2017
  • “...enterica STM0969 APC 16419480 + ++ S. enterica STM1477 APC 16419996 + + S. enterica STM2200 APC 16420738 ++ NT S. enterica STM2357 APC 16420900 + + + S. enterica STM3225 DAACS 16421782 ++ NT A. aeolicus Aq_1330 DAACS 15606533 ++ NT A. aeolicus Aq_031 DASS...”
  • “...mainly folded in both hosts. For the remaining five proteins (STM2913, STM3986, STM1360, STM3225 and STM2200), both, the properly folded and aggregated protein species were observed, and the ratios between them varied greatly from E. coli to P. stutzeri . In E. coli , with the...”
• Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae
  Bianchi, Scientific reports 2016
  • “...by Kaur et al . 19 . The LysP coding fragment was acquired by amplifying STM2200 from isolated S. typhimurium genomic DNA, using primer pair: Pr31/Pr32. The pBADcLIC-GFP fusion vector was amplified using primer pair: Pr33/Pr34 and a two-way ligation was performed with USER; the resulting...”
• A L-lysine transporter of high stereoselectivity of the amino acid-polyamine-organocation (APC) superfamily: production, functional characterization, and structure modeling
  Kaur, The Journal of biological chemistry 2014
  • “...heterologous production of the LysP-related transporter STM2200 from Salmonella typhimurium in Escherichia coli, its purification, and functional...”
  • “...functional interaction between basic amino acids and STM2200 was investigated by thermoanalytical methods, i.e. differential scanning and isothermal titration...”

Q8P9N1 Cationic amino acid transporter from Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
24% identity, 82% coverage

• Global gene expression analysis during germination in the chytridiomycete Blastocladiella emersonii.
  Salem-Izacc, Eukaryotic cell 2009 (no snippet)

Rv2320c PROBABLE CATIONIC AMINO ACID TRANSPORT INTEGRAL MEMBRANE PROTEIN ROCE from Mycobacterium tuberculosis H37Rv
24% identity, 84% coverage

• De novo histidine biosynthesis protects Mycobacterium tuberculosis from host IFN-γ mediated histidine starvation
  Dwivedy, Communications biology 2021
  • “...90 . The Mtb H37Rv genome encodes for a plethora of membrane transporters such as: Rv2320c (cationic amino acids), Rv0488 (lysine), Rv2564 (glutamine), Rv1280c (oligopeptide) and Rv1979c, which are capable of transporting amino acids 91 . However, no specific histidine transport mechanism(s) has been identified in...”
• Characterization of membrane vesicles released by Mycobacterium avium in response to environment mimicking the macrophage phagosome
  Chiplunkar, Future microbiology 2019
  • “...processes 44 2 A0A0H3A0D0 MAV_2087 Amino acid transporter Cell wall and cell processes 48 6 Rv2320c A0A0H3A0X6 MAV_4750 GluB bacterial extracellular solute-binding protein Cell wall and cell processes 36 2 Rv0411c A0A0H3A326 MAV_4059 Monoxygenase Intermediary metabolism and respiration 95 2 A0A0H3A3W0 MAV_0467 dppD ABC transporter, ATP-binding...”
• Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis
  Puniya, Scientific reports 2016
  • “...(PUNP5) HXPRT (hypoxanthine phosphoribosyltransferase Hypoxanthine) ( Rv3624c ) Purine Metabolism (PUNP5) ORNt (ornithine transport) ( Rv2320c ) Sugar Metabolism ( GMAND ) ME1 (malic enzyme NAD) ( Rv2332 ) Glycolysis ( GAPD , PGK , PYK ) DHNPA (dihydroneopterin aldolase) ( Rv3607c ) Folate Metabolism (DHPS2)...”
• In-Vivo Gene Signatures of Mycobacterium tuberculosis in C3HeB/FeJ Mice
  Gautam, PloS one 2015
  • “...of variety of other genes that code for the proteins like putative transporters e.g. Rv0283, Rv2320c, Rv1686c etc. and membrane protein Rv1671, Rv0954, Rv0426c etc. whose expression were either upregulated or did not change during course of infection. The sigma factor sigL dependent transcription of Rv2877c...”
• Physiology of mycobacteria
  Cook, Advances in microbial physiology 2009
  • “...Not surprisingly, M. tuberculosis has several genes encoding putative L-arginine uptake transporters: Rv0522, Rv1979c, Rv1999c, Rv2320c and Rv3253c ( Cole et al. , 1998 ). Transport of L-arginine, but not of L-lysine and L-ornithine, was reduced by 70% in a mutant of M. bovis BCG lacking...”
• Arginine homeostasis in J774.1 macrophages in the context of Mycobacterium bovis BCG infection
  Talaue, Journal of bacteriology 2006
  • “...several genes encoding putative L-arginine uptake systems (Rv0522, Rv2320c, Rv3253c, Rv1999c, and Rv1979c) in M. tuberculosis and M. bovis, most likely with...”
  • “...putative cationic amino acid permeases (encoded by Rv2320c, Rv1999c, and Rv3253c) that Downloaded from http://jb.asm.org/ on February 12, 2017 by University...”
• Modulation of J774.1 macrophage L-arginine metabolism by intracellular Mycobacterium bovis BCG
  Peteroy-Kelly, Infection and immunity 2003
  • “...RocE L-arginine transporter (annotated as Rv0522 and Rv2320c). The presence of multiple L-arginine transporters and catabolic pathways in mycobacteria suggests...”
  • “...is attributed to another L-arginine permease such as Rv2320c. Comparison of intracellular L-arginine transport and metabolism between wild-type BCG and AS1 will...”
• Amino acid transport and metabolism in mycobacteria: cloning, interruption, and characterization of an L-Arginine/gamma-aminobutyric acid permease in Mycobacterium bovis BCG
  Seth, Journal of bacteriology 2000
  • “...transport proteins. Two homologs were identified, Rv0522 and Rv2320c. Here, Rv0522 was cloned from BCG and used to construct a strain lacking the permease...”
  • “...a second rocE homolog discovered in the Sanger database (Rv2320c). Thus, as in the enterics (11, 53), L-arginine uptake is carried by more than one permease in...”

Smp_123010 putative cationic amino acid transporter from Schistosoma mansoni
26% identity, 57% coverage

• Combinatory microarray and SuperSAGE analyses identify pairing-dependently transcribed genes in Schistosoma mansoni males, including follistatin
  Leutner, PLoS neglected tropical diseases 2013
  • “...Smp_123300 (KC165687) S. mansoni follistatin; Smp_090140.2 - Ftz-F1 interacting protein; Smp_090520 - purin nucleoside phosphorylase; Smp_123010 cationic amino acid transporter; Smp_095360.x fatty acid binding protein; Smp_065580.x heterogeneous nuclear ribonucleoprotein k; Smp_033950 - Smad4; Smp_144390 - S. mansoni activin receptor; Smp_049760 TGFRI; Smp_093540.3 ActRI; Smp_124450 - ActRI/BMPRIa;...”
  • “...in the dataset of Williams et al. [36] . Also a cationic amino acid transporter (Smp_123010) (down-regulated in EM), a fatty acid binding protein (Smp_095360.x) (down-regulated in EM), and a heterogeneous nuclear ribonucleoprotein k (Smp_065580.x) (up-regulated in EM) showed the same direction of regulation in our...”
• Gene expression patterns in larval Schistosoma mansoni associated with infection of the mammalian host
  Parker-Manuel, PLoS neglected tropical diseases 2011
  • “...schistosomulum transcribed a different suite of transporters. Of these, two amino acid transporters (Smp_176930, and Smp_123010, the latter cationic), distinct from that already mentioned in the tegument category, showed the greatest change (19 and 6 fold) compared to the germ ball. Their enrichment may also be...”

LSA0189 Putative amino acid/polyamine transport protein from Lactobacillus sakei subsp. sakei 23K
25% identity, 76% coverage

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...transport and metabolism Transport/binding of amino acids LSA0125 lsa0125 Putative amino acid/polyamine transport protein 0.6 LSA0189 lsa0189 Putative amino acid/polyamine transport protein -0.7 LSA0311 lsa0311 Putative glutamate/aspartate:cation symporter -1.1 -1.0 LSA1037 lsa1037 Putative amino acid/polyamine transport protein 1.0 0.8 0.5 LSA1219 lsa1219 Putative cationic amino acid...”

CLM70_03985 amino acid permease from Acinetobacter baumannii
26% identity, 86% coverage

• Acquisition of plasmids conferring carbapenem and aminoglycoside resistance and loss of surface-exposed macromolecule structures as strategies for the adaptation of Acinetobacter baumannii CC104^O/CC15^P strains to the clinical setting
  Cameranesi, Microbial genomics 2020
  • “...ligase CVG52_12250 hypothetical protein Ab825 Ph-825-A 54.6 718987773665 CLM70_ 03610 tRNA-Arg-CCT CLM70_03370 HchA, protein deglycase CLM70_03985 Aminoacid permease Ph-825-B 62.3 15469821609384 CLM70_ 07550 IR (hypothetical protein-MFS transporter) CLM70_07545 hypothetical protein CLM70_08115 MFS transporter Ph-825-C 41.3 21006182141947 CLM70_ 10600 IR ( malG-zapE ) CLM70_10350 Malate synthase G...”

ABA1_03000 amino acid permease from Acinetobacter baumannii
26% identity, 76% coverage

• Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1
  Álvarez, Frontiers in microbiology 2020
  • “...Thirdly, in A1, AB0057 and A85 the prophage was flanked by the same genes aroP (ABA1_03000) and chaperone hsp31 gene (ABA1_03077) ( Supplementary Table 9 ). In the case of A144, the prophage was flanked by a putative signal peptide (ABAYE2757) and the same chaperone hsp31...”

LH92_RS05285 amino acid permease from Acinetobacter baumannii
27% identity, 76% coverage

• Importance of twitching and surface-associated motility in the virulence of Acinetobacter baumannii
  Corral, Virulence 2021
  • “...with the corresponding gene cloned, Km r , Zeo r , Gm r This work LH92_RS05285 MAR002 derivative strain with LH92 _ RS05285 ::pCR-BluntII-TOPO disruption, Km r , Zeo r This work LH92_RS05285 complemented LH92_RS05285 strain carrying the pBAV1K-T5-gfp plasmid with the corresponding gene cloned, Km...”
  • “...secretion system protein VgrG 2.00 S group LH92_RS00045 WP_047479431.1 ABC transporter ATP-binding protein 2.64 2.13 LH92_RS05285 WP_079267361.1 Amino acid permease 4.66 2.55 LH92_RS08005 WP_001162376.1 Phosphoglycerate mutase family protein 5.93 3.99 LH92_RS12010 WP_004840631.1 Multidrug efflux RND transporter outer membrane subunit AdeH 2.69 1.10 LH92_RS16065 WP_000521916.1 Sulfate ABC...”

AO353_16120 D-alanine and L-alanine transporter from Pseudomonas fluorescens FW300-N2E3
27% identity, 65% coverage

• mutant phenotype: Specific phenotype on D-alanine as the carbon source. Also important for utilizing L-alanine as a carbon source. Both of these phenotypes are conserved. For D-alanine as a nitrogen source, there is a mild phenotype, and it may be partly redundant with another amino acid transporter (AO353_04615:04600). Sometimes annotated as a glycine transporter, but neither it nor its orthologs are important on glycine.

LOC100168178 uncharacterized protein LOC100168178 from Acyrthosiphon pisum
24% identity, 63% coverage

• Whitefly genome expression reveals host-symbiont interaction in amino acid biosynthesis
  Upadhyay, PloS one 2015
  • “...48 ACYPI000550 (LOC100159152) Unitig_68785 253 Unitig_21655 57 Unitig_40249 36 ACYPI001018(LOC100159667) Unitig_47082 172 Unitig_49482 126 ACYPI008904 (LOC100168178) Unitig_52040 95 Unitig_52329 98 ACYPI008971 (LOC100168251) Unitig_36271 78 Conclusions Comprehensive analysis of the transcriptome data of the whitefly has provided important information regarding the mechanism of cooperation between the host...”
• Aphid amino acid transporter regulates glutamine supply to intracellular bacterial symbionts
  Price, Proceedings of the National Academy of Sciences of the United States of America 2014
  • “...ACYPI000550 (LOC100159152), ACYPI001018 (LOC100159667), ACYPI008904 (LOC100168178), Price et al. and ACYPI008971 (LOC100168251)--are expressed in bacteriocytes...”
  • “...ACYPI000550 (LOC100159152), ACYPI001018 (LOC100159667), ACYPI008904 (LOC100168178), and ACYPI008971 (LOC100168251) were amplified from A. pisum bacteriocyte...”

XF2207 cationic amino acid transporter from Xylella fastidiosa 9a5c
25% identity, 78% coverage

• Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon
  da, BMC microbiology 2010
  • “...-1.62 XF1121* 5,10-methylenetetrahydrofolate reductase -1.51 XF2699 transcription termination factor Rho -1.37 XF0180* hypothetical protein -1.03 XF2207 cationic amino acid transporter -0.80 Upregulated genes (negatively regulated by RpoN) XF1109 hypothetical protein 1.89 XF2343 recombination protein N 1.63 XF0887 mannosyltransferase 1.61 XF1830 nitrile hydratase activator 1.52 XF2551 conserved...”
• Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa
  Meidanis, Microbiology and molecular biology reviews : MMBR 2002
  • “...RND (HME) RND (HAE1) 2.A.3.3.1 2.A.1.6.2 MHS XF2094 XF2083 XF0243 XF0866 XF0408 XF2207 XF2208 XF1462 XF1609 12 11 12 6 12 9 11 11 8 9 10 8 14 10 11 8 No. of...”

SM12261_0999 APC family permease from Streptococcus mitis NCTC 12261
25% identity, 86% coverage

• Capsular Polysaccharide Expression in Commensal Streptococcus Species: Genetic and Antigenic Similarities to Streptococcus pneumoniae
  Skov, mBio 2016
  • “...gene (SM12261_0992), the rhamnosyltransferase WchF gene (SM12261_0993), a glycosyltransferase gene (SM12261_0994), the flippase Wzx gene (SM12261_0999), and the four rhamnose pathway genes rmlA to - D are shared with many serotypes of S.pneumoniae . Other genes were rare or absent among pneumococci, such as genes encoding...”

PSPPH_4866 proline-specific permease proY from Pseudomonas syringae pv. phaseolicola 1448A
25% identity, 65% coverage

• Transcriptional profile of P. syringae pv. phaseolicola NPS3121 at low temperature: physiology of phytopathogenic bacteria
  Arvizu-Gómez, BMC microbiology 2013
  • “...RNA 2'-phosphotransferase 1.55 PSPPH_4634 bmp family protein 2.99 PSPPH_4641 YccA 1.68 PSPPH_4717 dethiobiotin synthetase 2.09 PSPPH_4866 proline-specific permease proY 1.54 PSPPH_4925 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit 1.62 PSPPH_5142 oxaloacetate decarboxylase alpha subunit 2.35 The described functions were obtained from the literature. The up-regulated genes...”

A9497_09055 amino acid permease from Streptococcus thermophilus
25% identity, 85% coverage

• Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
  Tian, International journal of molecular sciences 2018
  • “...substrate-binding protein A9497_03375 A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545 Transporter A9497_02760 A9497_03620 A9497_09055 AKL23_RS02000 AKL23_RS02915 AKL23_06320 Permease Branched-chain amino acid A9497_00490 A9497_01930 A9497_07910 A9497_07915 AKL23_RS01775 AKL23_RS01780 AKL23_RS05525 AKL23_RS08285 ABC transporter permease A9497_04685 A9497_04690 AKL23_RS08280 AKL23_RS08285 Permease A9497_07905 AKL23_RS01770 ABC transporter substrate-binding protein Glutamine...”

B7D75_21325 amino acid permease from Pseudomonas paraeruginosa
26% identity, 65% coverage

• Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa
  Sood, Frontiers in microbiology 2019
  • “...branched-chain amino acids (BCAAs; Ile, Leu, and Val) ORTHOMCL3746 17.34394 0.000171 0.045382 Amino acid permease (B7D75_21325) Amino acid transporters ORTHOMCL4632 17.92312 0.000128 0.039327 Type IV pilus secretin PilQ (B7D75_26155) Involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion ORTHOMCL1798...”

MAV_2087 amino acid transporter from Mycobacterium avium 104
24% identity, 82% coverage

• Characterization of membrane vesicles released by Mycobacterium avium in response to environment mimicking the macrophage phagosome
  Chiplunkar, Future microbiology 2019
  • “...28 2 A0A0H2ZWB3 MAV_3084 amt ammonium transporter Cell wall and cell processes 44 2 A0A0H3A0D0 MAV_2087 Amino acid transporter Cell wall and cell processes 48 6 Rv2320c A0A0H3A0X6 MAV_4750 GluB bacterial extracellular solute-binding protein Cell wall and cell processes 36 2 Rv0411c A0A0H3A326 MAV_4059 Monoxygenase Intermediary...”

AKL23_RS02915 amino acid permease from Streptococcus thermophilus
25% identity, 85% coverage

• Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
  Tian, International journal of molecular sciences 2018
  • “...A9497_03375 A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545 Transporter A9497_02760 A9497_03620 A9497_09055 AKL23_RS02000 AKL23_RS02915 AKL23_06320 Permease Branched-chain amino acid A9497_00490 A9497_01930 A9497_07910 A9497_07915 AKL23_RS01775 AKL23_RS01780 AKL23_RS05525 AKL23_RS08285 ABC transporter permease A9497_04685 A9497_04690 AKL23_RS08280 AKL23_RS08285 Permease A9497_07905 AKL23_RS01770 ABC transporter substrate-binding protein Glutamine A9497_01790 A9497_06995...”

jhp0406 amino acid permease from Helicobacter pylori J99
25% identity, 74% coverage

• Growth phase-dependent response of Helicobacter pylori to iron starvation
  Merrell, Infection and immunity 2003
  • “...2.1 5.7 4.1 2.1 3.3 3.7 4.3 2.4 JHP0406 JHP0334 JHP1101 JHP1384 Iron(III) dicitrate transport protein, fecAI ABC transporter, ATP-binding protein Iron(III)...”
  • “...HP0942 *HP1017 HP1172 JHP0128 JHP0286 JHP0626 JHP0743 JHP0810 JHP0877 JHP0406 JHP1099 L-Lactate 2.7 2.5 6.4 8.2 22.0 2.7 2.4 2.6 2.0 2.1 4.0 3.3 10.8 2.5 2.4...”

lhv_1028 amino acid transporter from Lactobacillus helveticus DPC 4571
26% identity, 77% coverage

• Genome sequence and analysis of Lactobacillus helveticus
  Cremonesi, Frontiers in microbiology 2012
  • “...is a functional oligopeptide transporter lhv_2931 that is probably fulfilling the peptide transport role, whereas lhv_1028 and lhv_1375 act as amino acid transporters ( Callanan et al., 2008 ). L. helveticus has additional genes for fatty acid biosynthesis and specific amino acid metabolism, but notably fewer...”

PA14_54040 probable amino acid permease from Pseudomonas aeruginosa UCBPP-PA14
26% identity, 65% coverage

• A novel small RNA is important for biofilm formation and pathogenicity in Pseudomonas aeruginosa
  Taylor, PloS one 2017
  • “...PA14_51350 phnB Anthranilate synthase component II -1.39 0.22 PA14_52800 acsA Acetyl-coenzyme A synthetase +1.52 0.60 PA14_54040 Putative amino acid permease +1.08 0.58 PA14_55580 nemO Heme oxygenase -8.94 0.02 PA14_60100 dtd Deoxycytidine triphosphate deaminase -1.82 0.24 PA14_68670 Putative carboxypeptidase -2.03 0.35 PA14_71630 adhA Alcohol dehydrogenase -3.64 0.11...”

PA0789 probable amino acid permease from Pseudomonas aeruginosa PAO1
26% identity, 65% coverage

• Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
  Salvà-Serra, Frontiers in microbiology 2022
  • “...PA0605 AgtC AgtC 6 15 1.09 0.20 1.09 0.24 2.59 0.00 Down 1.12 0.08 WP_003085613.1 PA0789 - Probable amino acid permease 5 13 1.02 0.91 1.50 0.00 Up 4.69 0.00 Up 1.80 0.00 Lower WP_003085934.1 PA0889 AotQ Arginine/ornithine transport protein AotQ 3 9 1.09 0.58 1.24...”
• Differential transcription profiling of the phage LUZ19 infection process in different growth media
  Brandão, RNA biology 2021 (secret)
• Seawater salt-trapped Pseudomonas aeruginosa survives for years and gets primed for salinity tolerance
  Elabed, BMC microbiology 2019
  • “...cysT PA0282 2.55 0.0016 Probable amino acid permease PA3641 2.46 0.0012 Probable amino acid permease PA0789 2.37 0.0076 Probable ATP-binding component of ABC transporter PA3019* 2.24 0.0030 Metabolism/enzymes S-adenosylmethionine decarboxylase proenzyme speD PA0654* 2.66 0.00038 Aspartate ammonia-lyase aspA PA5429 2.56 0.0029 Sulfite reductase cysI PA1838 2.47...”
  • “...transporters are putative components of ABC transporters (PA2204, PA3019), and putative amino acid permeases (PA3641, PA0789). Additionally, three genes (a probable AGCS Na + /alanine/glycine symporter PA2252, a probable amino acid permease PA3641, and nqrB PA2998) involved in Na + ions transport (GO:0006814) were induced in...”
• The development of a new parameter for tracking post-transcriptional regulation allows the detailed map of the Pseudomonas aeruginosa Crc regulon
  Corona, Scientific reports 2018
  • “...dehydrogenase PutA 3,29 1,79 8,38 Transport putP PA0783 Sodium/proline symporter PutP 0,79 1,58 5,3 Transport PA0789 Probable amino acid permease 0,38 0,86 2,08 Iron pirA PA0931 Ferric enterobactin receptor PirA 0,29 0,97 2,48 Transport tolQ PA0969 TolQ protein 0,41 1,03 2,52 Transport tolR PA0970 TolR protein...”
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...periplasmic binding protein PA0322 PAK cationic amino acid APC family transporter PA0783 PAK proline/sodium transporter PA0789 PAK proline APC family transporter PA0866 PAK aromatic amino acid APC family transporter PA0888 PAK pili- arginine/ornithine ABC transporter periplasmic binding protein ( AotJ ) PA0889 PA01 arginine/ornithine ABC transporter...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...ECs0452, 5: ECs5186, 6: ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201,...”

MmuP / b0260 CP4-6 prophage; S-methyl-L-methionine transporter from Escherichia coli K-12 substr. MG1655 (see 3 papers)
mmuP / Q47689 CP4-6 prophage; S-methyl-L-methionine transporter from Escherichia coli (strain K12) (see 2 papers)
TC 2.A.3.1.10 / Q47689 S-Methylmethionine permease, MmuP from Escherichia coli (see 3 papers)
b0260 putative amino acid/amine transport protein from Escherichia coli str. K-12 substr. MG1655
SR35_01240 S-methylmethionine permease from Escherichia coli
26% identity, 67% coverage

• substrates: Methylmethionine, S-Methylmethionine
• luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling
  Wang, Journal of bacteriology 2005
  • “...b0621 b1407 b0076 b2723 b3683 b3028 b2968 b0579 b3220 b0260 b3046 b2919 b3906 b2060 b0790 b1720 b1010 b2797 b2993 b0042 b1001 b2549 b1311 b3141 b1012 b1571 lsrG...”
• Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA⁺)
  Jeong, Frontiers in microbiology 2017
  • “...exists only in K-12 MG1655 None b pepD (SR35_01230) ( gpt-ykfC ) IS 5 mmuP (SR35_01240) CP46 prophage (exclusive of IS 5 at the right end) and the upstream gpt-proA exist only in K-12 MG1655 quuD (SR35_02745) SR35_02750 IS 5 ( nmpC-borD ) ybcV (SR35_02760) Within...”

CG13248 uncharacterized protein from Drosophila melanogaster
27% identity, 57% coverage

• Animal amino acid sensor - A review
  Ke, Animal bioscience 2025
  • “...signaling process of DH44 neurons stimulated by L-Glu, L-Ala and L-Asp through the channel proteins CG13248 and CG4991. When the amino acid enters the cell, it inhibits the expression of GCN2, and then transmits the signal to DH44 neurons, and finally to DH44-R1/R2. L-Glu, L-glutamic; L-Ala,...”
• Differential amino acid transporter expression in adult Drosophila melanogaster tissues
  Wright, microPublication biology 2024
  • “...carcass, which houses the fat body and hemocytes, major mediators of the Drosophila immune response. CG13248 is expressed in all tissues examined but the ovary ( Fig. 1V ). CG13248 transports histidine in fly photoreceptors (Han et al., 2022) and is also highly expressed in neurons...”
  • “...CG1607, CD98hc, mnd, dmGlut, sbm, CG12773, Ctns, CG8026, Eaat1, CG4995, aralar1, CG13384, Ncc69, polyph, and CG13248 ). The ovary expresses all but three AAT transcripts, with 10 showing moderate to high expression levels ( CD98hc, dmGlut, sbm, CG12773, CG32079, CG8026, Cg7255, CG4995, Cg13384, and Ncc69 )....”
• Synaptic connectome of a neurosecretory network in theDrosophilabrain
  McKim, 2024
• Tadr is an axonal histidine transporter required for visual neurotransmission in Drosophila
  Han, eLife 2022
  • “...A2 CG30394 Yes Amino acid transmembrane transporter activity/SLC38A10 CG13743 Yes Amino acid transmembrane transporter activity/SLC38A11 CG13248 Yes Amino acid transmembrane transporter activity/SLC7A4 slif Yes Amino acid transmembrane transporter activity/SLC7A1 or A2 CG12773 Yes Amino acid transmembrane transporter activity/SLC12A8 NKCC Yes Amino acid transmembrane transporter activity/SLC12A3 ChT...”
  • “...CG13248-transfected cells, but not by Slif (Slimfast)-positive cells ( Figure 6A ). Next, we overexpressed CG13248 or Slif in tadr 2 mutant photoreceptor cells. The expression of CG13248 in tadr 2 mutant photoreceptor cells fully restored both ERG transients and phototaxis, whereas Slif did not. These...”
• Methionine restriction breaks obligatory coupling of cell proliferation and death by an oncogene Src in Drosophila
  Nishida, eLife 2021
  • “...Flybase FLYB: FBgn0005278 NA Gene Drosophila melanogaster samtor Flybase FLYB: FBgn0035035 NA Gene Drosophila melanogaster CG13248 Flybase FLYB: FBgn0036984 NA Gene Drosophila melanogaster tadr Flybase FLYB: FBgn0036984 NA Gene Drosophila melanogaster CG9413 Flybase FLYB: FBgn0030574 NA Gene Drosophila melanogaster jhl-21 Flybase FLYB: FBgn0028425 NA Gene Drosophila...”
  • “...and Miura, 2015 PMID: 32938923 F: 5'- GCCAACGGCGTTCATATC -3' R: 5'- GGCATATCCAAACATGATACCC -3' Sequence-based reagent CG13248 (primer) FlyPrimerBank PP18106 F: 5'- AAACCGATGCCTCAACACCTT -3' R: 5'- CAGTCAGCACGTAGATGCCA -3' Sequence-based reagent tadr (primer) FlyPrimerBank PP20579 F: 5'- CAGCCCGCTGTAAAACTAGC -3' R: 5'- GGCCAGAGCATCTAGCCAG -3' Sequence-based reagent CG9413 (primer) FlyPrimerBank...”
• Growth regulation by amino acid transporters in Drosophila larvae
  Manière, Cellular and molecular life sciences : CMLS 2020
  • “...directly stimulate DH44+brain neurons to increase in food consumption via a putative amino acid transporter, CG13248 [ 53 , 54 ]. In adult females, nutrients play also an important role in germline stem cells development. This requires specific nutrient-responsive signaling pathways which includes insulin/IGF signaling, TOR...”
• Recent advances in the neural regulation of feeding behavior in adult Drosophila
  Wang, Journal of Zhejiang University. Science. B 2019
  • “...a manner that requires putative amino acid transporters (CG13248 and CG4991). Essential amino acid-deficient (EAAD) food rejection is mediated by a group of...”
• A post-ingestive amino acid sensor promotes food consumption in Drosophila
  Yang, Cell research 2018
  • “...promote food consumption. Single-cell transcriptome analysis and immunostaining reveal that a putative amino acid transporter, CG13248, is enriched in DH44 + neurons. Knocking down CG13248 expression in DH44 + neurons blocks the increase in food consumption and eliminates calcium responses induced by dietary amino acids. Therefore,...”
  • “...key sensor to detect amino acids and to enhance food intake via a putative transporter CG13248. These results shed critical light on the regulation of protein homeostasis at organismal levels by the nervous system. issue-copyright-statement IBCB, SIBS, CAS 2018 Introduction Proteins are the most abundant macromolecules...”
• More

LSA1219 Putative cationic amino acid transport protein from Lactobacillus sakei subsp. sakei 23K
24% identity, 70% coverage

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...Putative glutamate/aspartate:cation symporter -1.1 -1.0 LSA1037 lsa1037 Putative amino acid/polyamine transport protein 1.0 0.8 0.5 LSA1219 lsa1219 Putative cationic amino acid transport protein 0.7 LSA1415 lsa1415 Putative amino acid/polyamine transport protein 1.1 0.7 LSA1424 lsa1424 Putative L-aspartate transport protein -1.4 -0.9 -1.2 LSA1435 lsa1435 Putative amino...”

PA14_25270 aromatic amino acid transport protein AroP1 from Pseudomonas aeruginosa UCBPP-PA14
26% identity, 87% coverage

• Loss of the Two-Component System TctD-TctE in Pseudomonas aeruginosa Affects Biofilm Formation and Aminoglycoside Susceptibility in Response to Citric Acid
  Taylor, mSphere 2019
  • “...ribosomal protein S6 2.58 PA14_15980 rimM 16S rRNA processing protein 2.59 PA14_73410 2.62 PA14_58570 2.68 PA14_25270 aroP1 Aromatic amino acid transport protein AroP1 2.76 PA14_44060 sdhC Succinate dehydrogenase (C subunit) 2.80 PA14_58120 mreD Rod shape-determining protein MreD 2.91 PA14_67560 typA Regulatory protein TypA 2.93 PA14_52340 3.04...”

CCNA_00435 L-proline transporter from Caulobacter crescentus NA1000
25% identity, 88% coverage

• mutant phenotype: Mildly important for growth with proline as the carbon or nitrogen source, and detrimental in most other conditions.

CAAT9_ARATH / Q9C5D6 Cationic amino acid transporter 9, chloroplastic from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT1G05940 CAT9 (CATIONIC AMINO ACID TRANSPORTER 9); cationic amino acid transmembrane transporter from Arabidopsis thaliana
26% identity, 67% coverage

• function: Permease involved in the transport of the cationic amino acids.
• Cellular export of sugars and amino acids: role in feeding other cells and organisms
  Kim, Plant physiology 2021
  • “..., AAP family protein PUT1 (At1g31820), AAP1 (At1g58360), cationic amino acid transporters CAT4 (At3g03720), CAT9 (At1g05940), and CAT2 (At1g58030) is indicated. The logit score for UmamiT45 was 14.2. Figure 4 The role of SWEETs and UmamiTs in Arabidopsis, rice, and maize. A, The role of SWEETs...”
• Transcriptome-Wide Analysis of Nitrogen-Regulated Genes in Tea Plant (Camellia sinensis L. O. Kuntze) and Characterization of Amino Acid Transporter CsCAT9.1
  Zhang, Plants (Basel, Switzerland) 2020
  • “...6 , it was observed that the growth of OE lines with Arabidopsis cat mutant (AT1G05940) background was comparable with the growth of the WT and the Arabidopsis cat mutant, particularly with respect to rosette leaves. The growth inhibition of OE lines in WT background was...”
• Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and Potassium Accumulation in Brassica napus L
  Alcock, Frontiers in plant science 2018
  • “...Cab002494.2 AT2G30320 3 10 207 Pseudouridine synthase family protein A3 GEM_Cab002494.2 Leaf K concentration Cab037725.3 AT1G05940 9 10 237 CATIONIC AMINO ACID TRANSPORTER 9 A9 GEM_Cab037664.1 Leaf K concentration Cab007712.1 AT5G10740 2 10 151 Protein phosphatase 2C family protein A10 GEM_Cab007712.1 Leaf K concentration Bo9g003730.1 AT4G01080...”
  • “...0.0 CYTOCHROME P450, FAMILY 86, SUBFAMILY A, POLYPEPTIDE 2 C9 GEM_Bo9g002280.1 Leaf K concentration Bo9g001030.1 AT1G05940 6 10 143 CATIONIC AMINO ACID TRANSPORTER 9 C9 GEM_Bo9g002280.1 Leaf K concentration Bo9g171810.1 AT5G10740 3 10 47 Protein phosphatase 2C family protein C9 GEM_Bo9g171810.1 Putative functions obtained from annotation...”
• The putative Cationic Amino Acid Transporter 9 is targeted to vesicles and may be involved in plant amino acid homeostasis
  Yang, Frontiers in plant science 2015
  • “...without nitrogen for 24 further weeks. DNA Cloning The full cDNA sequence of CAT9 ( At1g05940 ) that missed the STOP codon was cloned via BamHI and SmaI using the pCRblunt kit (Invitrogen) and inserted 5 in frame of the GFP sequence in a plant binary...”
• A tonoplast Glu/Asp/GABA exchanger that affects tomato fruit amino acid composition
  Snowden, The Plant journal : for cell and molecular biology 2015
  • “...(Table S1) and is a homologue of Arabidopsis thaliana cationic amino acid transporter 9 (CAT9; At1g05940; NP_563754.1). Whilst members of the CAT subfamily of transporters predominantly transport cationic amino acids, plasmamembranelocalised members of this family from Arabidopsis have been shown to possess the capacity for the...”
• The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis
  Elashry, Plant physiology and biochemistry : PPB 2013
  • “...0.6 0.03 At3g10600 AtCAT7 3.3 3 0.3 0.20 At1g17120 AtCAT8 6.5 5.6 0.9 a 0.00 At1g05940 AtCAT9 8.1 7 1.1 a 0.00 At5g05630 AtLAT1 3.5 3.7 0.2 0.43 At3g13620 ATLAT2 5.1 7 1.9 a 0.00 At1g31820 AtLAT3 4.6 3.9 0.7 0.07 At1g31830 AtLAT4 8.1 7.5 0.6...”
• A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture
  Jaquinod, Molecular & cellular proteomics : MCP 2007
  • “...46 KuP 2d Transp. NF NF At5g40670 At1g05940 At1g58030 At3g03720 At1g17120 At3g30390 At2g41190 At2g39130 At2g40420 At3g28960 At1g70330 31,007 60,138 67,072...”

YP1283 putative lysine-specific permease from Yersinia pestis biovar Medievalis str. 91001
27% identity, 78% coverage

• Context-Dependent Action of Scc4 Reinforces Control of the Type III Secretion System
  Gao, Journal of bacteriology 2020 (secret)

A9497_02760, AKL23_06320 amino acid permease from Streptococcus thermophilus
26% identity, 85% coverage

• Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
  Tian, International journal of molecular sciences 2018
  • “...ABC transporter substrate-binding protein A9497_03375 A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545 Transporter A9497_02760 A9497_03620 A9497_09055 AKL23_RS02000 AKL23_RS02915 AKL23_06320 Permease Branched-chain amino acid A9497_00490 A9497_01930 A9497_07910 A9497_07915 AKL23_RS01775 AKL23_RS01780 AKL23_RS05525 AKL23_RS08285 ABC transporter permease A9497_04685 A9497_04690 AKL23_RS08280 AKL23_RS08285 Permease A9497_07905 AKL23_RS01770 ABC transporter substrate-binding...”
  • “...A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545 Transporter A9497_02760 A9497_03620 A9497_09055 AKL23_RS02000 AKL23_RS02915 AKL23_06320 Permease Branched-chain amino acid A9497_00490 A9497_01930 A9497_07910 A9497_07915 AKL23_RS01775 AKL23_RS01780 AKL23_RS05525 AKL23_RS08285 ABC transporter permease A9497_04685 A9497_04690 AKL23_RS08280 AKL23_RS08285 Permease A9497_07905 AKL23_RS01770 ABC transporter substrate-binding protein Glutamine A9497_01790 A9497_06995 A9497_00730...”

CBO0389 amino acid permease from Clostridium botulinum A str. ATCC 3502
25% identity, 79% coverage

• Transcriptomic analysis of (group I) Clostridium botulinum ATCC 3502 cold shock response
  Dahlsten, PloS one 2014
  • “...and components of a putative ABC transporter was observed, as well as 16-fold induction of cbo0389 encoding a putative amino acid permease. The Effects of Prolonged Cold Exposure on the Transcriptome of C. botulinum ATCC 3502 The transcription of a large number of genes was markedly...”
  • “...were both down-regulated. Another strongly up-regulated gene (180-fold) 5 h after the cold shock was cbo0389 putatively encoding an amino acid permease. Additionally, the transcription of another putatively amino acid permease-encoding cbo0343 was 4.5-fold induced. Regulatory functions In total, 30 genes with predicted regulatory roles were...”

SPD_0887 amino acid permease family protein from Streptococcus pneumoniae D39
25% identity, 86% coverage

• Proteomic Adaptation of Streptococcus pneumoniae to the Antimicrobial Peptide Human Beta Defensin 3 (hBD3) in Comparison to Other Cell Surface Stresses
  Mücke, Microorganisms 2020
  • “...by hBD3, LL-37 stress caused a significant increase in BlpS, the transporters SPD_0076, SPD_0684, and SPD_0887, and the cell surface modification proteins TacF (SPD_1128), LicD1 (SPD_1129), and DltD (SPD_2002). The changes in cell surface modification proteins are thought to decrease the negative surface charge of pneumococci...”
• The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
  Yadav, PloS one 2015
  • “...family protein transporter activity transmembrane transport -4.2 (0.03) SPD_1170 oligopeptide ABC transporter activity -2.0 (0.04) SPD_0887 amino acid permease family protein amino acid transmembrane transporter activity -1.4 (0.05) SPD_1425 transporter, major facilitator family protein transporter activity transmembrane transport -4.2 (0.03) SPD_1409 sugar ABC transporter, ATP-binding protein...”
• Regulation of arginine acquisition and virulence gene expression in the human pathogen Streptococcus pneumoniae by transcription regulators ArgR1 and AhrC
  Kloosterman, The Journal of biological chemistry 2011
  • “...spd_0611 spd_0719 spd_0720 spd_0721 spd_0781 spd_0852 spd_0887 spd_0888 spd_0889 spd_1063 spd_1225 spd_1226 spd_1356 spd_1357 spd_1515 spd_1516 spd_1517...”

c2691 Lysine-specific permease from Escherichia coli CFT073
27% identity, 77% coverage

• The Saccharomyces cerevisiae Start-specific transcription factor Swi4 interacts through the ankyrin repeats with the mitotic Clb2/Cdc28 kinase and through its conserved carboxy terminus with Swi6
  Siegmund, Molecular and cellular biology 1996
  • “...can1-100 ssd1-d). The amino-terminally HA-tagged GAL1::SWI4 construct (c2691) was also transformed into a swi6 deletion strain (K2283 [36]; MATa swi6::TRP1...”

CadR / b2156 lysine:H⁺ symporter from Escherichia coli K-12 substr. MG1655 (see 15 papers)
lysP / P25737 lysine:H⁺ symporter from Escherichia coli (strain K12) (see 13 papers)
LYSP_ECOLI / P25737 Lysine-specific permease LysP; Lysine transporter LysP; Trigger transporter LysP from Escherichia coli (strain K12) (see 7 papers)
TC 2.A.3.1.2 / P25737 Lysine:H+ symporter. Forms a stable complex with CadC to allow lysine-dependent adaptation to acidic stress (Rauschmeier et al. 2013). The Salmonella orthologue is 95% identical to the E. coli protein and is highly specific for Lysine. Residues involved in lysine binding have been identified from Escherichia coli (see 5 papers)
lysP lysine-specific permease from Escherichia coli K12 (see 5 papers)
NP_416661 lysine:H(+) symporter from Escherichia coli str. K-12 substr. MG1655
b2156 lysine transporter from Escherichia coli str. K-12 substr. MG1655
27% identity, 77% coverage

• function: Permease involved in lysine uptake (PubMed:1315732, PubMed:24056175). In addition, functions as a lysine sensor that mediates the lysine-dependent regulation of the transcriptional activator CadC (PubMed:18086202, PubMed:24056175). In the absence of lysine, or at low lysine concentrations, LysP inhibits CadC by an interaction with the transmembrane domain of CadC. In the presence of lysine, LysP loses its ability to interact with and inhibit CadC, and acts as a lysine permease (PubMed:18086202, PubMed:24056175).
  catalytic activity: L-lysine(out) + H(+)(out) = L-lysine(in) + H(+)(in) (RHEA:28911)
  subunit: Interacts strongly with the transcriptional activator CadC in the absence of lysine or at low lysine concentrations (PubMed:18086202, PubMed:24056175). Interaction is markedly attenuated under increasing lysine levels (PubMed:24056175). Concomitant pH-dependent protonation of periplasmic amino acids in both proteins dissolves their electrostatic connections resulting in further destabilization of the CadC/LysP interaction (PubMed:24056175). Low pH promotes oligomerization of LysP (PubMed:24056175).
• substrates: H+, lysine
• New insights into the interplay between the lysine transporter LysP and the pH sensor CadC in Escherichia coli.
  Rauschmeier, Journal of molecular biology 2014 (PubMed)
  • GeneRIF: Upon induction, lysine-dependent conformational changes in LysP transduce the lysine signal via a direct conformational coupling to CadC without resolving the interaction completely.
• Identification of ArgP and Lrp as transcriptional regulators of lysP, the gene encoding the specific lysine permease of Escherichia coli.
  Ruiz, Journal of bacteriology 2011
  • GeneRIF: These results indicate that ArgP is a major regulator of lysP expression but that Lrp modulates lysP transcription under lysine-limiting conditions.
• The membrane-integrated transcriptional activator CadC of Escherichia coli senses lysine indirectly via the interaction with the lysine permease LysP.
  Tetsch, Molecular microbiology 2008 (PubMed)
  • GeneRIF: The results suggest a model according to which CadC is inactivated by an interaction with LysP at a low external lysine concentration.
• Topological analysis of the lysine-specific permease of Escherichia coli.
  Ellis, Microbiology (Reading, England) 1995 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...Cell inner membrane 469 P24207 PHEP Amino acid transport and metabolism Cell inner membrane 470 P25737 LYSP Amino acid transport and metabolism Cell inner membrane 471 P28306 MLTG General function prediction only Cell inner membrane 472 P30750 METN Inorganic ion transport and metabolism Cell inner membrane...”
• Identification and Engineering of Transporters for Efficient Melatonin Production in Escherichia coli
  Yang, Frontiers in microbiology 2022
  • “...) L-arginine efflux transporter UniProtKB P11667 (ARGO_ECOLI) LysP ( lysP ) lysine:H + symporter UniProtKB P25737 (LYSP_ECOLI) AcrA ( acrA ) Multidrug efflux pump subunit UniProtKB P0AE06 (ACRA_ECOLI) AcrB ( acrB ) Multidrug efflux pump subunit UniProtKB P31224 (ACRB_ECOLI) Growth curves of the five selected transporter...”
• Functional Characterization of the γ-Aminobutyric Acid Transporter from Mycobacterium smegmatis MC² 155 Reveals Sodium-Driven GABA Transport
  Pavić, Journal of bacteriology 2021
  • “...), YifK ( P27837 ), ProY ( P0AAE2 ), pheP ( P24207 ), LysP ( P25737 ) and YvbW ( O32257 ). A final alignment of this cluster was calculated using Mafft G-INS-I and consisted of 273 sequences. The best-fit evolutionary model for the alignment was...”
• Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae
  Van't, The FEBS journal 2020
  • “...Q9UPY5 corresponding to Lat1, Lat2, and Xct, respectively; and for bacterial, P24207 , P37460 , P25737 , P15993 , P0AAE0 , P25527 , P77610 , P39137 , and P42087 corresponding to PheP, ProY, LysP, AroP, CycA, GabP, AnsP, RocE, and HutM, respectively. This resulted in a...”
• The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
  Frick-Cheng, mBio 2020
  • “...Hypoxanthine phosphoribosyltransferase 2.1 b0125 ibaG Acid stress protein IbaG 2.2 b3190 lysP Lysine:H(+) symporter 2.1 b2156 opgC Protein required for succinyl modification of osmoregulated periplasmic glucans 2.6 b1047 ribE 6,7-Dimethyl-8-ribityllumazine synthase 2.1 b0415 rpmE 50S ribosomal subunit protein L31 2.7 b3936 suhB Inositol phosphate phosphatase 2.6...”
• Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12
  White-Ziegler, Journal of bacteriology 2007
  • “...lysC b4024 Aspartokinase III, lysine sensitive lysP b2156 Lysine-specific permease nanA b3225 N-Acetylneuraminate lyase (aldolase) tesA b0494 Acyl-coenzyme A...”
• Rapid identification and mapping of insertion sequences in Escherichia coli genomes using vectorette PCR
  Zhong, BMC microbiology 2004
  • “...based on flanking sequences amplified from both sides, and an additional insertion was identified in b2156 . IS150 The one known IS150 insertion was identified and no other. IS186 The three known IS186 insertions were identified based on flanking sequences amplified from both sides (Fig. 2...”
  • “...400 P P IS30 -a 4115565 b3927 - 692 186 P P IS30 -b 2246187 b2156 - 303* 445 P P P IS186 -a 4541184 b4314 - 606 534 P P a * indicates a fragment not recovered. b P, present. c Neither IS5-4 fragment is...”

SP_1001 amino acid permease family protein from Streptococcus pneumoniae TIGR4
25% identity, 86% coverage

• SP_0916 Is an Arginine Decarboxylase That Catalyzes the Synthesis of Agmatine, Which Is Critical for Capsule Biosynthesis in Streptococcus pneumoniae
  Ayoola, Frontiers in microbiology 2020
  • “...Spn are yet to be identified and characterized. Current annotation of Spn TIGR4 genome has SP_1001, a locus that encodes an amino acid permease family protein with the potential to transport amino acids, polyamines, and agmatine. Future studies to determine the substrate specificity of SP_1001 are...”

UTI89_C2430 lysine-specific permease from Escherichia coli UTI89
27% identity, 77% coverage

• Genetic requirements for uropathogenic <i>E. coli</i> proliferation in the bladder cell infection cycle
  Mediati, mSystems 2024
  • “...study UTI89_C2954 smpB SsrA-binding protein (degradation of stalled translation polypeptides) 3.69 2.66E-02 4.47E-01 This study UTI89_C2430 lysP Lysine-specific uptake transporter 3.60 2.85E-02 4.48E-01 ( 42 ) UTI89_C0235 aspV Aspartate tRNA 3.28 2.80E-02 4.59E-01 ( 43 ) UTI89_C2119 yecS Cystine ABC transporter integral membrane subunit 2.78 3.24E-02...”

TC 2.A.3.8.9 / Q19834 Heteromeric amino acid transporter #1 (transports most neutral aas with highest rates for Ala and Ser (Km≈100 μM)). They function by obligatory aa:aa exchange (Veljkovic et al., 2004b) (see paper)
NP_501707 Large neutral amino acids transporter small subunit 1 from Caenorhabditis elegans
27% identity, 76% coverage

• substrates: Amino acids
• Neural production of kynurenic acid in Caenorhabditis elegans requires the AAT-1 transporter.
  Lin, Genes & development 2020
  • GeneRIF: Neural production of kynurenic acid in Caenorhabditis elegans requires the AAT-1 transporter.
• l(2)01810 is a novel type of glutamate transporter that is responsible for megamitochondrial formation
  Shim, The Biochemical journal 2011
  • “...(NP_956273), Mmus Eaat2 (NP_035523), Hsap Eaat2 (NP_004162), Dmel Eaat2 (NP_001162844), Dmel genderblind (NP_651536), Cele aat-1 (NP_501707), Drer SLC7a11-like (XP_001919426), Mmus xCT (NP_036120), Hsap xCT (NP_055146), Dmel l(2)01810 (NP_620115), Dmel VGLUT (NP_608681), Cele eat-4 (NP_499023), Drer SLC17a7 (NP_001092225), Hsap VGLUT1 (NP_064705), Rnor VGLUT1 (NP_446311), Dmel arala1 (NP_733365),...”

PA3000 aromatic amino acid transport protein AroP1 from Pseudomonas aeruginosa PAO1
25% identity, 87% coverage

• Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
  Salvà-Serra, Frontiers in microbiology 2022
  • “...YfdC Conserved hypothetical protein 3 7 1.13 0.28 1.76 0.00 Down 3.81 0.00 Down WP_003091187.1 PA3000 AroP1 Aromatic amino acid transport protein AroP1 2 4 1.00 0.90 1.34 0.02 2.11 0.00 Up 1.27 0.04 WP_003091470.1 PA3188 GltG Probable permease of ABC sugar transporter 2 7 1.20...”
• Antimicrobial Activity of, and Cellular Pathways Targeted by, p-Anisaldehyde and Epigallocatechin Gallate in the Opportunistic Human Pathogen Pseudomonas aeruginosa
  Adewunmi, Applied and environmental microbiology 2020 (secret)
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...protein ( HisM ) PA2926 PAK histidine ABC transporter ATP binding protein ( HisP ) PA3000 PAK aromatic amino acid APC family transporter ( AroP1 ) PA3176 PA01 glutamate/sodium ion symporter ( GltS ) PA3560 PAK phosphotransferase system transporter fructose-specific IIBC component ( FruA ) PA3562...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...ECs0614, 2: ECs0116, 3: ECs4729, 4: ECs0452, 5: ECs5186, 6: ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421,...”

CTC_RS04695 APC family permease from Clostridium tetani E88
25% identity, 77% coverage

• Regulation of Clostridium tetani Neurotoxin Expression by Culture Conditions
  Pennings, Toxins 2022
  • “..., brown cluster). Apart from tetX , these included acyl-CoA dehydrogenase (CTC_RS10685), amino acid permease (CTC_RS04695), ethanolamine utilization protein (CTC_RS11165), and five hypothetical proteins (CTC_RS05450, CTC_RS08030, CTC_RS08110, CTC_RS10695, CTC_RS13650). When adjacent clusters were included, we found a set of 20 DEGs for which the overall gene...”

XP_683623 high affinity cationic amino acid transporter 1 isoform X1 from Danio rerio
23% identity, 61% coverage

• Sequence analysis and spatiotemporal developmental distribution of the Cat-1-type transporter slc7a1a in zebrafish (Danio rerio).
  Ellingsen, Fish physiology and biochemistry 2020
  • GeneRIF: Sequence analysis and spatiotemporal developmental distribution of the Cat-1-type transporter slc7a1a in zebrafish (Danio rerio).

XP_039296923 cationic amino acid transporter 4 from Nilaparvata lugens
26% identity, 61% coverage

• Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species (Nilaparvata lugens)
  Yue, Frontiers in physiology 2021
  • “...67035.3 8.49 + NlAPC17 XP_039296817 Nlug17189-TA chr14 15988763 16025229 611 13 15 66179.6 8.42 NlAPC18 XP_039296923 Nlug20896-TA chr14 18470291 18500414 628 10 14 67808.4 6.34 NlAPC19 XP_039296913 Nlug21374-TA chr14 17485099 17501514 475 8 10 51234.1 6.39 NlAPC20 XP_039301531 Nlug28084-TA Sf7363 758 10624 222 6 3 23926.7...”

YintA_01003466 COG0833: Amino acid transporters from Yersinia intermedia ATCC 29909
27% identity, 66% coverage

• Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909)
  Babujee, PloS one 2013
  • “...protein -3.5 12.1 10.3 AEH-0003449 YintA_01003465 mmuM CP4-6 prophage; S-methylmethionine:homocysteine methyltransferase -2.7 12.8 11.4 AEH-0003450 YintA_01003466 mmuP CP4-6 prophage; predicted S-methylmethionine transporter -2 12.3 11.3 AEH-0000386 YintA_01000389 ybhB putative Phospholipid-binding protein -1.8 12.8 12 Bold fonts represent genes present only in Y. intermedia ATCC29909 Analysis of...”

BAT1_MOUSE / Q9QXA6 b(0,+)-type amino acid transporter 1; b(0,+)AT1; Glycoprotein-associated amino acid transporter b0,+AT1; Solute carrier family 7 member 9 from Mus musculus (Mouse) (see 2 papers)
XP_006540108 B(0,+)-type amino acid transporter 1 isoform X1 from Mus musculus
26% identity, 76% coverage

• function: Associates with SLC3A1 to form a functional transporter complex that mediates the electrogenic exchange between cationic amino acids and neutral amino acids, with a stoichiometry of 1:1 (By similarity) (PubMed:10588648). Has system b(0,+)-like activity with high affinity for extracellular cationic amino acids and L-cystine and lower affinity for intracellular neutral amino acids (By similarity). Substrate exchange is driven by high concentration of intracellular neutral amino acids and the intracellular reduction of L-cystine to L- cysteine (By similarity). Required for reabsorption of L-cystine and dibasic amino acids across the brush border membrane in renal proximal tubules (By similarity).
  catalytic activity: L-leucine(out) + L-arginine(in) = L-leucine(in) + L- arginine(out) (RHEA:71059)
  catalytic activity: L-histidine(out) + L-arginine(in) = L-histidine(in) + L- arginine(out) (RHEA:71063)
  catalytic activity: L-phenylalanine(out) + L-arginine(in) = L-phenylalanine(in) + L-arginine(out) (RHEA:71067)
  catalytic activity: L-cysteine(out) + L-arginine(in) = L-cysteine(in) + L- arginine(out) (RHEA:71071)
  catalytic activity: L-cystine(out) + L-arginine(in) = L-cystine(in) + L- arginine(out) (RHEA:71075)
  catalytic activity: L-lysine(out) + L-arginine(in) = L-lysine(in) + L- arginine(out) (RHEA:70827)
  subunit: Disulfide-linked heterodimer composed of the catalytic light chain subunit SLC7A9 and the heavy chain subunit SLC3A1. The heterodimer is the minimal functional unit. Assembles in heterotetramers (dimers of heterodimers) and higher order oligomers; the oligomerization is mediated by SLC3A1 likely to prevent degradation and facilitate heteromer trafficking to the plasma membrane (By similarity) (PubMed:10588648). Interacts with CAV1 (By similarity).
• Unraveling the Proteomic Landscape of Intestinal Epithelial Cell-Derived Exosomes in Mice.
  Ding, Frontiers in physiology 2022
  • “...0.845 0.402 Not Enterocyte 28 P18242 Ctsd Cathepsin D 70.48 0.823 0.511 Not Enterocyte 29 Q9QXA6 Slc7a9 b(0, +)-type amino acid transporter 1 54.43 0.806 0.082 Not Enterocyte 30 O88329 Myo1a Unconventional myosin-Ia 4066.40 0.771 0.000 Not Enterocyte 31 Q8VDN2 Atp1a1 Sodium/potassium-transporting ATPase subunit alpha-1 19959.97...”
• Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics
  Simionato, BMC evolutionary biology 2007
  • “...gw.168.63.1, gene similar to the uncharacterized Drosophila CG13990 gene; B = estExt_fgenesh1_pm.C_570004, gene similar to Q9QXA6 (Glycoprotein-associated amino acid transporter b0+AT1) from Mus musculus ; C = fgenesh1_pg.scaffold_57000051, gene similar to Drosophila CG18497 . See text and additional file 16 for details. bHLHs from non bilaterians...”
• Tissue distribution, hormonal regulation, ontogeny, diurnal expression, and induction of mouse cystine transporters Slc3a1 and Slc7a9.
  Wu, Free radical research 2020
  • GeneRIF: Tissue distribution, hormonal regulation, ontogeny, diurnal expression, and induction of mouse cystine transporters Slc3a1 and Slc7a9.
• Slc7a9 knockout mouse is a good cystinuria model for antilithiasic pharmacological studies.
  Font-Llitjós, American journal of physiology. Renal physiology 2007 (PubMed)
  • GeneRIF: A new protocol with d-penicillamine to validate our Slc7a9 knockout mouse model for the study of the therapeutic effect of drugs in the treatment of cystine lithiasis is reported.
• Molecular cloning of mouse amino acid transport system B0, a neutral amino acid transporter related to Hartnup disorder.
  Bröer, The Journal of biological chemistry 2004 (PubMed)
  • GeneRIF: mouse amino acid transport system B0 is a neutral amino acid transporter related to Hartnup disorder
• Slc7a9-deficient mice develop cystinuria non-I and cystine urolithiasis.
  Feliubadaló, Human molecular genetics 2003 (PubMed)
  • GeneRIF: Slc7a9-deficient mice develop cystinuria non-I and cystine urolithiasis
• rBAT-b(0,+)AT heterodimer is the main apical reabsorption system for cystine in the kidney.
  Fernández, American journal of physiology. Renal physiology 2002 (PubMed)
  • GeneRIF: a decreasing expression gradient of heterodimeric rBAT-b(0,+)AT along the proximal tubule is responsible for virtually all apical cystine reabsorption

Minf_1788 Amino acid transporter from Methylacidiphilum infernorum V4
24% identity, 86% coverage

• Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
  Hou, Biology direct 2008
  • “...the acidic environment M. infernorum encodes a glutamate decarboxylase (Minf_0102) and a potential glutamate/-aminobutyrate antiporter (Minf_1788), as well as an arginine decarboxylase (biosynthetic, Minf_2107) and a potential arginine/agmatine antiporter (Minf_1531). These enzyme/transporter pairs could potentially counteract acidification of the cytoplasm by binding excess H + ions...”

CTR1_MOUSE / Q09143 High affinity cationic amino acid transporter 1; CAT-1; CAT1; Ecotropic retroviral leukemia receptor; Ecotropic retrovirus receptor; ERR; EcoR; Solute carrier family 7 member 1; System Y+ basic amino acid transporter from Mus musculus (Mouse) (see 7 papers)
TC 2.A.3.3.1 / Q09143 System Y+ high affinity basic amino acid transporter (CAT1) (ecotropic retrovival leukemia virus receptor (ERR)) (transports arginine, lysine and ornithine; Na+-independent) from Mus musculus (Mouse) (see 2 papers)
Slc7a1 / RF|NP_031539.3 high affinity cationic amino acid transporter 1 from Mus musculus
NP_031539 high affinity cationic amino acid transporter 1 from Mus musculus
23% identity, 63% coverage

• function: High-affinity, low capacity permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine) in non-hepatic tissues.
  function: (Microbial infection) Acts as a receptor for the ecotropic murine retroviral leukemia virus.
  catalytic activity: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: L-lysine(in) = L-lysine(out) (RHEA:70935)
  catalytic activity: L-ornithine(in) = L-ornithine(out) (RHEA:71199)
  catalytic activity: L-homoarginine(in) = L-homoarginine(out) (RHEA:71203)
  subunit: Interacts with TM4SF5; the interaction is negatively regulated by arginine (By similarity). Forms tissue-specific complexes with ASL, ASS1 and nitric oxide synthase NOS1 or NOS3; the complex regulates cell-autonomous L-arginine synthesis and citrulline recycling while channeling extracellular L-arginine to nitric oxide synthesis pathway (PubMed:22081021).
• substrates: Arginine, Ornithine, lysine
• The solute carrier SLC7A1 may act as a protein transporter at the blood-brain barrier.
  Kurtyka, European journal of cell biology 2024 (PubMed)
  • GeneRIF: The solute carrier SLC7A1 may act as a protein transporter at the blood-brain barrier.
• Cationic amino acid transporter-1 (CAT-1) promotes fibroblast-like synoviocyte proliferation and cytokine secretion by taking up L-arginine in rheumatoid arthritis.
  Lu, Arthritis research & therapy 2022
  • GeneRIF: Cationic amino acid transporter-1 (CAT-1) promotes fibroblast-like synoviocyte proliferation and cytokine secretion by taking up L-arginine in rheumatoid arthritis.
• Endothelial-specific overexpression of cationic amino acid transporter-1 prevents loss of kidney function in heart failure.
  Giam, Clinical science (London, England : 1979) 2020 (PubMed)
  • GeneRIF: Endothelial-specific overexpression of cationic amino acid transporter-1 prevents loss of kidney function in heart failure.
• MCD diet-induced steatohepatitis is associated with alterations in asymmetric dimethylarginine (ADMA) and its transporters.
  Di, Molecular and cellular biochemistry 2016 (PubMed)
  • GeneRIF: A time-dependent decrease in serum and tissue ADMA and increase in mRNA expression of DDAH-1 and PRMT-1 as well as higher rates of mRNA expression of CAT-1 and lower rates of CAT-2A and CAT-2B were found after 8-week MCD diet.
• Endothelial cationic amino acid transporter-1 overexpression blunts the effects of oxidative stress on pressor responses to behavioural stress in mice.
  Rajapakse, Clinical and experimental pharmacology & physiology 2014 (PubMed)
  • GeneRIF: Endothelial CAT-1 overexpression can counter the ability of oxidative stress.
• Nitric oxide signalling pathway in Duchenne muscular dystrophy mice: up-regulation of L-arginine transporters.
  Ramachandran, The Biochemical journal 2013
  • GeneRIF: L-argine transporters CAT-1 and CAT-2A expression and function are significantly increased in Duchenne muscular dystrophy mice.
• GRB2 interaction with the ecotropic murine leukemia virus receptor, mCAT-1, controls virus entry and is stimulated by virus binding.
  Chen, Journal of virology 2012
  • GeneRIF: findings suggest a novel role for GRB2 in ecotropic MLV entry and infection by facilitating mCAT-1 trafficking
• A bifunctional intronic element regulates the expression of the arginine/lysine transporter Cat-1 via mechanisms involving the purine-rich element binding protein A (Pur alpha).
  Huang, The Journal of biological chemistry 2009
  • GeneRIF: analysis of how a bifunctional intronic element regulates the expression of the arginine/lysine transporter Cat-1 via mechanisms involving the purine-rich element binding protein A (Pur alpha)
• More
• A multi-hierarchical approach reveals d-serine as a hidden substrate of sodium-coupled monocarboxylate transporters.
  Wiriyasermkul, eLife 2024
  • “...p-Value of 8 hr IRI/ sham Peptides Score Mascot Abundance in sham * Increased Slc7a1/Cat1 Q09143 0.8 0.12 1.3 0.01 1 131 2.6E+06 Slc1a5/Asct2 P51912 0.4 0.10 0.7 0.09 4 767 1.5E+07 Decreased Slc36a1/Pat1 Q8K4D3 1.2 0.08 1.0 0.12 3 103 5.4E+06 Slc2a5/Glut5 Q9WV38 1.2 0.01...”
• NEAT1 inhibits the angiogenic activity of cerebral arterial endothelial cells by inducing the M1 polarization of microglia through the AMPK signaling pathway.
  Chen, Cellular & molecular biology letters 2024
  • “...SETD7 4.29 Q8VDV8 Mitd1 MIT domain-containing protein 1 4.09 Q08857 Cd36 Platelet glycoprotein 4 4.05 Q09143 Slc7a1 High affinity cationic amino acid transporter 1 3.83 Q8BP40 Acp6 Lysophosphatidic acid phosphatase type 6 3.79 Q69ZQ2 Isy1 Pre-mRNA-splicing factor ISY1 homolog 3.48 Q9ET26 Rnf114 E3 ubiquitin-protein ligase RNF114...”
• Proteomic Analysis of Protective Effects of Dl-3-n-Butylphthalide against mpp + -Induced Toxicity via downregulating P53 pathway in N2A Cells
  Zhao, Proteome science 2023
  • “...domain-containing protein 1 0.027175 Q14B01 Rnf113a2 Ring finger protein 113A2 0.000267 Q0PD20 Rab34 Rab34 0.023811 Q09143 Slc7a1 High affinity cationic amino acid transporter 1 0.032001 Q08509 Eps8 Epidermal growth factor receptor kinase substrate 8 0.006738 Q07813 Bax Apoptosis regulator BAX 0.018148 Q05915 Gch1 GTP cyclohydrolase 1...”
• TMT-Based Quantitative Proteomic Analysis Reveals the Effect of Bone Marrow Derived Mesenchymal Stem Cell on Hair Follicle Regeneration
  Zhang, Frontiers in pharmacology 2021
  • “...L-dopachrome tautomerase Dct 4.457 1.73E-05 3.564 1.64E-04 Q9QXD6 Fructose-1,6-bisphosphatase 1 Fbp1 4.31 1.53E-03 2.421 4.01E-02 Q09143 High affinity cationic amino acid transporter 1 Slc7a1 3.674 1.24E-02 2.487 3.50E-02 P02798 Metallothionein-2 Mt2 3.479 1.81E-04 2.281 8.23E-03 Q8R100 Calcium homeostasis modulator protein 5 Calhm5 3.469 2.35E-02 2.506 4.53E-02...”
• Efficient isolation of brain capillary from a single frozen mouse brain for protein expression analysis.
  Ogata, Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 2021
• Regulation of the V-ATPase along the endocytic pathway occurs through reversible subunit association and membrane localization.
  Lafourcade, PloS one 2008
  • “...2 40 O55143 endoplasmic reticulum calcium ATPase 2 Ion transport 107.98 114784 3.45 2 41 Q09143 High affinity cationic amino acid transporter 1 Ion transport 98.32 67048 3.94 2 42 Q91VS7 Microsomal glutathione S-transferase 1 Ion transport 83.61 17409 7.59 1 43 Q8VDN2 Na(+)/K(+) ATPase alpha-1...”

Z3413 lysine-specific permease from Escherichia coli O157:H7 EDL933
27% identity, 77% coverage

• The gluconeogenesis pathway is involved in maintenance of enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content
  Bertin, PloS one 2014
  • “...high-affinity transport system 11.34 2.3E-06 Z1031 glnQ Component of glutamine high-affinity transport system 8.47 4.6E-05 Z3413 lysP Lysine-specific permease 2.11 7.2E-03 Z0715 pheP Phenylalanine-specific transport system 2.20 2.8E-03 Gluconeogenic amino acids are both carbon and nitrogen sources for many bacteria: ammonia is first release due to...”

RT0297 AtrC1-like cationic amino acid transporter protein from Rickettsia typhi str. wilmington
25% identity, 82% coverage

• Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, Rickettsia typhi
  Dreher-Lesnick, BMC microbiology 2008
  • “...septation protein [Rickettsia typhi str. Wilmington] 0.6 (0.4, 0.9, 0.6) Amino acid transport and metabolism RT0297 AtrC1-like cationic amino acid transporter protein [Rickettsia typhi str. Wilmington] 0.6 (0.3, 0.6, 1.8) RT0473 cysteine desulfurase [Rickettsia typhi str. Wilmington] 0.6 (0.7, 0.7, 0.5) RT0118 glutamine transport system permease...”

CCNA_01242 amino acid permease from Caulobacter crescentus NA1000
26% identity, 73% coverage

• A Genome-Wide Analysis of Adhesion in <i>Caulobacter crescentus</i> Identifies New Regulatory and Biosynthetic Components for Holdfast Assembly
  Hershey, mBio 2019
  • “...uncharacterized genes from these clusters of mutants for detailed examination of holdfast defects. Disruption of CCNA_01242 , which encodes a predicted amino acid permease, led to the strongest nonadhesion fitness profile of any gene in the cheesecloth passaging experiment ( Fig.5A ). However, the CCNA_01242 strain...”
  • “...significant adhesion defect under any conditions tested ( Fig.5C ; see also TableS2 ). Instead, CCNA_01242 had an unusual, biphasic growth profile. In complex medium, the log phase was shorter than that shown by the wild type, leading to a lower level of optical density (OD)...”

CTR1_RAT / P30823 High affinity cationic amino acid transporter 1; CAT-1; CAT1; Ecotropic retroviral leukemia receptor; Ecotropic retrovirus receptor; EcoR; Solute carrier family 7 member 1; System Y+ basic amino acid transporter from Rattus norvegicus (Rat) (see paper)
23% identity, 63% coverage

• function: High-affinity, low capacity permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine) in non-hepatic tissues.
  function: (Microbial infection) Acts as a receptor for the ecotropic murine retroviral leukemia virus.
  catalytic activity: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: L-lysine(in) = L-lysine(out) (RHEA:70935)
  catalytic activity: L-ornithine(in) = L-ornithine(out) (RHEA:71199)
  catalytic activity: L-homoarginine(in) = L-homoarginine(out) (RHEA:71203)
  subunit: Interacts with TM4SF5; the interaction is negatively regulated by arginine (By similarity). Forms tissue-specific complexes with ASL, ASS1 and nitric oxide synthase NOS1 or NOS3; the complex regulates cell-autonomous L-arginine synthesis and citrulline recycling while channeling extracellular L-arginine to nitric oxide synthesis pathway (By similarity).
• Proteomic analysis of immature rat pups brain in response to hypoxia and ischemia challenge.
  Yang, International journal of clinical and experimental pathology 2014

PMI0841 lysine-specific permease from Proteus mirabilis HI4320
26% identity, 77% coverage

• Pathogenesis of <i>Proteus mirabilis</i> Infection
  Armbruster, EcoSal Plus 2018 (secret)

Htur_0566 amino acid permease-associated region from Haloterrigena turkmenica DSM 5511
26% identity, 52% coverage

• Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
  Anderson, PloS one 2011
  • “...a UspA protein, and some are both fused and adjacent to UspA family proteins (e.g. Htur_0566). This appears to be specific for the APC family as other potential amino acid symporters of the neurotransmittersodium symporter (NSS) family and the dicarboxylate/amino acidcation symporter (DAACS) family are not...”

HMPREF9571_RS04615 amino acid permease from Cutibacterium acnes HL043PA2
25% identity, 64% coverage

• Proteomic and transcriptomic analyses of Cutibacterium acnes biofilms and planktonic cultures in presence of epinephrine
  Gannesen, AIMS microbiology 2024
  • “...Forward TCTAGGCCTGGTGTTGAGGT Reverse GACCGTCCATTCTTGGGTGT 3 HMPREF9571_RS03355 iron ABC transporter permease Forward ACGAGCCGACAAATCACCTT Reverse ATGTCTGCAGTCCGTTCCAG 4 HMPREF9571_RS04615 amino acid permease Forward AGGTCAAGGGCATCAACGAG Reverse AAGGAGATGGCGAACAGTGG 5 HMPREF9571_RS09715 hypothetical protein Forward GATTTCGGGGTGTCTGTCGT Reverse AGAACCGGGAACTTCGTGTC 6 HMPREF9571_RS01930 CsbD family protein Forward TTTTTCGCCGCTGTCTTGTG Reverse TTCCCGATTGAACTGCGACA 7 HMPREF9571_RS04360 antitoxin Forward TCTTCGATAAGGCCAAGGACG Reverse...”
  • “...samples at the concentration of 5 nM ( Table 4 ), and the putative permease HMPREF9571_RS04615 (ALT35263.1) was downregulated with a similar fold change as in the previous sample pair. Therefore, at least this gene can be considered as a putative target for epinephrine-mediated regulation. These...”

Q3UTL4 Cationic amino acid transporter C-terminal domain-containing protein from Mus musculus
22% identity, 63% coverage

• The ubiquitin ligase Cullin5^SOCS2 regulates NDR1/STK38 stability and NF-κB transactivation
  Paul, Scientific reports 2017
  • “...P08030 Adenine phosphoribosyltransferase Aprt 3.618 0.844 12 19.724 Q5SSZ5 Tensin-3 Tns3 3.978 0.840 1 58.725 Q3UTL4 High affinity cationic amino acid transporter 1 Slc7a1 2.364 0.835 3 67.107 Q8VDF2 E3 ubiquitin-protein ligase UHRF1 Uhrf1 3.938 0.829 20 87.555 Q9CPY1 39S ribosomal protein L51, mitochondrial Mrpl51 3.421...”

PP0660 amino acid transporter, AAT family from Pseudomonas putida KT2440
23% identity, 78% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

CAAT2_ARATH / Q9ASS7 Cationic amino acid transporter 2, vacuolar from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
TC 2.A.3.3.13 / Q9ASS7 Cationic amino acid transporter 2, vacuolar from Arabidopsis thaliana (see 4 papers)
AT1G58030 CAT2 (CATIONIC AMINO ACID TRANSPORTER 2); amino acid transmembrane transporter from Arabidopsis thaliana
25% identity, 65% coverage

• function: Permease involved in the transport of the cationic amino acids.
• substrates: Amino acids
• Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis
  Bellin, Molecules (Basel, Switzerland) 2023
  • “...2.01 1.58 0.70 0.72 PL nucleotide AT1G61800 GPT2 5.90 7.61 0.39 1.65 PL Glc6P, TP AT1G58030 CAT2 1.40 1.32 0.62 TP amino acid AT5G40890 CLCa 2.34 1.50 0.56 TP Cl, nitrate AT3G16240 TIP2.1 3.42 3.74 0.48 0.97 TP H 2 O AT3G26520 TIP1.2 2.08 1.85 0.49...”
• Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress
  Shen, Frontiers in plant science 2022
  • “...inhibited during the salt treatment. Similarly, we found some stress related genes such as CAT2 (AT1G58030), XTH6 (AT5G65730), XTH22 / TCH4 (AT5G57560), HSFA2 (AT2G26150), NRT2.6 (AT3G45060), HSP70-2 (AT5G02490), COR15A (AT2G42540), COR15B (AT2G42530), NAC13 (AT1G32870), VSP2 (AT5G24770) that were upregulated in Col-0 under salt/normal but downregulated in...”
• Cellular export of sugars and amino acids: role in feeding other cells and organisms
  Kim, Plant physiology 2021
  • “...protein PUT1 (At1g31820), AAP1 (At1g58360), cationic amino acid transporters CAT4 (At3g03720), CAT9 (At1g05940), and CAT2 (At1g58030) is indicated. The logit score for UmamiT45 was 14.2. Figure 4 The role of SWEETs and UmamiTs in Arabidopsis, rice, and maize. A, The role of SWEETs and UmamiTs during...”
• Transcription factor CDF4 promotes leaf senescence and floral organ abscission by regulating abscisic acid and reactive oxygen species pathways in Arabidopsis
  Xu, EMBO reports 2020 (secret)
• Transcription of putative tonoplast transporters in response to glyphosate and paraquat stress in Conyza bonariensis and Conyza canadensis and selection of reference genes for qRT-PCR
  Moretti, PloS one 2017
  • “...of a cationic amino acid transporter (CAT), [ 22 ]. In Arabidopsis , both CAT2 (AT1G58030) and CAT4 (AT3G03720) encode CATs which are primarily localized to the tonoplast [ 23 ], making them appropriate candidates for the vacuolar sequestration of paraquat. In glyphosate-paraquat-resistant (GPR) Conyza spp...”
  • “...4e -105 CATIONIC AMINO ACID TRANSPORTER 4 (CAT4) NM_111243.7 AT3G03720 JSWR01002601.1 77 2e -37 NM_179491.2 AT1G58030 83 5-ENOL-PYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) NM_130093.2 AT2G45300 AY545666; JSWR01004464.1 78 7e -41 AY545667; JSWR01002887.1 77 3e -39 AY545668; JSWR01015937.1 71 2e -23 a Gene nomenclature followed Arabidopsis thaliana genes. b Arabidopsis...”
• Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function"
  Quanbeck, Frontiers in plant science 2012
  • “...(the minimum number of detected metabolic changes was 4 metabolites, associated with the mutation in At1g58030), 55 mutant alleles show between 10 and 30 metabolic changes, and 9 mutant alleles showed more than 30 altered metabolite abundances; the highest number of detected altered metabolites being 46....”
• DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns
  Rigal, The EMBO journal 2012
  • “...genes for H3K9me2 demethylation, all genes but one (AT1G58030) showed ectopic CHG methylation in the ibm1 mutant background compared with the WT. Among these,...”
• Transcriptome analysis reveals absence of unintended effects in drought-tolerant transgenic plants overexpressing the transcription factor ABF3
  Abdeen, BMC genomics 2010
  • “...transporter family protein 1.017 1.540 1.826 263918_at At2g36590 Proline transporter 3 (ProT3) 1.907 1.845 245868_at At1g58030 Cationic amino acid transporter 2 (CAT2) -1.406 260543_at At2g43330 Inositol transporter 1 (AtINT1) 1.118 0.160 262756_at At1g16370 Organic cation/carnitine transporter 6 (AtOCT6)/carbohydrate transmembrane transporte 1.992 245499_at At4g16480 Inositol transporter 4...”
• More

CAAT4_ARATH / Q8W4K3 Cationic amino acid transporter 4, vacuolar from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
TC 2.A.3.3.14 / Q8W4K3 Cationic amino acid transporter 4, vacuolar from Arabidopsis thaliana (see 4 papers)
NP_001154586 cationic amino acid transporter 4 from Arabidopsis thaliana
25% identity, 65% coverage

• function: Permease involved in the transport of the cationic amino acids.
• substrates: Amino acids
• Characterization of the putative amino acid transporter genes AtCAT2, 3 &4: the tonoplast localized AtCAT2 regulates soluble leaf amino acids.
  Yang, Journal of plant physiology 2014 (PubMed)
  • GeneRIF: Two members of a small subfamily of the cationic amino acid transporters, AtCAT2 and AtCAT4, were primarily localized at the tonoplast when tagged with GFP. The closely related AtCAT3, by contrast, was detected in the endoplasmic reticulum membrane.

Q8VIA9 Ecotropic retrovirus receptor from Rattus norvegicus
23% identity, 63% coverage

• Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture.
  Cui, Proteomics 2009
  • “...isoform 1 IPI00400615.1 1.63 1.16 2 Q6PCU2 297566 Cationic amino acid transporter-1 IPI00190498.1 1.81NA 1 Q8VIA9 25648 Fragile X mental retardation gene 1, autosomal homolog IPI00373184.2 3.19 0.34 3 Q5XI81 361927 Mitochondrial 2-oxoglutarate/malate carrier protein IPI00231261.6 1.97NA 1 P97700 64201 Na-K-Cl cotransporter IPI00212590.1 2.34NA 1 Q9QX10...”

XF0408 amino acid transporter from Xylella fastidiosa 9a5c
25% identity, 83% coverage

• Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa
  Meidanis, Microbiology and molecular biology reviews : MMBR 2002
  • “...(HME) RND (HME) RND (HAE1) 2.A.3.3.1 2.A.1.6.2 MHS XF2094 XF2083 XF0243 XF0866 XF0408 XF2207 XF2208 XF1462 XF1609 12 11 12 6 12 9 11 11 8 9 10 8 14 10 11 8 No....”

Dhaf_1325 amino acid permease-associated region from Desulfitobacterium hafniense DCB-2
27% identity, 74% coverage

• Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction
  Kim, BMC microbiology 2012
  • “...converts tryptophan to indole, pyruvate, and ammonia were identified in association with two permease genes (Dhaf_1325 and Dhaf_2459). These gene sets were also observed in Y51 (DSY4041-4042 and DSY1331-1332). Complete biosynthetic pathways are present for the formation of amino acids, nucleic acid precursors, as well as...”

HP1017 amino acid permease (rocE) from Helicobacter pylori 26695
25% identity, 71% coverage

• <i>Helicobacter pylori</i> Efflux Pumps: A Double-Edged Sword in Antibiotic Resistance and Biofilm Formation
  Krzyżek, International journal of molecular sciences 2024
  • “...potassium ion transport), HP0497 (sodium and chlorine ion transport), HP0939 (YckJ, amino acid transport) and HP1017 (RocE, amino acid transport). It was proved that the average expression of genes encoding these four transporters was significantly higher in clinical strains with clarithromycin resistance than in susceptible ones....”
  • “...SpoT Is Involved in the Clarithromycin Tolerance of Helicobacter pylori by Upregulating the Transporters HP0939, HP1017, HP0497, and HP0471 Antimicrob. Agents Chemother. 2017 61 e02011-16 10.1128/AAC.02011-16 28242673 64. Cai Y. Wang C. Chen Z. Xu Z. Li H. Li W. Sun Y. Transporters HP0939, HP0497, and...”
• Clarithromycin sustained-release tablet may be an improper therapy for the eradication of Helicobacter pylori
  Zuo, Therapeutic advances in gastroenterology 2024
  • “...SpoT locus is involved in H. pylori tolerance to clarithromycin by upregulating the transporters HP0939, HP1017, HP0497, and HP0471. For antibiotic-resistant strains, higher drug concentrations may result in superior bactericidal effects. This may explain why the sustained-release tablets were less effective than the dispersible tablets in...”
  • “...SpoT is involved in the clarithromycin tolerance of Helicobacter pylori by upregulating the transporters HP0939, HP1017, HP0497, and HP0471 . Antimicrob Agents Chemother 2017 ; 61 ( 5 ): e02011e02016. 41 Chen CL Wu IT Wu DC , et al . Independent risk factors predicting eradication...”
• Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance
  Ansari, Clinical microbiology reviews 2022 (secret)
• The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
  Xu, Frontiers in microbiology 2021
  • “...1.1314 HP0943 dadA 1.293 HP0985 Predicted gene 1.0004 HP1000 Para 1.4507 HP1002 Predicted gene 1.3929 HP1017 rocE 1.704 HP1020 ispDF 1.2427 HP1021 cheY 1.6902 HP1022 Predicted gene 1.0345 HP1027 fur 1.1997 HP1047 rbfA 1.0606 HP1051 Predicted gene 1.1447 HP1080 Membrane protein 1.3598 HP1081 Predicted gene 1.5337...”
• Trends in Helicobacter pylori resistance to clarithromycin: from phenotypic to genomic approaches
  Marques, Microbial genomics 2020
  • “...spoT [bifunctional (p)ppGpp synthase] gene is involved in tolerance to CLA, upregulating transporter genes (HP0939, HP1017, HP0497 and HP0471) [ 49 ]. Overall, the mechanisms besides mutations in 23S rRNA appear to potentiate the effect of ribosomal mutations by interfering either with other translation machinery or...”
  • “...spot Is involved in the clarithromycin tolerance of Helicobacter pylori by upregulating the Transporters HP0939, HP1017, HP0497, and HP0471 Antimicrob Agents Chemother 2017 61 10.1128/AAC.02011-16 50 Malfertheiner P Megraud F O'Morain CA Gisbert JP Kuipers EJ et al Management of Helicobacter pylori infection-the maastricht v/florence consensus...”
• The Bifunctional Enzyme SpoT Is Involved in the Clarithromycin Tolerance of Helicobacter pylori by Upregulating the Transporters HP0939, HP1017, HP0497, and HP0471
  Geng, Antimicrobial agents and chemotherapy 2017
  • “...SpoT Is Involved in the Clarithromycin Tolerance of Helicobacter pylori by Upregulating the Transporters HP0939, HP1017, HP0497, and HP0471 SpoT and H. pylori Adaption to Clarithromycin Geng et al. Geng Xiwen a Li Wen a Chen Zhenghong b Gao Sizhe a Hong Wei b Ge Xiaoran...”
  • “...SpoT is involved in the clarithromycin tolerance of Helicobacter pylori by upregulating the transporters HP0939, HP1017, HP0497, and HP0471. Antimicrob Agents Chemother 61:e02011-16. https://doi.org/10.1128/AAC.02011-16 . 27 2 2017 24 4 2017 5 2017 24 4 2017 61 5 e02011-16 16 9 2016 23 10 2016 21...”
• Characterisation of worldwide Helicobacter pylori strains reveals genetic conservation and essentiality of serine protease HtrA
  Tegtmeyer, Molecular microbiology 2016
  • “...genome sequence of strain 26695, the htrA locus comprises 6,288 bp and contained six genes/domains (HP1017 to HP1022) organised in tight linkage (Fig. 1 A). In this scheme, the htrA gene is separated into two genes, called HP1018 and HP1019 (Tomb etal ., 1997 ). However,...”
  • “...htrA gene region Region/domain Gene n Size a (bp) Polymorphism Selection P H HD D HP1017 ( rocE ) Amino acid permease 53 1560 291 50 0.998 0.04176 0.50786 HP1018/1019 ( htrA ) Serine protease 53 1428 296 50 0.997 0.04963 0.10142 HP1020 Conserved hypothetical protein...”
• Metabolism and genetics of Helicobacter pylori: the genome era
  Marais, Microbiology and molecular biology reviews : MMBR 1999
  • “...gene from Bacillus subtilis encoding arginase, and ORF HP1017, with similarity to the rocE gene encoding an arginine transporter. Moreover, an aliphatic amidase...”

NP_001012631 high affinity cationic amino acid transporter 1 from Sus scrofa
24% identity, 64% coverage

• Transmissible gastroenteritis virus infection decreases arginine uptake by downregulating CAT-1 expression.
  Xia, Veterinary research 2018
  • GeneRIF: High performance liquid chromatography (HPLC) analyses showed that Transmissible gastroenteritis virus infection leads to reduced arginine uptake at 48 hours post-infection (hpi). Expression of cationic amino acid transporter 1 (CAT-1) was attenuated as well.
• Dietary arginine supplementation enhances intestinal expression of SLC7A7 and SLC7A1 and ameliorates growth depression in mycotoxin-challenged pigs.
  Yin, Amino acids 2014 (PubMed)
  • GeneRIF: Arginine supplementation enhances small intestinal expression of SLC7A7 and SLC7A1.
• Expression of cationic amino acid transporters, carcass traits, and performance of growing pigs fed low-protein amino acid-supplemented versus high protein diets.
  Morales, Genetics and molecular research : GMR 2013 (PubMed)
  • GeneRIF: Changes in the expression of b(0,+) and CAT-1 in pigs fed on amino acid supplemented versus high proteins diets.
• Expression profiles of miRNA-122 and its target CAT1 in minipigs (Sus scrofa) fed a high-cholesterol diet.
  Cirera, Comparative medicine 2010
  • GeneRIF: Data show that in minipigs, increased weight and cholesterol resulting from a high-cholesterol diet are correlated with a decrease in the expression of miRNA-122, and that gene expression levels of CAT1 do not differ between groups.
• Molecular cloning, characterization, and chromosomal assignment of porcine cationic amino acid transporter-1.
  Cui, Genomics 2005 (PubMed)
  • GeneRIF: Radiation hybrid mapping data indicate that the porcine SLC7A1 maps to the distal end of the short arm of pig chromosome 11

AT3G03720 CAT4 (CATIONIC AMINO ACID TRANSPORTER 4); cationic amino acid transmembrane transporter from Arabidopsis thaliana
25% identity, 49% coverage

• Cellular export of sugars and amino acids: role in feeding other cells and organisms
  Kim, Plant physiology 2021
  • “...-coexpressed UmamiTs , AAP family protein PUT1 (At1g31820), AAP1 (At1g58360), cationic amino acid transporters CAT4 (At3g03720), CAT9 (At1g05940), and CAT2 (At1g58030) is indicated. The logit score for UmamiT45 was 14.2. Figure 4 The role of SWEETs and UmamiTs in Arabidopsis, rice, and maize. A, The role...”
• Transcription of putative tonoplast transporters in response to glyphosate and paraquat stress in Conyza bonariensis and Conyza canadensis and selection of reference genes for qRT-PCR
  Moretti, PloS one 2017
  • “...amino acid transporter (CAT), [ 22 ]. In Arabidopsis , both CAT2 (AT1G58030) and CAT4 (AT3G03720) encode CATs which are primarily localized to the tonoplast [ 23 ], making them appropriate candidates for the vacuolar sequestration of paraquat. In glyphosate-paraquat-resistant (GPR) Conyza spp ., reduced translocation...”
  • “...MRP8 (M11) NM_112148.3 AT3G13090 JSWR01014711.1 67 4e -105 CATIONIC AMINO ACID TRANSPORTER 4 (CAT4) NM_111243.7 AT3G03720 JSWR01002601.1 77 2e -37 NM_179491.2 AT1G58030 83 5-ENOL-PYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) NM_130093.2 AT2G45300 AY545666; JSWR01004464.1 78 7e -41 AY545667; JSWR01002887.1 77 3e -39 AY545668; JSWR01015937.1 71 2e -23 a Gene nomenclature...”
• Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
  Wan, Genome biology 2015
  • “...AT5G53530, AT5G01990, AT3G55320, AT4G13750, AT1G16820, AT1G77140, AT5G05570, AT5G07770, AT2G21340, AT2G27460, AT1G74720, AT1G47550, AT5G66380, AT5G47490, AT5G08470, AT3G03720, AT5G61310, AT5G62600, AT5G11980, AT1G56290, AT2G20840, AT2G15240, AT4G39420, AT5G07980, [ 15 21 ] Defense or stress response AT1G63770, AT1G64790, AT1G67090, AT1G80030, AT2G05580, AT2G27380, AT2G35510, AT2G42560, AT3G20290, AT3G22640, AT3G49600, AT4G01210, AT4G04920, AT4G08230,...”
• The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis
  Elashry, Plant physiology and biochemistry : PPB 2013
  • “...0.2 0.43 At1g58032 AtCAT2 not available on GeneChip At5g36940 AtCAT3 7.8 6 1.8 a 0.00 At3g03720 AtCAT4 6.7 5.4 1.3 0.03 At2g34960 AtCAT5 3.5 3.1 0.4 0.24 At5g04770 AtCAT6 5.3 5.9 0.6 0.03 At3g10600 AtCAT7 3.3 3 0.3 0.20 At1g17120 AtCAT8 6.5 5.6 0.9 a 0.00...”
• A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture
  Jaquinod, Molecular & cellular proteomics : MCP 2007
  • “...2d Transp. NF NF At5g40670 At1g05940 At1g58030 At3g03720 At1g17120 At3g30390 At2g41190 At2g39130 At2g40420 At3g28960 At1g70330 31,007 60,138 67,072 63,597...”

XP_069905166 high affinity cationic amino acid transporter 1 from Oryctolagus cuniculus
23% identity, 63% coverage

• Rabbit SLC15A1, SLC7A1 and SLC1A1 genes are affected by site of digestion, stage of development and dietary protein content.
  Liu, Animal : an international journal of animal bioscience 2019 (PubMed)
  • GeneRIF: Real time-PCR results indicated that SLC15A1, SLC7A1 and SLC1A1 genes throughout the rabbits' entire development and were expressed in all tested rabbit digestive sites, including the stomach, duodenum, jejunum, ileum, colon and cecum.

H281DRAFT_04042 phenylacetate transporter from Paraburkholderia bryophila 376MFSha3.1
26% identity, 74% coverage

• mutant phenotype: Specifically important for phenylacetate utilization.

F1QGJ2 B(0,+)-type amino acid transporter 1 from Danio rerio
26% identity, 76% coverage

• The zebrafish cationic amino acid transporter/glycoprotein-associated family: sequence and spatiotemporal distribution during development of the transport system b^0,+ (slc3a1/slc7a9)
  Ellingsen, Fish physiology and biochemistry 2021
  • “...the zebrafish Slc3a1 and Slc7a9 proteins using their primary sequences (UniProtKB peptide IDs: F1QEA9 and F1QGJ2, respectively; see Table S1 ). The search for templates directly targeted the human heteromeric amino acid transporter b 0,+ AT-rBAT complex bound to the arginine structure (Protein Data Bank Acc....”

BAT1_RABIT / Q9N1R6 b(0,+)-type amino acid transporter 1; b(0,+)AT; 4F2-LC6; Glycoprotein-associated amino acid transporter b0,+AT1; Solute carrier family 7 member 9 from Oryctolagus cuniculus (Rabbit) (see paper)
26% identity, 76% coverage

• function: Mediates the electrogenic exchange between cationic amino acids and neutral amino acids, with a stoichiometry of 1:1 (By similarity). Has system b(0,+)-like activity with high affinity for extracellular cationic amino acids and L-cystine and lower affinity for intracellular neutral amino acids (By similarity). Substrate exchange is driven by high concentration of intracellular neutral amino acids and the intracellular reduction of L-cystine to L-cysteine (By similarity). Required for reabsorption of L-cystine and dibasic amino acids across the brush border membrane in renal proximal tubules (By similarity).
  catalytic activity: L-leucine(out) + L-arginine(in) = L-leucine(in) + L- arginine(out) (RHEA:71059)
  catalytic activity: L-histidine(out) + L-arginine(in) = L-histidine(in) + L- arginine(out) (RHEA:71063)
  catalytic activity: L-phenylalanine(out) + L-arginine(in) = L-phenylalanine(in) + L-arginine(out) (RHEA:71067)
  catalytic activity: L-cysteine(out) + L-arginine(in) = L-cysteine(in) + L- arginine(out) (RHEA:71071)
  catalytic activity: L-cystine(out) + L-arginine(in) = L-cystine(in) + L- arginine(out) (RHEA:71075)
  catalytic activity: L-lysine(out) + L-arginine(in) = L-lysine(in) + L- arginine(out) (RHEA:70827)
  subunit: Disulfide-linked heterodimer composed of the catalytic light chain subunit SLC7A9 and the heavy chain subunit. The heterodimer is the minimal functional unit. Assembles in heterotetramers (dimers of heterodimers) and higher order oligomers (By similarity). Interacts with CAV1 (By similarity).

XCC1343 S-methylmethionine transporter from Xanthomonas campestris pv. campestris str. ATCC 33913
27% identity, 65% coverage

• A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage
  Pruvost, PloS one 2014
  • “...36 polymorphic TR loci were identified. Five of these were not further considered because (i) Xcc1343, Xcc1742 and Xcc2572 did not provide amplicons for all X. citri pv. citri strains; (ii) Xcc3912 and its flanking regions were found twice in the IAPAR 306 genome; and (iii)...”

ABA1_03676 amino acid permease from Acinetobacter baumannii
25% identity, 65% coverage

• Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1
  Holt, Microbial genomics 2016
  • “...ABA1_02860 ( gyrA ) DNA gyrase, A subunit 81 TCATTA SL NS (4) Drug resistance ABA1_03676 Proline-specific permease proY 331 AGTGGT SG NS () Transport ABA1_03708 DNA-3-methyladenine glycosylase 1 24 GGCGGT GG S () * NS, non-synonymous; S, synonymous. (), both the indicated substitution and its...”

ABZJ_03790 amino acid permease from Acinetobacter baumannii MDR-ZJ06
25% identity, 65% coverage

• Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach
  Hua, Frontiers in cellular and infection microbiology 2017
  • “...0.001813 ABZJ_00922 hypothetical protein 1.07121 5.599955 7.64E-05 0.000424 ABZJ_01907 response regulator 1.07682 6.813752 2.94E-07 2.90E-06 ABZJ_03790 gamma-aminobutyrate permease 1.07931 8.18838 3.71E-05 0.000227 ABZJ_00882 hypothetical protein 1.07943 9.751157 2.22E-11 4.34E-10 ABZJ_01078 hypothetical protein 1.08109 10.14275 5.68E-14 1.49E-12 ABZJ_01132 glutamate dehydrogenase/leucine dehydrogenase 1.08366 7.760303 2.14E-07 2.24E-06 ABZJ_03802 putative...”

NP_001041574 B(0,+)-type amino acid transporter 1 from Canis lupus familiaris
26% identity, 76% coverage

• SLC7A9 cDNA cloning and mutational analysis of SLC3A1 and SLC7A9 in canine cystinuria.
  Harnevik, Mammalian genome : official journal of the International Mammalian Genome Society 2006 (PubMed)
  • GeneRIF: Mutation analysis of 2 cystinuria disease genes revealed one SLC7A9 mutation (A217T) and two SLC3A1 mutations (I192V and S698G) in French and English Bulldogs that affect nonconserved amino acid residues, arguing against functional impact on the proteins.

EF2047 amino acid permease family protein from Enterococcus faecalis V583
25% identity, 78% coverage

• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...protein protein protein protein protein protein protein protein protein EF2047 EF2058 EF2059 EF2226 EF2364 EF2377 EF2485 EF2509 EF2641 EF2642 0 0 0 0 0.73 0 0 0...”

HD73_0562 amino acid permease from Bacillus thuringiensis serovar kurstaki str. HD73
26% identity, 67% coverage

• Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis
  Peng, Frontiers in microbiology 2015
  • “...Quaternary ammonium compound-resistance protein 2.377 HD73_0560 Biotin carboxyl carrier protein - HD73_0561 Hypothetical protein - HD73_0562 Amino-acid permease rocC - HD73_1024 Proline racemase 62.621 HD73_1025 Hypothetical protein 3.687 HD73_1070 Glutamine amidotransferase, class I 5.429 HD73_2540 L-lysine 2,3-aminomutase 2.685 HD73_2541 Cytoplasmic protein 2.296 HD73_3140 Hypothetical protein 73.623...”

FPSM_00250 amino acid permease from Flavobacterium psychrophilum
22% identity, 82% coverage

• Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum
  Gliniewicz, BMC microbiology 2015
  • “...PBP 1A 155877 100 A>T 43 FPSM_00129 Leu71Phe Putative exported protein 283611 80 A>T 10 FPSM_00250 Asn522Ile Amino acid permease 325469 100 T>A 4 FPSM_00287 Met1Leu Thioredoxin 488182 100 A>C 4 FPSM_00425 Gln466Pro DNA primase 514297 86.4 C>T 162 FPSM_00445 Ala11Thr Malonyl-CoA-[acyl-carrier-protein] transacylase 548737 100 A>T...”

NP_001007330 solute carrier family 7, member 3 from Danio rerio
24% identity, 61% coverage

• Genetic ablation of solute carrier family 7a3a leads to hepatic steatosis in zebrafish during fasting.
  Gu, Hepatology (Baltimore, Md.) 2014 (PubMed)
  • GeneRIF: null mutants have hepatic steatosis

HUTT_PSEFS / C3K810 L-histidine transporter HutT from Pseudomonas fluorescens (strain SBW25) (see 2 papers)
PFLU0368 putative histidine ABC transport system, permease from Pseudomonas fluorescens SBW25
25% identity, 65% coverage

• function: Major high-affinity histidine transporter (PubMed:22225938). Binds and catalyzes the uptake of histidine into the cell (By similarity). Functions as an histidine:proton symporter with high specificity for histidine (By similarity). Required for histidine utilization, but not for competitive colonization of sugar beet seedlings (PubMed:16735749).
  catalytic activity: L-histidine(out) + n H(+)(out) = L-histidine(in) + n H(+)(in) (RHEA:76379)
  disruption phenotype: The mutant grows normally on urocanate but shows delayed growth on histidine (PubMed:22225938). The deletion mutant grows normally on minimal medium with glucose and ammonia and on minimal medium with proline as a sole carbon and nitrogen source, but not when histidine is the sole source of carbon and nitrogen (PubMed:16735749). The deletion mutant is not compromised in its ability to colonize sugar beet seedlings (PubMed:16735749).
• Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25
  Zhang, Genetics 2007
  • “...encode an ABC-type transport system and pflu0362 and pflu0368 encode predicted permeases 1/2pflu0368 is required for histidine utilization (Zhang et al. 2006)....”

CV1138 proline-specific permease from Chromobacterium violaceum ATCC 12472
26% identity, 66% coverage

• Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis
  Lau, Cell & bioscience 2011
  • “...Proline and glycine betaine uptake - CV1197 - - Proline-specific permease proY Proline uptake - CV1138 - - Osmoprotectant transport system substrate-binding protein - Osmoprotectants uptake - CV1195 CV4392 - - Osmoprotectant transport system permease protein - Osmoprotectants uptake - CV1194 CV1196 CV4393 CV4395 - -...”

XP_039296817 cationic amino acid transporter 2-like isoform X1 from Nilaparvata lugens
24% identity, 66% coverage

• Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species (Nilaparvata lugens)
  Yue, Frontiers in physiology 2021
  • “...124016.4 7.73 NlAPC16 XP_039296825 Nlug17187-TA chr14 16084741 16128173 615 21 14 67035.3 8.49 + NlAPC17 XP_039296817 Nlug17189-TA chr14 15988763 16025229 611 13 15 66179.6 8.42 NlAPC18 XP_039296923 Nlug20896-TA chr14 18470291 18500414 628 10 14 67808.4 6.34 NlAPC19 XP_039296913 Nlug21374-TA chr14 17485099 17501514 475 8 10 51234.1...”

E2QU34 Cationic amino acid transporter 1 from Canis lupus familiaris
24% identity, 62% coverage

• Exosome proteomes reveal glycolysis-related enzyme enrichment in primary canine mammary gland tumor compared to metastases.
  Kim, Proteome science 2024
  • “...659060 E2R1I9 166180 206360 226490 501360 428540 371000 CON__P02676 164330 148880 173720 117990 180290 168060 E2QU34 163970 142220 158390 92954 156900 153320 J9P652 163480 132150 155460 149480 410710 350310 E2RCZ6 162040 207100 242930 50159 69357 63185 J9P6J1 160770 237630 278570 663940 385130 354120 CON__Q2KJF1 160630 242730...”

CDBI1_00900 APC family permease from Clostridioides difficile BI1
27% identity, 50% coverage

• The Alternative Sigma Factor SigL Influences Clostridioides difficile Toxin Production, Sporulation, and Cell Surface Properties
  Clark, Frontiers in microbiology 2022
  • “...q -value Motif sequence CD0166-0165 630 CD630_01650 putative amino acid transporter 26.888 0.001 TGGCATAATAATTGCTTA BI-1 CDBI1_00900 amino acid permease 26.888 0.001 TGGCATAATAATTGCTTA CDC1 Not identified CD2699-CD2697 630 CD630_26970 putative peptidase, M20D family 22.888 0.007 TGGCATAAGTTTTGCTTA BI-1 CDBI1_13130 amidohydrolase 22.888 0.007 TGGCATAAGTTTTGCTTA CDC1 Not identified CD0284-0289 630...”

HUTT_PSEPK / Q88CZ8 L-histidine transporter HutT from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
PP5031, PP_5031 amino acid transporter from Pseudomonas putida KT2440
25% identity, 65% coverage

• function: Major high-affinity histidine transporter (PubMed:34245008). Binds and catalyzes the uptake of histidine into the cell (PubMed:34245008). Functions as an histidine:proton symporter with high specificity for histidine (PubMed:34245008).
  catalytic activity: L-histidine(out) + n H(+)(out) = L-histidine(in) + n H(+)(in) (RHEA:76379)
  disruption phenotype: Deletion of the gene severely impairs growth on histidine.
• Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
  Schmidt, Applied and environmental microbiology 2022 (secret)
• Transport and kinase activities of CbrA of Pseudomonas putida KT2440
  Wirtz, Scientific reports 2020
  • “...generated a strain devoid of cbrA and other genes for putative histidine transporters [ hutT (PP_5031, encodes the main inducible histidine transporter) and hutXW (PP_3558/PP_3559, encode a putative periplasmic binding protein and an integral membrane component of a putative ABC transporter) 19 . In addition, hutH...”
• FinR Regulates Expression of nicC and nicX Operons, Involved in Nicotinic Acid Degradation in Pseudomonas putida KT2440
  Xiao, Applied and environmental microbiology 2018
  • “...PP_4625 PP_4626 PP_4735 PP_4736 PP_4737 PP_5029 PP_5030 PP_5031 PP_5032 PP_5033 PP_5036 PP_5073 PP_5269 PP_5270 PP_5338 PP_5549 Log2 fold change 2.207 2.856...”
• The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents
  Duque, Journal of bacteriology 2007
  • “...PP4403 PP4561 PP4739 PP4870 PP4933 PP5029 PP5030 PP5031 PP5032 PP5033 PP5035 Formate dehydrogenase accessory protein FdhD Outer membrane protein OprG Fructose...”
  • “...PP4523 PP4548 PP4624 PP4870 PP5028 PP5029 PP5030 PP5031 PP5032 PP5033 PP5036 PP5390 PP5392 Conserved hypothetical protein Pyridine nucleotide transhydrogenase,...”
• Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25
  Zhang, Genetics 2007
  • “...HutH (36) HutH (84) HutT (84) HutI (70) PP5032 PP5032 PP5031 PP5030 HutG (75) PP5029 (73) HutG (72) Not available PP5036 (82) PA5106 (76) (38) (97) (86) (80)...”

SSUSC84_1836 putative S-methylmethionine permease from Streptococcus suis SC84
SSU1814 S-methylmethionine permease from Streptococcus suis P1/7
25% identity, 67% coverage

• Comparative transcriptomic analysis reveal genes involved in the pathogenicity increase of Streptococcus suis epidemic strains
  Wang, Virulence 2022
  • “...E SSUSC84_1606 SSU1580 MUN40_02765 5,10-methylenetetrahydrofolate reductase MetF E SSUSC84_1835 SSU1813 - Homocysteine S-methyltransferaseMmuM UDC20 E SSUSC84_1836 SSU1814 - Amino acid transporterMmuP E 4h SSUSC84_0130 SSU0135 MUN40_01225 Folate family ECF transporter S component UDC3 E -: absent in the corresponding genome. RNA-Seq sequencing and gene expression analysis...”
  • “...displayed a downregulation. Except for homologous genes of three DEGs SSUSC84_0921 , SSUSC84_1835 , and SSUSC84_1836 absent in the 891591 genome, the remaining 25 DEGs belonged to core genes of three genomes. The homologous genes of SSUSC84_1406 , SSUSC84_1605 , and SSUSC84_1606 were also upregulated in...”
• Comparative transcriptomic analysis reveal genes involved in the pathogenicity increase of Streptococcus suis epidemic strains
  Wang, Virulence 2022
  • “...SSUSC84_1606 SSU1580 MUN40_02765 5,10-methylenetetrahydrofolate reductase MetF E SSUSC84_1835 SSU1813 - Homocysteine S-methyltransferaseMmuM UDC20 E SSUSC84_1836 SSU1814 - Amino acid transporterMmuP E 4h SSUSC84_0130 SSU0135 MUN40_01225 Folate family ECF transporter S component UDC3 E -: absent in the corresponding genome. RNA-Seq sequencing and gene expression analysis Illumina...”

NP_004164 cationic amino acid transporter 4 from Homo sapiens
O43246 Cationic amino acid transporter 4 from Homo sapiens
27% identity, 54% coverage

• Association of serotonin and dopamine gene pathways with behavioral subphenotypes in dementia.
  Proitsi, Neurobiology of aging 2012 (PubMed)
  • GeneRIF: Observational study of gene-disease association, gene-gene interaction, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
• Influence of serotonin transporter gene polymorphisms on clozapine response in Brazilian schizophrenics.
  Kohlrausch, Journal of psychiatric research 2010 (PubMed)
  • GeneRIF: Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
• The role of clinical variables, neuropsychological performance and SLC6A4 and COMT gene polymorphisms on the prediction of early response to fluoxetine in major depressive disorder.
  Gudayol-Ferré, Journal of affective disorders 2010 (PubMed)
  • GeneRIF: Clinical trial of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
• Characterization of de novo diffuse large B-cell lymphoma with a translocation of c-myc and immunoglobulin genes.
  Kikuchi, Leukemia research 2008 (PubMed)
  • GeneRIF: These results suggest a heterogeneous immunophenotype and genotype for c-myc/Ig DLBCL, with CD10(-)/BCL6(+)/MUM1(-) cases the most frequent.
• Comparative analysis of ZAP-70 expression and Ig VH mutational status in B-cell chronic lymphocytic leukemia.
  Muñoz, Cytometry. Part B, Clinical cytometry 2007 (PubMed)
  • GeneRIF: ZAP-70 reactivity using a T-cell marker as a control allows to identify the majority of patients with an unmutated Ig VH genotype.
• Expression of solute carrier 7A4 (SLC7A4) in the plasma membrane is not sufficient to mediate amino acid transport activity.
  Wolf, The Biochemical journal 2002
  • GeneRIF: expression in cell membrane is not sufficient for amino acid transport (SOLUTE CARRIER SLC7A4)
• Analysis of the genomic organization of the human cationic amino acid transporters CAT-1, CAT-2 and CAT-4.
  Hammermann, Amino acids 2001 (PubMed)
  • GeneRIF: analysis of the genomic organization
• Predicting Drug-Target Interactions Based on the Ensemble Models of Multiple Feature Pairs
  Wang, International journal of molecular sciences 2021
  • “...In addition, two predicted drugtarget pairs were demonstrated as interactions (Lysine (DB00194) interacts with SLC7A4 (O43246) [ 40 , 41 ], and Micafungin (DB01141) interacts with FKSA (A2QLK4)) [ 42 , 43 ]. 5. Conclusions In this work, an algorithm based on the Ensemble models of...”
• The Concise Guide to PHARMACOLOGY 2013/14: transporters
  Alexander, British journal of pharmacology 2013
  • “...Common abbreviation CAT1 CAT2 CAT3 CAT4 HGNC, UniProt SLC7A1, P30825 SLC7A2, P52569 SLC7A3, Q8WY07 SLC7A4, O43246 SLC7A14, Q8TBB6 Substrates L-arginine, L-lysine, L-ornithine, L-histidine L-arginine, L-lysine, L-ornithine, L-histidine L-arginine, L-lysine, L-ornithine Glycoprotein-associated amino acid transporters are 12 TM proteins, which heterodimerize with members of the SLC3 family...”

AO356_18530 L-tyrosine transporter from Pseudomonas fluorescens FW300-N2C3
25% identity, 77% coverage

• mutant phenotype: Specific phenotype with tyrosine as the nitrogen source. Not important if phenylalanine is the nitrogen source.

GBAA0492 amino acid permease family protein from Bacillus anthracis str. 'Ames Ancestor'
26% identity, 67% coverage

• An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics
  Okinaka, BMC genomics 2011
  • “...aa GBAA0382 47140 ABC transporter, substrate binding W * GBAA0414 435861 Hypothetical protein I V GBAA0492 488260 Amino Acid permease family A V GBAA0715 734957 ABC phosphate binding protein Q * GBAA0925 935719 Putative lipoprotein E G GBAA1301 1248597 PAP 2 family protein S N GBAA1858...”

SG0465 aromatic amino acid transport protein from Sodalis glossinidius str. 'morsitans'
26% identity, 74% coverage

• Metabolic networks of Sodalis glossinidius: a systems biology approach to reductive evolution
  Belda, PloS one 2012
  • “...always present in all minimal networks under nutrient-rich conditions, but not under nutrient-limited conditions, was SG0465, coding for an aromatic amino acid permease (AroP), responsible for transporting the biomass constituents histidine, phenylalanine, tyrosine and tryptophan in both E. coli K12 iJR904 and S. glossinidius networks. The...”

BAT1_HUMAN / P82251 b(0,+)-type amino acid transporter 1; b(0,+)AT1; Glycoprotein-associated amino acid transporter b0,+AT1; Solute carrier family 7 member 9 from Homo sapiens (Human) (see 16 papers)
TC 2.A.3.8.19 / P82251 B(0,+)-type amino acid transporter 1 (B(0,+)AT) (Glycoprotein-associated amino acid transporter b0,+AT1) (Solute carrier family 7 member 9) from Homo sapiens (see 9 papers)
XP_011524704 B(0,+)-type amino acid transporter 1 isoform X1 from Homo sapiens
26% identity, 76% coverage

• function: Associates with SLC3A1 to form a functional transporter complex that mediates the electrogenic exchange between cationic amino acids and neutral amino acids, with a stoichiometry of 1:1 (PubMed:16825196, PubMed:32494597, PubMed:32817565, PubMed:8663357). Has system b(0,+)-like activity with high affinity for extracellular cationic amino acids and L-cystine and lower affinity for intracellular neutral amino acids (PubMed:16825196, PubMed:32494597, PubMed:8663357). Substrate exchange is driven by high concentration of intracellular neutral amino acids and the intracellular reduction of L-cystine to L- cysteine (PubMed:8663357). Required for reabsorption of L-cystine and dibasic amino acids across the brush border membrane in renal proximal tubules.
  catalytic activity: L-leucine(out) + L-arginine(in) = L-leucine(in) + L- arginine(out) (RHEA:71059)
  catalytic activity: L-histidine(out) + L-arginine(in) = L-histidine(in) + L- arginine(out) (RHEA:71063)
  catalytic activity: L-phenylalanine(out) + L-arginine(in) = L-phenylalanine(in) + L-arginine(out) (RHEA:71067)
  catalytic activity: L-cysteine(out) + L-arginine(in) = L-cysteine(in) + L- arginine(out) (RHEA:71071)
  catalytic activity: L-cystine(out) + L-arginine(in) = L-cystine(in) + L- arginine(out) (RHEA:71075)
  catalytic activity: L-lysine(out) + L-arginine(in) = L-lysine(in) + L- arginine(out) (RHEA:70827)
  subunit: Disulfide-linked heterodimer composed of the catalytic light chain subunit SLC7A9 and the heavy chain subunit SLC3A1. The heterodimer is the minimal functional unit. Assembles in heterotetramers (dimers of heterodimers) and higher order oligomers; the oligomerization is mediated by SLC3A1 likely to prevent degradation and facilitate heteromer trafficking to the plasma membrane (PubMed:16825196, PubMed:32494597, PubMed:32817565). Interacts with CAV1 (By similarity).
• substrates: Amino acids
• Interpretation of SLC3A1 and SLC7A9 variants in cystinuria patients: The significance of the PM3 criterion and protein stability.
  Lee, Urolithiasis 2023
  • GeneRIF: Interpretation of SLC3A1 and SLC7A9 variants in cystinuria patients: The significance of the PM3 criterion and protein stability.
• Population genetics analysis of SLC3A1 and SLC7A9 revealed the etiology of cystine stone may be more than what our current genetic knowledge can explain.
  Wu, Urolithiasis 2023 (PubMed)
  • GeneRIF: Population genetics analysis of SLC3A1 and SLC7A9 revealed the etiology of cystine stone may be more than what our current genetic knowledge can explain.
• SLC7A9 as a Potential Biomarker for Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma.
  Baba, Annals of surgical oncology 2022 (PubMed)
  • GeneRIF: SLC7A9 as a Potential Biomarker for Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma.
• Clinical profile of a Polish cohort of children and young adults with cystinuria.
  Tkaczyk, Renal failure 2021
  • GeneRIF: Clinical profile of a Polish cohort of children and young adults with cystinuria.
• Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
  Wu, Proceedings of the National Academy of Sciences of the United States of America 2020
  • GeneRIF: Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
• In silico analysis of SLC3A1 and SLC7A9 mutations in Iranian patients with Cystinuria.
  Mahdavi, Molecular biology reports 2018 (PubMed)
  • GeneRIF: Study shows that various computational tools were able to distinguish cystinuria-causing mutations from benign polymorphisms. Only missense mutation V142A had a benign effect on the protein structure and function of SLC7A9. The intron variant c.604+66C>G in SLC7A9 gene probably affected the splicing process.
• Clinical, Biochemical, and Genetic Findings of Cystinuria in Chinese Children.
  Ma, Clinical laboratory 2018 (PubMed)
  • GeneRIF: A homozygous c.325G>A mutation in cationic amino cid transport proteins (SLC7A9) was identified in two patients, and six neutral and basic amino acid transporter protein (SLC3A1) mutations were found in five patients.
• A Novel Mutation in SLC7A9 Gene in Cystinuria.
  Fazaeli, Iranian journal of kidney diseases 2017 (PubMed)
  • GeneRIF: A new variation in exon 4 of the SLC7A9 gene was identified in cystinuria patients, which was insertion of 1 adenine nucleotide between 2 cytosine nucleotides in position c.213-214insA.
• More
• Predicting hotspots for disease-causing single nucleotide variants using sequences-based coevolution, network analysis, and machine learning.
  Zheng, PloS one 2024
  • “...association and relative motions. 10.1371/journal.pone.0302504.g003 Fig 3 Results for amino acid transporter 1 (Uniprot id: P82251). (a) Four contact maps constructed from coevolution analysis by DeepMetaPSICOV (DMP), RaptorX (RX), SPOT-Contact (SC), and the predicted structure by AlphaFold (AF) (only those contacts with probability >0.1 are shown)....”
• They all rock: A systematic comparison of conformational movements in LeuT-fold transporters.
  Licht, bioRxiv : the preprint server for biology 2024
  • “...alanine X-ray 2.86 C _BasC A8UCQ5 6F2G (A) I op n/a X-ray 2.92 Hs BAT1 P82251 6LI9 (B) I op arginine cryo-EM 2.3 Ec GadC P63235 4DJK (A) I op n/a X-ray 3.097 Hs LAT2 Q9UHI5 7CMI (B) I op leucine cryo-EM 2.9 Hs xCT Q9UPY5...”
• Compendium of causative genes and their encoded proteins for common monogenic disorders.
  Apgar, Protein science : a publication of the Protein Society 2022
• Identify Molecular Mechanisms of Jiangzhi Decoction on Nonalcoholic Fatty Liver Disease by Network Pharmacology Analysis and Experimental Validation.
  Wang, BioMed research international 2020
  • “...Nuclear receptor subfamily 1 group H member 3 19 P13716 210 ALAD Aminolevulinate dehydratase 20 P82251 11136 SLC7A9 Solute carrier family 7 member 9 21 Q8N159 162417 NAGS N-Acetylglutamate synthase 22 P21549 189 AGXT Alanine-glyoxylate and serine-pyruvate aminotransferase 23 P34896 6470 SHMT1 Serine hydroxymethyltransferase 1 24...”
• Effects of Mutations and Ligands on the Thermostability of the l-Arginine/Agmatine Antiporter AdiC and Deduced Insights into Ligand-Binding of Human l-Type Amino Acid Transporters.
  Ilgü, International journal of molecular sciences 2018
  • “...of the used proteins are: P60061 (AdiC), Q01650 (SCL7A5), Q92536 (SLC7A6), Q9UM01 (SLC7A7), Q9UHI5 (SLC7A8), P82251 (SLC7A9), Q9NS82 (SLC7A10), Q9UPY5 (SLC7A11), and Q8TCU3 (SLC7A13). 3.5. Homology Models and Ligand Docking We show a previously published homology model of LAT1 bound to phenylalanine, which was built based...”
• THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
  Alexander, British journal of pharmacology 2017
  • “...SLC7A6 SLC7A9 SLC7A10 SLC7A11 SLC7A13 HGNC, UniProt SLC7A7 , Q9UM01 SLC7A6 , Q92536 SLC7A9 , P82251 SLC7A10 , Q9NS82 SLC7A11 , Q9UPY5 SLC7A13 , Q8TCU3 Common abreviation y+LAT1 y+LAT2 b 0,+ AT Asc1 xCT Inhibitors quisqualate (pIC 50 5.3) [ 164 ] Comments CAT4 appears to...”
• The Concise Guide to PHARMACOLOGY 2015/16: Transporters
  Alexander, British journal of pharmacology 2015
  • “...0,+ AT HGNC, UniProt SLC7A8 , Q9UHI5 SLC7A7 , Q9UM01 SLC7A6 , Q92536 SLC7A9 , P82251 Nomenclature Asctype amino acid transporter 1 Cystine/glutamate transporter AGT1 Systematic nomenclature SLC7A10 SLC7A11 SLC7A13 Common abreviation Asc1 xCT HGNC, UniProt SLC7A10 , Q9NS82 SLC7A11 , Q9UPY5 SLC7A13 , Q8TCU3 Comments...”
• State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.
  Farrah, Journal of proteome research 2014
  • “...0 0 4 2 glomerulus UBE2Q2 Q8WVN8 Ubiquitin-conjugating enzyme E2 Q2 0 0 0 SLC7A9 P82251 B(0,+)-type amino acid transporter 1 0 0 0 CPS1 P31327 Carbamoyl-phosphate synthase [ammonia], mitochondrial 0 0 0.012 SLC22A2 O15244 Solute carrier family 22 member 2 3.1 0 0 44 2...”
• More

LYSP_LACLM / A2RNZ6 Lysine-specific permease LysP; Lysine transporter LysP from Lactococcus lactis subsp. cremoris (strain MG1363) (see paper)
llmg_2477 lysine specific permease from Lactococcus lactis subsp. cremoris MG1363
24% identity, 68% coverage

• function: Permease involved in lysine uptake.
  catalytic activity: L-lysine(out) + H(+)(out) = L-lysine(in) + H(+)(in) (RHEA:28911)
  disruption phenotype: Deletion of the gene abolishes high-affinity lysine uptake without affecting growth on free amino acids.
• Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs
  van, Frontiers in microbiology 2017
  • “...7.2 NCDO_2243/7 llmg_2309/13 arcABD1C1C2 : arginine deiminase pathway 10.9 2.1 2.8 0.7 2.2 0.6 NCDO_2384 llmg_2477 lysP : Lysine-specific permease 8.0 2.1 4.9 TRANSPORTERS, ABC/PTC/PORIN NCDO_0184 llmg_0454 bglP: PTS system. trehalose-specific IIB component 17.4 2.4 3.2 NCDO_0191 llmg_0446 msmK: Multiple sugar ABC transporter. ATP-binding protein 3.0...”
• Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
  Chen, Scientific reports 2015
  • “...L. lactis . For the other genes, which play minor roles in the thermal tolerance, llmg_2477 and llmg_2541 encodes lysine specific permease and cation transporting ATPase, respectively. They could be involved in the aforementioned transport process for nutrients supplement and ion homeostasis. The role of TrmD...”
  • “...RNA polymerase subunit beta GluLys 2358022 SNP GA cdsA Phosphatidate cytidylyltransferase ProLeu 2434453 SNP GA llmg_2477 Lysine specific permease AlaSer 2497054 SNP GA llmg_2541 Cation transporting ATPase AlaThr 1322282- llmg_1349- DEL 1334514 llmg_1358 a Reference position refers to the genome sequence of L. lactis MG1363 (GenBank...”
• Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR
  Pinto, PloS one 2011
  • “...llmg_2163 Putative stress-responsive transcriptional regulator 11.88 2.5*10 9 llmg_2420 Putative uncharacterized protein 1.29 9.7*10 3 llmg_2477 Lysine-specific permease 2.91 6.3*10 6 A full-genome DNA microarray analysis was performed, comparing L. lactis NZ9000 (pNZ bcaP -H6) and L. lactis NZ9000 (pNZ8048; empty vector control) (See Experimental Procedures)....”

NP_001265934 cationic amino acid transporter 2, vacuolar-like from Solanum lycopersicum
25% identity, 60% coverage

• Bacterial production and reconstitution in proteoliposomes of Solanum lycopersicum CAT2: a transporter of basic amino acids and organic cations.
  Regina, Plant molecular biology 2017 (PubMed)
  • GeneRIF: CAT2 is a transporter of basic amino acids and organic cations. [CAT2]

AAA1_MOUSE / P63115 Asc-type amino acid transporter 1; Asc-1; D-serine transporter; Solute carrier family 7 member 10 from Mus musculus (Mouse) (see 5 papers)
AAA1_RAT / P63116 Asc-type amino acid transporter 1; Asc-1; D-serine transporter; Solute carrier family 7 member 10 from Rattus norvegicus (Rat) (see paper)
TC 2.A.3.8.13 / P63115 The Asc-type small neutral D- and L-amino acid:H+ symport transporter-1, Asc-1 (Slc7a10). Also transports amino acid related compounds. Heterodimeric; associates with 4F2hc (TC# 8.A.9.2.1) Most highly expressed in brain and lung, but to a lesser degree in placenta and small intestine. from Mus musculus (Mouse) (see 3 papers)
Slc7a10 Asc-type amino acid transporter 1 from Mus musculus (see paper)
27% identity, 66% coverage

• function: Associates with SLC3A2/4F2hc to form a functional heterodimeric complex that translocates small neutral L- and D-amino acids across the plasma membrane. Preferentially mediates exchange transport, but can also operate via facilitated diffusion (By similarity) (PubMed:10734121). Acts as a major transporter for glycine, L- and D-serine in the central nervous system. At the spinal cord and brainstem regulates glycine metabolism and glycinergic inhibitory neurotransmission by providing for glycine de novo synthesis from L- serine and glycine recycling from astrocytes to glycinergic motor neurons (PubMed:25755256, PubMed:27759100). At Schaffer collateral-CA1 synapses mediates D-serine and glycine release that modulates post- synaptic activation of NMDA receptors and excitatory glutamatergic transmission (By similarity). May regulate D-serine release from mesenchymal progenitors located in developing subcutaneous adipose tissue, favoring white adipocyte over thermogenic beige adipocyte lineage commitment (PubMed:33707431).
  catalytic activity: L-alanine(in) + glycine(out) = L-alanine(out) + glycine(in) (RHEA:74019)
  catalytic activity: L-serine(out) + L-alanine(in) = L-serine(in) + L-alanine(out) (RHEA:74023)
  catalytic activity: L-threonine(out) + L-alanine(in) = L-threonine(in) + L- alanine(out) (RHEA:74027)
  catalytic activity: L-cysteine(out) + L-alanine(in) = L-cysteine(in) + L- alanine(out) (RHEA:74031)
  catalytic activity: 2-aminoisobutanoate(out) + L-alanine(in) = 2- aminoisobutanoate(in) + L-alanine(out) (RHEA:74063)
  catalytic activity: D-serine(out) + L-alanine(in) = D-serine(in) + L-alanine(out) (RHEA:74035)
  catalytic activity: D-alanine(out) + L-alanine(in) = D-alanine(in) + L- alanine(out) (RHEA:74039)
  catalytic activity: L-valine(out) + L-alanine(in) = L-valine(in) + L-alanine(out) (RHEA:74047)
  catalytic activity: L-alanine(in) + L-methionine(out) = L-alanine(out) + L- methionine(in) (RHEA:74043)
  catalytic activity: beta-alanine(out) + L-alanine(in) = beta-alanine(in) + L- alanine(out) (RHEA:74059)
  catalytic activity: D-cysteine(out) + L-alanine(in) = D-cysteine(in) + L- alanine(out) (RHEA:74055)
  catalytic activity: D-threonine(out) + L-alanine(in) = D-threonine(in) + L- alanine(out) (RHEA:74051)
  catalytic activity: D-isoleucine(out) + D-serine(in) = D-isoleucine(in) + D- serine(out) (RHEA:74299)
  catalytic activity: D-serine(in) = D-serine(out) (RHEA:29455)
  subunit: Disulfide-linked heterodimer with the amino acid transport protein SLC3A2/4F2hc.
  disruption phenotype: Mutant mice develop hyperekplexia-like phenotype due to impaired glycinergic inhibitory transmission. Administration of glycine and L-serine reverses the phenotype.
• function: Associates with SLC3A2/4F2hc to form a functional heterodimeric complex that translocates small neutral L- and D-amino acids across the plasma membrane. Preferentially mediates exchange transport, but can also operate via facilitated diffusion (By similarity) (PubMed:23426681). Acts as a major transporter for glycine, L- and D-serine in the central nervous system. At the spinal cord and brainstem regulates glycine metabolism and glycinergic inhibitory neurotransmission by providing for glycine de novo synthesis from L- serine and glycine recycling from astrocytes to glycinergic motor neurons (By similarity). At Schaffer collateral-CA1 synapses mediates D-serine and glycine release that modulates post-synaptic activation of NMDA receptors and excitatory glutamatergic transmission (PubMed:23426681). May regulate D-serine release from mesenchymal progenitors located in developing subcutaneous adipose tissue, favoring white adipocyte over thermogenic beige adipocyte lineage commitment (By similarity).
  catalytic activity: L-alanine(in) + glycine(out) = L-alanine(out) + glycine(in) (RHEA:74019)
  catalytic activity: L-serine(out) + L-alanine(in) = L-serine(in) + L-alanine(out) (RHEA:74023)
  catalytic activity: L-threonine(out) + L-alanine(in) = L-threonine(in) + L- alanine(out) (RHEA:74027)
  catalytic activity: L-cysteine(out) + L-alanine(in) = L-cysteine(in) + L- alanine(out) (RHEA:74031)
  catalytic activity: 2-aminoisobutanoate(out) + L-alanine(in) = 2- aminoisobutanoate(in) + L-alanine(out) (RHEA:74063)
  catalytic activity: D-serine(out) + L-alanine(in) = D-serine(in) + L-alanine(out) (RHEA:74035)
  catalytic activity: D-alanine(out) + L-alanine(in) = D-alanine(in) + L- alanine(out) (RHEA:74039)
  catalytic activity: L-valine(out) + L-alanine(in) = L-valine(in) + L-alanine(out) (RHEA:74047)
  catalytic activity: L-alanine(in) + L-methionine(out) = L-alanine(out) + L- methionine(in) (RHEA:74043)
  catalytic activity: beta-alanine(out) + L-alanine(in) = beta-alanine(in) + L- alanine(out) (RHEA:74059)
  catalytic activity: D-cysteine(out) + L-alanine(in) = D-cysteine(in) + L- alanine(out) (RHEA:74055)
  catalytic activity: D-threonine(out) + L-alanine(in) = D-threonine(in) + L- alanine(out) (RHEA:74051)
  catalytic activity: D-isoleucine(out) + D-serine(in) = D-isoleucine(in) + D- serine(out) (RHEA:74299)
  catalytic activity: D-serine(in) = D-serine(out) (RHEA:29455)
  subunit: Disulfide-linked heterodimer with the amino acid transport protein SLC3A2/4F2hc.
• substrates: Amino Acid derivatives, D-Amino Acids, H+, L-Amino Acids

BCI_0393 lysine-specific permease from Baumannia cicadellinicola str. Hc (Homalodisca coagulata)
27% identity, 65% coverage

• Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
  Wu, PLoS biology 2006
  • “...(GapA) (BCI_0443), general amino acid ABC transporter (BCI_0250, BCI_02070208), arginine/lysine ABC transporter (BCI_03230326), lysine permease (BCI_0393), proton/sodium-glutamate symport protein (BCI_0108), and aspartate ammonia-lyase AspA (BCI_0593), We are grateful to Heather Costa for assistance with sharpshooter collecting in Riverside and to Colin Dale and Wendy Smith for...”

PA0866 aromatic amino acid transport protein AroP2 from Pseudomonas aeruginosa PAO1
26% identity, 75% coverage

• The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa
  Kotecka, International journal of molecular sciences 2021
  • “...PA2264, and amino acid metabolism PA3459, PA5170 (ArcD), PA5100 (HutU), PA2015 (LiuA), PA2016 (LiuR), and PA0866 (AroP2). Among these, the PA3458 binding site with the highest fold enrichment was found in the promoter region of the PA3459 PA3461 . RNA-seq analysis showed significantly decreased expression of...”
  • “...exert the effect on gene expression regulation as exemplified by PA1596 , PA2247 , or PA0866 as target genes of PA3458, but the molecular mechanism of gene expression control in this way requires further studies. The weaker PA3458 interactions with less conserved binding sites scattered in...”
• Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa
  Sonnleitner, PloS one 2012
  • “...crcZ vs. wt PA0755 opdH 5,9 2,05 cis -aconitate porin OpdH AAGAACAA (25 to 18) PA0866 aroP2 4,73 aromatic amino acid transport protein AACAAUAA (33 to 12) PA0887 acsA 3,41 2,51 3,27 7,98 2,88 3,62 acetyl-coenzyme A synthetase AACAAAAACAA (35 to 25) PA0996 pqsA 3,55 3,49...”
• Characterization of the Pseudomonas aeruginosa transcriptional response to phenylalanine and tyrosine
  Palmer, Journal of bacteriology 2010
  • “...PA1000 PA1001 PA1002 Aromatic amino acid catabolism PA0865 PA0866 PA0870 PA0871 PA0872 PA0873 PA1999 PA2000 PA2001 PA2002 PA2006 PA2007 PA2008 PA2009 Other...”
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...amino acid APC family transporter PA0783 PAK proline/sodium transporter PA0789 PAK proline APC family transporter PA0866 PAK aromatic amino acid APC family transporter PA0888 PAK pili- arginine/ornithine ABC transporter periplasmic binding protein ( AotJ ) PA0889 PA01 arginine/ornithine ABC transporter membrane protein ( AotQ ) PA0890...”
• Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum
  Palmer, Journal of bacteriology 2007
  • “...acid transport and degradation Gene Function or class PA0782 PA0865 PA0866 PA0870 PA0871 PA0872 PA0897 putA hpd aroP2 phhC phhB phhA aruG 4.3 66 13 9 5 32 3...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...ECs0116, 3: ECs4729, 4: ECs0452, 5: ECs5186, 6: ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743,...”
• Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
  Palmer, Journal of bacteriology 2005
  • “...ORFa Amino acid transport and degradation PA0782 PA0865 PA0866 PA0870 PA0871 PA0872 PA0897 PA0898 PA2001 PA2007 PA2008 PA2009 PA2247 PA2248 PA2249 PA2250 PA3766...”

J3U91_01734 APC family permease from Oenococcus oeni
24% identity, 76% coverage

• Analysis of Transcriptomic Response to SO₂ by Oenococcus oeni Growing in Continuous Culture
  Onetto, Microbiology spectrum 2021
  • “...malolactic enzyme 0.45 1.15 0.31 0.84 J3U91_01682 abfA; alpha- l- arabinofuranosidase ND 1.05 ND 0.61 J3U91_01734 APA; basic amino acid/polyamine antiporter, APA family ND 1.34 ND 0.90 J3U91_01750 alr; alanine racemase 0.29 1.25 0.29 0.75 J3U91_01778 kdgR; LacI family transcriptional regulator, kdg operon repressor ND 1.29...”

SCO2914 amino acid permease from Streptomyces coelicolor A3(2)
27% identity, 65% coverage

• Deletion of a cyclic AMP receptor protein homologue diminishes germination and affects morphological development of Streptomyces coelicolor
  Derouaux, Journal of bacteriology 2004
  • “...in amino acids) SCO2545 SCO3571 SCO2914 SCO3945 SCO4280 SCO4281(c) SCO4562 SCO4561(c) SCO5029 SCO5864 GTATGTGACCTAGATCACATCA ATCCTTGTGACAGATCACACTGTT...”

CAAT3_ARATH / Q8GYB4 Cationic amino acid transporter 3, mitochondrial from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G36940 CAT3 (CATIONIC AMINO ACID TRANSPORTER 3); basic amino acid transmembrane transporter/ cationic amino acid transmembrane transporter from Arabidopsis thaliana
26% identity, 56% coverage

• function: Permease involved in the transport of the cationic neutral or acidic amino acids.
• DEG10 contributes to mitochondrial proteostasis, root growth, and seed yield in Arabidopsis
  Huber, Journal of experimental botany 2019
  • “...bp between intron 9 of the Cationic Amino Acid Transporter 3 gene ( CATR3 ; At5g36940, previously referred to as CAT3 , although this is commonly used for Catalase 3 ) and exon 8 of DEG10 ( Fig. 4A ). Since we did not find any...”
• Overexpression of a tomato miR171 target gene SlGRAS24 impacts multiple agronomical traits via regulating gibberellin and auxin homeostasis
  Huang, Plant biotechnology journal 2017
  • “...1 allergen and extensin 1.16 1.23 Solyc12g014580.1 Pollen allergen Ole e 6 1.14 1.29 Solyc10g081460.1 AT5G36940 CAT3, involved in amino acid transport 1.1 1.06 Solyc09g010090.2 AT3G52600 Cell wall invertase 2, involved in sucrose catabolic process 1.33 1.23 Solyc01g107830.2 AT3G53160.1 UDPglycosyltransferase superfamily protein 2.66 3.4 Hormone signallingrelated...”
• Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
  Wan, Genome biology 2015
  • “...AT2G07687, AT2G07698, AT2G07741, AT2G41700, AT3G08650, AT3G08960, AT3G17430, AT3G20560, AT3G20920, AT3G46830, AT4G00630, AT4G00800, AT4G38920, AT4G39850, AT5G27970, AT5G36940, AT5G53530, AT5G01990, AT3G55320, AT4G13750, AT1G16820, AT1G77140, AT5G05570, AT5G07770, AT2G21340, AT2G27460, AT1G74720, AT1G47550, AT5G66380, AT5G47490, AT5G08470, AT3G03720, AT5G61310, AT5G62600, AT5G11980, AT1G56290, AT2G20840, AT2G15240, AT4G39420, AT5G07980, [ 15 21 ] Defense or...”
• The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis
  Elashry, Plant physiology and biochemistry : PPB 2013
  • “...4.6 0.6 0.13 At4g21120 AtCAT1 4.4 4.6 0.2 0.43 At1g58032 AtCAT2 not available on GeneChip At5g36940 AtCAT3 7.8 6 1.8 a 0.00 At3g03720 AtCAT4 6.7 5.4 1.3 0.03 At2g34960 AtCAT5 3.5 3.1 0.4 0.24 At5g04770 AtCAT6 5.3 5.9 0.6 0.03 At3g10600 AtCAT7 3.3 3 0.3 0.20...”

TC 2.A.3.1.18 / K7VV21 The lysine specific transporter, LysP of 488 aas and 12 TMSs from Lactococcus lactis subsp. cremoris UC509.9
24% identity, 68% coverage

• substrates: lysine

CD2465 amino acid transporter from Clostridium difficile 630
26% identity, 75% coverage

• Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile
  Saujet, PLoS genetics 2013
  • “...CD1789 Putative membrane protein, DUF421 family 0.61 G + CD1789-CD1788 CD1788 Conserved hypothetical protein 0.43 CD2465 Putative amino acid/polyamine transporter 0.36 0.52 G + stress CD1567 cotG putative manganese catalase 0.25 0.27 G + CD2845 rbr Rubrerythrin 0.14 0.27 G + CD1631 sodA Superoxide dismutase (Mn)...”
  • “...recently identified [48] . Nine genes encoding probable membrane proteins (CD0792, CD0793, CD1677, CD1789, CD2051, CD2465, CD2635, CD2636, CD3551.1) were downregulated in the sigG mutant and these proteins may be involved in germination. 55% of our G -controlled genes encode proteins associated to the spore in...”
• Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores
  Lawley, Journal of bacteriology 2009
  • “...substrate-binding proteins for ABC transporters. Only one transporter (CD2465), predicted to facilitate the import of amino acids, is found in the spore...”

P42087 Putative histidine permease from Bacillus subtilis (strain 168)
BSU39390 histidine permease from Bacillus subtilis subsp. subtilis str. 168
27% identity, 67% coverage

• Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae.
  Van't, The FEBS journal 2020
  • “...P37460 , P25737 , P15993 , P0AAE0 , P25527 , P77610 , P39137 , and P42087 corresponding to PheP, ProY, LysP, AroP, CycA, GabP, AnsP, RocE, and HutM, respectively. This resulted in a population of 450, 105, and 835 sequences for yeast, mammalian, and bacterial proteins,...”
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU32740 BSU32750 No No 3DHW 3DHW E. coli E. coli BSU39390 No BSU09130 No Yes BSU36900 Yes Yes BSU09460 No BSU33330 No Yes Yes Yes 3.6.3.14 3.6.3.14 Yes S...”

BAT1_RAT / P82252 b(0,+)-type amino acid transporter 1; b(0,+)AT; Glycoprotein-associated amino acid transporter b0,+AT1; Solute carrier family 7 member 9 from Rattus norvegicus (Rat) (see 2 papers)
TC 2.A.3.8.15 / P82252 The b0,+ amino acid (cystine) transporter associated with the cystinuria-related type II membrane glycoprotein, BAT1 which forms a heterodimer with rBAT (TC# 8.A.9.1.1). Present in the apical membrane of renal proximal tubules from Rattus norvegicus (Rat) (see 2 papers)
26% identity, 76% coverage

• function: Associates with SLC3A1 to form a functional transporter complex that mediates the electrogenic exchange between cationic amino acids and neutral amino acids, with a stoichiometry of 1:1 (By similarity) (PubMed:10506124). Has system b(0,+)-like activity with high affinity for extracellular cationic amino acids and L-cystine and lower affinity for intracellular neutral amino acids (By similarity). Substrate exchange is driven by high concentration of intracellular neutral amino acids and the intracellular reduction of L-cystine to L- cysteine (By similarity). Required for reabsorption of L-cystine and dibasic amino acids across the brush border membrane in renal proximal tubules (By similarity).
  catalytic activity: L-leucine(out) + L-arginine(in) = L-leucine(in) + L- arginine(out) (RHEA:71059)
  catalytic activity: L-histidine(out) + L-arginine(in) = L-histidine(in) + L- arginine(out) (RHEA:71063)
  catalytic activity: L-phenylalanine(out) + L-arginine(in) = L-phenylalanine(in) + L-arginine(out) (RHEA:71067)
  catalytic activity: L-cysteine(out) + L-arginine(in) = L-cysteine(in) + L- arginine(out) (RHEA:71071)
  catalytic activity: L-cystine(out) + L-arginine(in) = L-cystine(in) + L- arginine(out) (RHEA:71075)
  catalytic activity: L-lysine(out) + L-arginine(in) = L-lysine(in) + L- arginine(out) (RHEA:70827)
  subunit: Disulfide-linked heterodimer composed of the catalytic light chain subunit SLC7A9 and the heavy chain subunit SLC3A1. The heterodimer is the minimal functional unit. Assembles in heterotetramers (dimers of heterodimers) and higher order oligomers; the oligomerization is mediated by SLC3A1 likely to prevent degradation and facilitate heteromer trafficking to the plasma membrane (By similarity) (PubMed:10506124). Interacts with CAV1 (PubMed:16358225).
• substrates: Cystine

AROP_CORGL / Q46065 Aromatic amino acid transport protein AroP; General aromatic amino acid permease from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) (see paper)
TC 2.A.3.1.12 / Q46065 Aromatic amino acid permease, AroP from Corynebacterium glutamicum (Brevibacterium flavum) (see 2 papers)
cg1257 aromatic amino acid transporter from Corynebacterium glutamicum ATCC 13032
25% identity, 73% coverage

• function: Permease that is involved in the active transport across the cytoplasmic membrane of all three aromatic amino acids, phenylalanine, tyrosine and tryptophan.
  catalytic activity: L-phenylalanine(in) + H(+)(in) = L-phenylalanine(out) + H(+)(out) (RHEA:28923)
  catalytic activity: L-tryptophan(in) + H(+)(in) = L-tryptophan(out) + H(+)(out) (RHEA:28879)
  catalytic activity: L-tyrosine(in) + H(+)(in) = L-tyrosine(out) + H(+)(out) (RHEA:28875)
  disruption phenotype: Mutants show reduced aromatic amino acids uptake.
• substrates: Histidine, phenylalanine, tryptophan, tyrosine
• Functional Characterization of the γ-Aminobutyric Acid Transporter from Mycobacterium smegmatis MC² 155 Reveals Sodium-Driven GABA Transport
  Pavić, Journal of bacteriology 2021
  • “...subtilis GabP ( P46349 ), Streptomyces coelicolor ( Q9L202 ), and Corynebacterium glutamicum AroP ( Q46065 ), a protein characterized as an aromatic amino acid transporter. The second group has a less varied taxonomic distribution and comprises mainly Actinobacteria sequences, including MsGabP and MtbGabP, but also...”
• Anaerobic growth of Corynebacterium glutamicum via mixed-acid fermentation
  Michel, Applied and environmental microbiology 2015
  • “...NCgl0464 gapP Cg0953 Cg1016 Cg1105 Cg1167 Cg1169 Cg1257 Cg1305 Cg1314 Cg2537 Cg2539 Cg2563 Cg3080 Cg3357 NCgl0799 NCgl0856 NCgl0929 NCgl0985 NCgl0986 NCgl1062...”

y4036 aromatic amino acid permease from Yersinia pestis KIM
24% identity, 65% coverage

• LPS modification promotes maintenance of Yersinia pestis in fleas
  Aoyagi, Microbiology (Reading, England) 2015
  • “...The 17B4 mutation is located between y4035 (hypothetical) and y4036 (proY), and may 635 K. L. Aoyagi and others affect the promoter of y4035, interfering with...”

XAC4354 amino acid transporter from Xanthomonas axonopodis pv. citri str. 306
24% identity, 85% coverage

• The citrus plant pathogen Xanthomonas citri has a dual polyamine-binding protein
  Cremonesi, Biochemistry and biophysics reports 2021
  • “...(PuuA/PuuP), an amino acid transporter (H + ) symporter, the proteins XAC3863/3864, XAC1841/1842 (YhdG) and XAC4354 (YhdG) forming three distinct cationic amino acid/polyamine antiporters, and the proteins XAC0856 to XAC0860 ( Fig. 2 ). The latter was previously described as the components of an oligopeptide ABC...”

CTR2_HUMAN / P52569 Cationic amino acid transporter 2; CAT-2; CAT2; Low affinity cationic amino acid transporter 2; Solute carrier family 7 member 2 from Homo sapiens (Human) (see 3 papers)
TC 2.A.3.3.8 / P52569 Low affinity cationic amino acid transporter 2 (CAT-2) (CAT2) (Solute carrier family 7 member 2) from Homo sapiens (see 6 papers)
XP_016869235 cationic amino acid transporter 2 isoform X1 from Homo sapiens
23% identity, 56% coverage

• function: Functions as a permease involved in the transport of the cationic amino acids (L-arginine, L-lysine, L-ornithine and L- homoarginine); the affinity for its substrates differs between isoforms created by alternative splicing (PubMed:28684763, PubMed:9174363). May play a role in classical or alternative activation of macrophages via its role in arginine transport (By similarity).
  function: [Isoform 1]: Functions as a permease that mediates the transport of the cationic amino acids (L-arginine, L-lysine, L- ornithine and L-homoarginine). Shows a much higher affinity for L- arginine and L-homoarginine than isoform 2.
  function: [Isoform 2]: Functions as a low-affinity, high capacity permease involved in the transport of the cationic amino acids (L- arginine, L-lysine, L-ornithine and L-homoarginine).
  catalytic activity: [Isoform 1]: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: [Isoform 2]: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: L-lysine(in) = L-lysine(out) (RHEA:70935)
  catalytic activity: L-ornithine(in) = L-ornithine(out) (RHEA:71199)
  catalytic activity: [Isoform 1]: L-homoarginine(in) = L-homoarginine(out) (RHEA:71203)
  catalytic activity: [Isoform 2]: L-homoarginine(in) = L-homoarginine(out) (RHEA:71203)
• substrates: Amino acids
• System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation.
  Borisov, International journal of molecular sciences 2020
  • “...SERPINC1 Antithrombin-III UniProtKB: P36955 SERPINF1 Pigment epithelium-derived factor UniProtKB: Q86VZ5 SGMS1 Phosphatidylcholine:ceramide cholinephosphotransferase 1 UniProtKB: P52569 SLC7A2 Cationic amino acid transporter 2 UniProtKB: P52569 SLC7A2 Cationic amino acid transporter 2 UniProtKB: Q15797 SMAD1 Mothers against decapentaplegic homolog 1 UniProtKB: P84022 SMAD3 Mothers against decapentaplegic homolog 3...”
• LocText: relation extraction of protein localizations to assist database curation
  Cejuela, BMC bioinformatics 2018
  • “...the tonoplast in transformed Arabidopsis protoplasts, PMID (PubMed Identifier) 15377779, the relationship of CAT2 (UniProtKB: P52569) localized to tonoplast (GO:0009705) must be established. Most existing GO annotation methods either coarsely associate all pairs of entities that are co-mentioned in a same sentence or otherwise aggregate the...”
• THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
  Alexander, British journal of pharmacology 2017
  • “...2 Systematic nomenclature SLC7A1 SLC7A2 SLC7A3 SLC7A5 SLC7A8 HGNC, UniProt SLC7A1 , P30825 SLC7A2 , P52569 SLC7A3 , Q8WY07 SLC7A5 , Q01650 SLC7A8 , Q9UHI5 Common abreviation CAT1 CAT2 CAT3 LAT1 LAT2 Substrates Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine ,...”
• The Concise Guide to PHARMACOLOGY 2015/16: Transporters
  Alexander, British journal of pharmacology 2015
  • “...SLC7A3 SLC7A5 Common abreviation CAT1 CAT2 CAT3 LAT1 HGNC, UniProt SLC7A1 , P30825 SLC7A2 , P52569 SLC7A3 , Q8WY07 SLC7A5 , Q01650 Substrates Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine Nomenclature Ltype amino acid...”
• The Concise Guide to PHARMACOLOGY 2013/14: transporters
  Alexander, British journal of pharmacology 2013
  • “...SLC7A2 SLC7A3 SLC7A4 SLC7A14 Common abbreviation CAT1 CAT2 CAT3 CAT4 HGNC, UniProt SLC7A1, P30825 SLC7A2, P52569 SLC7A3, Q8WY07 SLC7A4, O43246 SLC7A14, Q8TBB6 Substrates L-arginine, L-lysine, L-ornithine, L-histidine L-arginine, L-lysine, L-ornithine, L-histidine L-arginine, L-lysine, L-ornithine Glycoprotein-associated amino acid transporters are 12 TM proteins, which heterodimerize with members...”
• Elevated SLC7A2 expression is associated with an abnormal neuroinflammatory response and nitrosative stress in Huntington's disease.
  Gaudet, Journal of neuroinflammation 2024
  • GeneRIF: Elevated SLC7A2 expression is associated with an abnormal neuroinflammatory response and nitrosative stress in Huntington's disease.
• SLC7A2-Mediated Lysine Catabolism Inhibits Immunosuppression in Triple Negative Breast Cancer.
  Sun, Critical reviews in eukaryotic gene expression 2024 (PubMed)
  • GeneRIF: SLC7A2-Mediated Lysine Catabolism Inhibits Immunosuppression in Triple Negative Breast Cancer.
• Lower SLC7A2 expression is associated with enhanced multidrug resistance, less immune infiltrates and worse prognosis of NSCLC.
  Jiang, Cell communication and signaling : CCS 2023
  • GeneRIF: Lower SLC7A2 expression is associated with enhanced multidrug resistance, less immune infiltrates and worse prognosis of NSCLC.
• Integrated Amino Acids and Transcriptome Analysis Reveals Arginine Transporter SLC7A2 Is a Novel Regulator of Myogenic Differentiation.
  Huang, International journal of molecular sciences 2023
  • GeneRIF: Integrated Amino Acids and Transcriptome Analysis Reveals Arginine Transporter SLC7A2 Is a Novel Regulator of Myogenic Differentiation.
• SLC7A2 deficiency promotes hepatocellular carcinoma progression by enhancing recruitment of myeloid-derived suppressors cells.
  Xia, Cell death & disease 2021
  • GeneRIF: SLC7A2 deficiency promotes hepatocellular carcinoma progression by enhancing recruitment of myeloid-derived suppressors cells.
• Human cationic amino acid transporters are not affected by direct nitros(yl)ation.
  Hobbach, Amino acids 2020 (PubMed)
  • GeneRIF: Human cationic amino acid transporters are not affected by direct nitros(yl)ation.
• SLC7A2 serves as a potential biomarker and therapeutic target for ovarian cancer.
  Sun, Aging 2020
  • GeneRIF: SLC7A2 serves as a potential biomarker and therapeutic target for ovarian cancer.
• Genetic variation in SLC7A2 interacts with calcium and magnesium intakes in modulating the risk of colorectal polyps.
  Sun, The Journal of nutritional biochemistry 2017
  • GeneRIF: genetic association studies in population in Tennessee: Data suggest that an SNP in SLC7A2 (rs2720574) is associated with response to dietary calcium and magnesium in prevention of colorectal polyps and colorectal ademonas.
• More

ADIC_SALTY / P60066 Arginine/agmatine antiporter from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
STM14_5166 arginine/agmatine antiporter from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
P60065 Arginine/agmatine antiporter from Salmonella typhi
25% identity, 84% coverage

• function: Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach (Probable). Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons (PubMed:19578361). Probably undergoes several conformational states in order to translocate the substrate across the membrane; keeps the substrate accessible to only 1 side of the membrane at a time by opening and closing 3 membrane-internal gates (By similarity).
  catalytic activity: agmatine(in) + L-arginine(out) = agmatine(out) + L- arginine(in) (RHEA:29651)
  subunit: Homodimer; each subunit has its own individual transport capacity.
• Utilizing nutrient type compounds as anti-bacterial compounds: arginine and cysteine inhibit Salmonella survival in egg white
  Ben-Porat, Frontiers in bioengineering and biotechnology 2024
  • “...hisM histidine/lysine/arginine/ornithine transport protein 1.50 0.44912 0.93284 STM14_2899 hisQ histidine/lysine/arginine/ornithine transport protein 0.76 0.59059 0.97854 STM14_5166 yjdE, adiC arginine:agmatin antiporter 1.00 0.58828 0.97854 Arginine metabolism STM14_5357 STM14_5357 putative arginine repressor 2.97 0.14279 0.63919 STM14_5169 adi catabolic arginine decarboxylase 2.68 0.17457 0.69005 STM14_3729 speA arginine decarboxylase 1.01...”
• High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding
  Ilgü, BMC biology 2021
  • “...O157:H7 (P60063), PotE E. coli K12 (P0AAF1), CadB E. coli K12 (P0AAE8), hAdiC Salmonella typhi (P60065), hAdiC Shigella flexneri (P60064), hCadB Vibrio cholerae (WP_000097425.1) and hAdiC Yersinia enterocolitica (WP_174848373.1). Positions with a single, fully conserved residue are indicated by (*), conservation between groups of strongly and...”
• They all rock: A systematic comparison of conformational movements in LeuT-fold transporters.
  Licht, bioRxiv : the preprint server for biology 2024
  • “...n/a X-ray 2.73 Dr SCL38A9 Q08BA4 6C08 (C) I op arginine X-ray 3.17 St AdiC P60066 3NCY (A) O op n/a X-ray 3.2 Mm AgcS Q6LX42 6CSE (M) O oc alanine X-ray 3.24 Mj ApcT Q58026 3GIA (A) I op n/a X-ray 2.32 Gk ApcT Q5L1G5...”
• Role of transmembrane domain 8 in substrate selectivity and translocation of SteT, a member of the L-amino acid transporter (LAT) family
  Bartoccioni, The Journal of biological chemistry 2010
  • “...of the SteT (Swiss-Prot O34739) and AdiC (Swiss-Prot P60066) sequences (supplemental Fig. S1), which exhibit only 22% sequence identity, was aided by comparison...”

YPO4015 amino acid permease from Yersinia pestis CO92
24% identity, 65% coverage

• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937). Table 1 Results of the algorithm on the COGs database # % Pairs with score below threshold, not tested 1021764 44.0 Pairs with score above threshold...”

CTR1_HUMAN / P30825 High affinity cationic amino acid transporter 1; CAT-1; CAT1; Ecotropic retroviral leukemia receptor homolog; Ecotropic retrovirus receptor homolog; Solute carrier family 7 member 1; System Y+ basic amino acid transporter from Homo sapiens (Human) (see 4 papers)
TC 2.A.3.3.9 / P30825 High affinity cationic amino acid transporter 1 (CAT-1) (CAT1) (Ecotropic retroviral leukemia receptor homologue) (Ecotropic retrovirus receptor homologue) (ERR) (Solute carrier family 7 member 1) (System Y+ basic amino acid transporter) from Homo sapiens (see 6 papers)
23% identity, 64% coverage

• function: High-affinity, low capacity permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine) in non-hepatic tissues.
  catalytic activity: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: L-lysine(in) = L-lysine(out) (RHEA:70935)
  catalytic activity: L-ornithine(in) = L-ornithine(out) (RHEA:71199)
  catalytic activity: L-homoarginine(in) = L-homoarginine(out) (RHEA:71203)
  subunit: Interacts with TM4SF5; the interaction is negatively regulated by arginine (PubMed:30956113). Forms tissue-specific complexes with ASL, ASS1 and nitric oxide synthase NOS1 or NOS3; the complex regulates cell-autonomous L-arginine synthesis and citrulline recycling while channeling extracellular L-arginine to nitric oxide synthesis pathway (By similarity).
• substrates: Amino acids
• Isolation method of brain microvessels from small frozen human brain tissue for blood-brain barrier protein expression analysis.
  Ogata, Fluids and barriers of the CNS 2024
  • “...- SLC6A12 P48065 Detected only in Bcap - SLC2A1 (GLUT1) P11166 122 4.66E-06 SLC7A1 (ATRC1) P30825 36.7 8.42E-05 SLC16A1 (MCT1) P53985 15.8 5.55E-02 SLC5A6 (SMVT) Q9Y289 15.3 9.17E-03 SLC9A3R2 (NHERF2) Q15599 12.0 3.42E-05 SLC38A3 (SNAT3) Q99624 7.41 9.82E-04 SLC7A5 (LAT1) Q01650 5.92 6.38E-05 SLC30A1 (ZNT1) Q9Y6M5...”
• Surfaceome Profiling of Cell Lines and Patient-Derived Xenografts Confirm FGFR4, NCAM1, CD276, and Highlight AGRL2, JAM3, and L1CAM as Surface Targets for Rhabdomyosarcoma
  Timpanaro, International journal of molecular sciences 2023
  • “...PE = 1 SV = 2 3.58 10 8 6.30 10 8 0.817 18 82 P30825 SLC7A1 High affinity cationic amino acid transporter 1 OS = Homo sapiens OX = 9606 GN = SLC7A1 PE = 1 SV = 1 1.97 10 8 7.64 10 7...”
• Neurodevelopmental signatures of narcotic and neuropsychiatric risk factors in 3D human-derived forebrain organoids.
  Notaras, Molecular psychiatry 2021
  • “...Dehydrogenase E1 Component DHKTD1, Mitochonondrial Q96HY7 0.018748869 SLC7A1 High Affinity Cationic Amino Acid Transporter 1 P30825 0.021172737 PIK3C2B Phosphatidylinositol 4-Phosphate 3-Kinase C2 Domain-Containing Subunit Beta O00750 0.021899148 SORBS1 Sorbin and SH3 Domain-Containing Protein 1 Q9BX66-4 0.024998617 HSPA9 Stress-70 Protein, Mitochondrial P38646 0.027136132 CCDC47 Coiled-Coil domain-Containing Protein...”
• Humoral Immunity Profiling of Subjects with Myalgic Encephalomyelitis Using a Random Peptide Microarray Differentiates Cases from Controls with High Specificity and Sensitivity
  Singh, Molecular neurobiology 2018
  • “...715 119.7 7 NP_060868 CACNA2D3 Calcium voltage-gated channel auxiliary subunit alpha2delta 3 1091 121.2 5 P30825 SLC7A1 Solute carrier family 7 member 1 629 125.8 4 NP_004557 PFKFB3 6-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 520 130 4 XP_011509718 ACOXL Acyl-CoA oxidase-like 547 136.8 Previous studies have proposed that HERV elements...”
• Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line
  Jia, Molecular & cellular proteomics : MCP 2017
  • “...Q9Y265 SARS QARS MAN2B1 LEPRE1 RUVBL1 Q9UGQ3 SLC2A6 P30825 P53618 Q9Y678 Q96RQ1 SLC7A1 COPB1 COPG1 ERGIC2 O15431 O14980 SLC31A1 XPO1 O00400 P48723 Q07021...”
• THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
  Alexander, British journal of pharmacology 2017
  • “...amino acid transporter 2 Systematic nomenclature SLC7A1 SLC7A2 SLC7A3 SLC7A5 SLC7A8 HGNC, UniProt SLC7A1 , P30825 SLC7A2 , P52569 SLC7A3 , Q8WY07 SLC7A5 , Q01650 SLC7A8 , Q9UHI5 Common abreviation CAT1 CAT2 CAT3 LAT1 LAT2 Substrates Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine...”
• Glycomic and sialoproteomic data of gastric carcinoma cells overexpressing ST3GAL4.
  Mereiter, Data in brief 2016
  • “...P21589 5-nucleotidase LDNdeYSTQELGK N333 1.67 0.0479 E P26006 Integrin alpha-3 ELAVPDGYTNdeRTGAVYLCPLTAHK N86 2.68 0.0433 AM P30825 High affinity cationic amino acid transporter 1 LCLNNdeDTK N235 3.48 0.0297 TT LCLNdeNdeDTK N234 3.01 0.0342 P35613 Basigin ALMNdeGSESR N268 2.91 0.0342 P P42892 Endothelin-converting enzyme 1 NdeSSVEAFK N632 1.89...”
• The Concise Guide to PHARMACOLOGY 2015/16: Transporters
  Alexander, British journal of pharmacology 2015
  • “...nomenclature SLC7A1 SLC7A2 SLC7A3 SLC7A5 Common abreviation CAT1 CAT2 CAT3 LAT1 HGNC, UniProt SLC7A1 , P30825 SLC7A2 , P52569 SLC7A3 , Q8WY07 SLC7A5 , Q01650 Substrates Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine Nomenclature...”
• More

B2R728 cDNA, FLJ93255, highly similar to Homo sapiens solute carrier family 7 (cationic amino acidtransporter, y+ system), member 1 (SLC7A1), mRNA from Homo sapiens
23% identity, 64% coverage

• Pharmacoproteomic analysis reveals that metapristone (RU486 metabolite) intervenes E-cadherin and vimentin to realize cancer metastasis chemoprevention
  Yu, Scientific reports 2016
  • “...4 0.527* 11 437 27 J3KQA0 Synaptotagmin I, isoform CRA_b 10 0.694* 12 119 15.4 B2R728 cDNA, FLJ9325 4 0.603* 13 133 23.1 Q13308-2 Isoform 2 of Inactive tyrosine-protein kinase 7 6 0.324** 14 2854 46 A8K28 cDNA FLJ78433 25 0.523* 15 226 12.8 Q9ULX6 A-kinase...”

SPy0016 putative amino acid permease from Streptococcus pyogenes M1 GAS
24% identity, 82% coverage

• Large-scale identification of serotype 4 Streptococcus pneumoniae virulence factors
  Hava, Molecular microbiology 2002 (secret)

RR42_RS28305 L-threonine:H+ symporter from Cupriavidus basilensis FW507-4G11
25% identity, 65% coverage

• mutant phenotype: Specifically important for utilizing threonine as a carbon source

CTR3_HUMAN / Q8WY07 Cationic amino acid transporter 3; CAT-3; CAT3; Cationic amino acid transporter y+; Solute carrier family 7 member 3 from Homo sapiens (Human) (see paper)
TC 2.A.3.3.10 / Q8WY07 Cationic amino acid transporter 3 (CAT-3) (CAT3) (Cationic amino acid transporter y+) (Solute carrier family 7 member 3) from Homo sapiens (see 5 papers)
NP_001041629 cationic amino acid transporter 3 from Homo sapiens
24% identity, 63% coverage

• function: Uniporter that mediates the uptake of cationic L-amino acids such as L-arginine, L-lysine and L-ornithine (PubMed:11591158). The transport is sodium ions- and pH-independent, moderately trans- stimulated and is mediated by passive diffusion (PubMed:11591158).
  catalytic activity: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: L-lysine(in) = L-lysine(out) (RHEA:70935)
  catalytic activity: L-ornithine(in) = L-ornithine(out) (RHEA:71199)
• substrates: Amino acids
• Comparative Bioinformatic Analysis of the Proteomes of Rabbit and Human Sex Chromosomes
  Pinto-Pinho, Animals : an open access journal from MDPI 2024
  • “...acid transporter B(0+) TM PM P48029 SLC6A8 Sodium- and chloride-dependent creatine transporter 1 TM PM Q8WY07 SLC7A3 Cationic amino acid transporter 3 TM PM Q92581 SLC9A6 Sodium/hydrogen exchanger 6 SP+TM PM Q96T83 SLC9A7 Sodium/hydrogen exchanger 7 SP+TM PM Q9H156 SLITRK2 SLIT- and NTRK-like protein 2 SP+TM...”
• The Expression of Rab8, Ezrin, Radixin and Moesin in the Ciliary Body of Cynomolgus Monkeys.
  Tanabe, Juntendo Iji zasshi = Juntendo medical journal 2022
  • “...0.00 1 37 Catenin alpha-1 P35221 100008.6 2.00 1 38 Cationic amino acid transporter 3 Q8WY07 67125.6 1.90 2 39 CD59 glycoprotein P13987 14167.8 8.60 4 40 CD9 antigen P21926 25399.0 5.30 2 41 Centromere protein C 1 Q03188 106860.4 1.30 1 42 Citrate synthase, mitochondrial...”
• THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
  Alexander, British journal of pharmacology 2017
  • “...SLC7A1 SLC7A2 SLC7A3 SLC7A5 SLC7A8 HGNC, UniProt SLC7A1 , P30825 SLC7A2 , P52569 SLC7A3 , Q8WY07 SLC7A5 , Q01650 SLC7A8 , Q9UHI5 Common abreviation CAT1 CAT2 CAT3 LAT1 LAT2 Substrates Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine , Lhistidine Lornithine ,...”
• The Concise Guide to PHARMACOLOGY 2015/16: Transporters
  Alexander, British journal of pharmacology 2015
  • “...abreviation CAT1 CAT2 CAT3 LAT1 HGNC, UniProt SLC7A1 , P30825 SLC7A2 , P52569 SLC7A3 , Q8WY07 SLC7A5 , Q01650 Substrates Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine , Lhistidine Lornithine , Larginine , Llysine Nomenclature Ltype amino acid transporter 2 y+L...”
• Comprehensive quantitative comparison of the membrane proteome, phosphoproteome, and sialiome of human embryonic and neural stem cells
  Melo-Braga, Molecular & cellular proteomics : MCP 2014
  • “...Level ID Protein Description Protein Ratio Q9BV40 Q8WY07 Q14126 Q96SQ9 Q10589 Q15833 P20339 P21709 Q01650 P11169 Q96QD8 P20337 P17302 Q14571 P08195...”
• The Concise Guide to PHARMACOLOGY 2013/14: transporters
  Alexander, British journal of pharmacology 2013
  • “...SLC7A4 SLC7A14 Common abbreviation CAT1 CAT2 CAT3 CAT4 HGNC, UniProt SLC7A1, P30825 SLC7A2, P52569 SLC7A3, Q8WY07 SLC7A4, O43246 SLC7A14, Q8TBB6 Substrates L-arginine, L-lysine, L-ornithine, L-histidine L-arginine, L-lysine, L-ornithine, L-histidine L-arginine, L-lysine, L-ornithine Glycoprotein-associated amino acid transporters are 12 TM proteins, which heterodimerize with members of the...”
• Hypomorphic variants of cationic amino acid transporter 3 in males with autism spectrum disorders.
  Nava, Amino acids 2015
  • GeneRIF: rare hypomorphic variants of SLC7A3 exist in male individuals, SLC7A3 variants possibly contribute to the etiology of autism spectrum disorders in male subjects in association with other genetic factors
• Genetic ablation of solute carrier family 7a3a leads to hepatic steatosis in zebrafish during fasting.
  Gu, Hepatology (Baltimore, Md.) 2014 (PubMed)
  • GeneRIF: knockdown impaired AMPK-PPAR-alpha signaling and resulted in lipid accumulation under glucose starvation in liver cells
• Differential topochemistry of three cationic amino acid transporter proteins, hCAT1, hCAT2 and hCAT3, in the adult human brain.
  Jäger, Amino acids 2013 (PubMed)
  • GeneRIF: CAT1, CAT2, and CAT3 localized in adult brains but with uneven distribution.
• Activation of classical protein kinase C reduces the expression of human cationic amino acid transporter 3 (hCAT-3) in the plasma membrane.
  Rotmann, The Biochemical journal 2006
  • GeneRIF: It is concluded that similar to hCAT-1, hCAT-3 activity is decreased by PKC via reduction of transporter molecules in the plasma membrane.
• Monovalent cation conductance in Xenopus laevis oocytes expressing hCAT-3.
  Gilles, Biochimica et biophysica acta 2005 (PubMed)
  • GeneRIF: is concluded that hCAT-3 is a passive transport system that conducts monovalent cations including L-Arg.

YjdD / b4115 arginine:agmatine antiporter from Escherichia coli K-12 substr. MG1655 (see 3 papers)
adiC / P60061 arginine:agmatine antiporter from Escherichia coli (strain K12) (see 2 papers)
ADIC_ECOLI / P60061 Arginine/agmatine antiporter from Escherichia coli (strain K12) (see 6 papers)
ADIC_ECO57 / P60063 Arginine/agmatine antiporter from Escherichia coli O157:H7 (see 3 papers)
TC 2.A.3.2.5 / P60061 Homodimeric electrogenic arginine (Km=80μM):agmatine antiporter, AdiC, involved in extreme acid resistance (Fang et al., 2007; Gong et al., 2003; Iyer et al., 2003). A projection structure at 6.5 Å resolution has been published (Casagrande et al., 2008), and the 3.2 Å resolution X-ray structure was determined by Fang et al., 2009 and Gao et al., 2009 from Escherichia coli (see 6 papers)
adiC / GB|AAN45533.1 arginine/agmatine antiporter from Shigella flexneri (see 6 papers)
S3622 putative amino acid/amine transport protein from Shigella flexneri 2a str. 2457T
NP_418539 arginine:agmatine antiporter from Escherichia coli str. K-12 substr. MG1655
P60064 Arginine/agmatine antiporter from Shigella flexneri
b4115 arginine:agmatin from Escherichia coli str. K-12 substr. MG1655
Z5717 putative amino acid/amine transport protein, cryptic from Escherichia coli O157:H7 EDL933
26% identity, 84% coverage

• function: Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach (Probable). Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons (PubMed:12867448, PubMed:14594828, PubMed:19578361, PubMed:21368142). Probably undergoes several conformational states in order to translocate the substrate across the membrane; keeps the substrate accessible to only 1 side of the membrane at a time by opening and closing 3 membrane-internal gates (Probable).
  catalytic activity: agmatine(in) + L-arginine(out) = agmatine(out) + L- arginine(in) (RHEA:29651)
  subunit: Homodimer; each subunit has its own individual transport capacity.
  disruption phenotype: Loss of arginine-dependent acid resistance. No coupled transport of arginine and agmatine (PubMed:12867448, PubMed:14594828). No effect on levels of AdiA (PubMed:12867448).
• function: Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach (Probable). Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons (PubMed:19478139, PubMed:25136114). Probably undergoes several conformational states in order to translocate the substrate across the membrane; keeps the substrate accessible to only 1 side of the membrane at a time by opening and closing 3 membrane-internal gates (Probable).
  catalytic activity: agmatine(in) + L-arginine(out) = agmatine(out) + L- arginine(in) (RHEA:29651)
  subunit: Homodimer;each subunit has its own individual transport capacity.
• substrates: Arginine
  tcdb comment: Protonation of glutamate 208 induces release of agmatine in the outward-facing conformation (Zomot and Bahar, 2011). The 3.0 Å structure of an Arg-bound form in an open-to-out conformation completed the picture of the major states of the porter during the transport cycle (Kowalczyk et al., 2011). Aromatic residues may regulate access to both the outward- and inward-facing states (Krammer et al. 2016). Both the glutamate- and arginine (AdiC; TC# 2.A.3.2.5)-dependent acid resistance systems increase the internal pH and reverse the transmembrane potential (Richard and Foster 2004)
• Regulation of the yjjQ-bglJ operon, encoding LuxR-type transcription factors, and the divergent yjjP gene by H-NS and LeuO
  Stratmann, Journal of bacteriology 2008
  • “...S3604 S3606 S3608 S3610 S3612 S3614 S3616 S3618 S3620 S3622 S3631 S3633 S3635 S3637 S3638 S3641 S3642 S3645 S3646 S3663 S3665 S3667 S3669 S3671 S3673 S3675...”
• Unveiling the Mechanism of Arginine Transport through AdiC with Molecular Dynamics Simulations: The Guiding Role of Aromatic Residues.
  Krammer, PloS one 2016
  • GeneRIF: The mechanism of arginine transport through AdiC has been described using molecular dynamics simulations.
• Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.
  Ilgü, Proceedings of the National Academy of Sciences of the United States of America 2016
  • GeneRIF: We have solved the crystal structures of wild-type AdiC in the presence and absence of the substrate agmatine at 2.6-A and 2.2-A resolution.we present a potential mechanism for conformational changes of the AdiC transport cycle involved in the release of agmatine into the periplasmic space of E. coli.
• They all rock: A systematic comparison of conformational movements in LeuT-fold transporters.
  Licht, bioRxiv : the preprint server for biology 2024
  • “...(B) O op JX-075 d cryo-EM 2.9 6JMQ (A) I op cryo-EM 3.31 Ec AdiC P60061 3LRB (A) O op n/a X-ray 3.61 3L1L (A) O oc arginine X-ray 3 Vp SGLT P96169 3DH4 (A) I oc galactose b X-ray 2.7 2XQ2 (A) I op n/a...”
• Identification of an Acidic Amino Acid Permease Involved in d-Aspartate Uptake in the Yeast Cryptococcus humicola
  Imanishi, Microorganisms 2021
  • “...S1: Comparison of amino acid sequences of ChAap4 and ChAap5 with E. coli AdiC (UniProKB: P60061) and three yeast dicarboxylic amino acid permeases: Dip5p ( S. cerevisiae ), PcDip5 ( P. chrysogenum ), and AgtA ( A. nidulans ). Figure S2: Exon-intron structures of ChAAP4 ,...”
  • “...transmembrane (TM) region 1 and 6 of ChAap4 and ChAap5 with E. coli AdiC (UniProKB: P60061) and three yeast dicarboxylic amino acid permeases: Dip5p ( S. cerevisiae ), PcDip5 ( P. chrysogenum ), and AgtA ( A. nidulans ). Transmembrane (TM) regions were predicted by Phobius...”
• High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding
  Ilgü, BMC biology 2021
  • “...The UniProt ID or NCBI reference sequence codes are as follows: AdiC E. coli K12 (P60061), AdiC E. coli O104:H4 (A0A0E0Y6U0), AdiC E. coli O157:H7 (P60063), PotE E. coli K12 (P0AAF1), CadB E. coli K12 (P0AAE8), hAdiC Salmonella typhi (P60065), hAdiC Shigella flexneri (P60064), hCadB Vibrio...”
• Effects of Mutations and Ligands on the Thermostability of the l-Arginine/Agmatine Antiporter AdiC and Deduced Insights into Ligand-Binding of Human l-Type Amino Acid Transporters
  Ilgü, International journal of molecular sciences 2018
  • “...Omega [ 31 ] was used. The UniProtKB/Swiss-Prot entry codes of the used proteins are: P60061 (AdiC), Q01650 (SCL7A5), Q92536 (SLC7A6), Q9UM01 (SLC7A7), Q9UHI5 (SLC7A8), P82251 (SLC7A9), Q9NS82 (SLC7A10), Q9UPY5 (SLC7A11), and Q8TCU3 (SLC7A13). 3.5. Homology Models and Ligand Docking We show a previously published homology...”
• Insights into the Structure, Function, and Ligand Discovery of the Large Neutral Amino Acid Transporter 1, LAT1
  Singh, International journal of molecular sciences 2018
  • “...(P32837, Saccharomyces cerevisiae ), Cat6 (Q9LZ20, Arabidopsis thaliana ), GadC (P63235, Escherichia coli ), AdiC (P60061, E. coli ), CadB (P0AAE8, E. coli ), and PotE (P0AAF1, E. coli ). The multiple sequence alignment and phylogenetic tree data were generated using Clustal Omega [ 72 ]....”
• YjeH Is a Novel Exporter of l-Methionine and Branched-Chain Amino Acids in Escherichia coli
  Liu, Applied and environmental microbiology 2015
  • “...the secondary structure analysis of YjeH (P39277), AdiC (P60061), PotE (P0AAF1), and CadB (P0AAE8) from E. coli were performed using ESPript 3.0...”
  • “...Met and BCAAs. Sequence alignments of YjeH (P39277), AdiC (P60061), PotE (P0AAF1), and CadB (P0AAE8) showed that YjeH was arranged in 12 TMSs in which many...”
• High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding
  Ilgü, BMC biology 2021
  • “...follows: AdiC E. coli K12 (P60061), AdiC E. coli O104:H4 (A0A0E0Y6U0), AdiC E. coli O157:H7 (P60063), PotE E. coli K12 (P0AAF1), CadB E. coli K12 (P0AAE8), hAdiC Salmonella typhi (P60065), hAdiC Shigella flexneri (P60064), hCadB Vibrio cholerae (WP_000097425.1) and hAdiC Yersinia enterocolitica (WP_174848373.1). Positions with a...”
• High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding
  Ilgü, BMC biology 2021
  • “...coli K12 (P0AAF1), CadB E. coli K12 (P0AAE8), hAdiC Salmonella typhi (P60065), hAdiC Shigella flexneri (P60064), hCadB Vibrio cholerae (WP_000097425.1) and hAdiC Yersinia enterocolitica (WP_174848373.1). Positions with a single, fully conserved residue are indicated by (*), conservation between groups of strongly and weakly similar properties are...”
• Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli
  Iyer, Journal of bacteriology 2003
  • “...spanning 12 amino acids of unknown function, designated yjdE (b4115) and now named adiC by us and, recently, by others (12). The adiC gene is a homologue...”
• Escherichia coli gene expression responsive to levels of the response regulator EvgA
  Masuda, Journal of bacteriology 2002
  • “...hdeD yhiE yhiU yhiV gadA yiiS proP b4113 basR b4115 yjdE Decreased expression b0553 nmpC b2167 b2168 b2169 fruA fruK fruB b2943 galP Mean Outer membrane porin...”
• Genome-wide expression profiling in Escherichia coli K-12
  Richmond, Nucleic acids research 1999
  • “...b1888 cheA -8.0 -3.3 Sensory transducer kinase b4115 yjdE -8.0 2.5 Putative amino acid/amine transport protein, cryptic b1676 pykF -8.3 -9.2...”
• Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
  Segura, BMC genomics 2018
  • “...NDE Z4993 xylH D-xylose transport system (permease protein) NDE NDE 2.03 1.36E-03 2.07 1.01E-03 NDE Z5717 yjdE Arginine:agmatine antiporter 2.43 8.29E-03 NDE 3.76 1.94E-05 NDE 3.19 3.64E-04 Z0461 z0461 Fucose transporter (optimal import) 2.66 1.23E-03 3.00 3.12E-04 2.33 6.92E-03 4.75 1.65E-09 NDE 3.61E-04 Z1245 z1245 Putative...”
• Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
  Landstorfer, BMC genomics 2014
  • “...(29) 2.8 (14) 4.5 (13) 2.1 (3) 3.0 (11) 2.2 (6) 7.7 (257) 8.5 (140) Z5717 arginine:agmatin antiporter 1 (5) 0.2 (3) 5.7 (0) 3.2 (0) 1.3 (11) 5.7 (0) 0.5 (1) 3.9 (46) 7.5 (528) 1.8 (9) 5.7 (0) Z5719 biodegradative arginine decarboxylase 1 (3)...”

ROCE_BACSU / P39137 Amino-acid permease RocE from Bacillus subtilis (strain 168) (see paper)
TC 2.A.3.1.11 / P39137 L-Arginine permease, RocE from Bacillus subtilis (see 3 papers)
BSU40330 arginine/ornithine/gamma-aminobutyrate permease from Bacillus subtilis subsp. subtilis str. 168
28% identity, 67% coverage

• function: Putative transport protein involved in arginine degradative pathway. Probably transports arginine or ornithine
• substrates: Arginine
• rocF affects the production of tetramethylpyrazine in fermented soybeans with Bacillus subtilis BJ3-2
  Liu, BMC biotechnology 2022
  • “...Down BSU37770 3233.527 117.411 4.78 1.57E-07 2.20E-05 Down BSU01600 79.028 3.085 4.63 1.29E-05 1.02E-03 Down BSU40330 4924.789 203.326 4.6 4.62E-07 6.02E-05 Down BSU37760 2661.551 110.143 4.59 4.99E-07 6.28E-05 Down BSU01630 639.373 31.384 4.34 2.85E-06 3.06E-04 Down BSU40340 9319.344 465.809 4.32 2.35E-06 2.60E-04 Down BSU18310 796.701 42.378...”
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...No 3V8F P. horikoshii Major H/Na-glutamate symport protein BSU40330 No 3LRB E. coli Amino acid permease BSU03220 No 2XQ2 Vibrio parahaemolyticus High-affinity...”
• Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae.
  Van't, The FEBS journal 2020
  • “...bacterial, P24207 , P37460 , P25737 , P15993 , P0AAE0 , P25527 , P77610 , P39137 , and P42087 corresponding to PheP, ProY, LysP, AroP, CycA, GabP, AnsP, RocE, and HutM, respectively. This resulted in a population of 450, 105, and 835 sequences for yeast, mammalian,...”

LBA1086 amino acid permease from Lactobacillus acidophilus NCFM
26% identity, 76% coverage

• Microarray analysis of a two-component regulatory system involved in acid resistance and proteolytic activity in Lactobacillus acidophilus
  Azcarate-Peril, Applied and environmental microbiology 2005
  • “...substrate-binding protein LBA1080 putative methionine synthase metK LBA1086 amino acid permease LBA1135 macrolide efflux protein LBA1211 homoserine kinase khsE...”

CGS9114_RS03560 aromatic amino acid transport protein AroP from Corynebacterium glutamicum S9114
25% identity, 73% coverage

• Improvement in L-ornithine production from mannitol via transcriptome-guided genetic engineering in Corynebacterium glutamicum
  Nie, Biotechnology for biofuels and bioproducts 2022
  • “...1.43 aroC Down CGS9114_RS06245 3-Dehydroquinate synthase 1.41 aroB Down CGS9114_RS06240 Shikimate kinase 1.31 aroK Down CGS9114_RS03560 Aromatic amino acid transport protein AroP 1.14 aroP Down Improvement of l -ornithine production by manipulating novel transcriptome analysis-guided targets using a promoter or terminator insertion approach From the transcriptome...”

NP_730006 minidiscs, isoform C from Drosophila melanogaster
27% identity, 65% coverage

• A LAT1-Like Amino Acid Transporter Regulates Neuronal Activity in the Drosophila Mushroom Bodies.
  Delescluse, Cells 2024
  • GeneRIF: A LAT1-Like Amino Acid Transporter Regulates Neuronal Activity in the Drosophila Mushroom Bodies.
• Direct Sensing of Nutrients via a LAT1-like Transporter in Drosophila Insulin-Producing Cells.
  Manière, Cell reports 2016
  • GeneRIF: Direct sensing of nutrients via a LAT1-like transporter Mnd in Drosophila insulin-producing cells has been demonstrated.
• Drosophila expresses a CD98 transporter with an evolutionarily conserved structure and amino acid-transport properties.
  Reynolds, The Biochemical journal 2009
  • GeneRIF: Data show that CG2791 and two Drosophila homologues of the mammalian CD98 light chains, Mnd (Minidiscs) and JhI-21, are required for normal levels of System L transport.

NP_001021789 Amino acid transporter from Caenorhabditis elegans
25% identity, 76% coverage

• Aromatic amino acid transporter AAT-9 of Caenorhabditis elegans localizes to neurons and muscle cells.
  Veljkovic, The Journal of biological chemistry 2004 (PubMed)
  • GeneRIF: AAT-9 is expressed in excitable cells of the nematode head and pharynx in which it may provide a pathway for aromatic amino acid transport

TC 2.A.3.8.10 / Q9NA91 Aromatic amino acid exchanger, AAT-9 (Veljkovic et al., 2004b) from Caenorhabditis elegans (see paper)
25% identity, 74% coverage

• substrates: Histidine, phenylalanine, tryptophan, tyrosine

YPO3201 probable proline-specific permease from Yersinia pestis CO92
22% identity, 81% coverage

• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937). Table 1 Results of the algorithm on the COGs database # % Pairs with score below threshold, not tested 1021764 44.0 Pairs with score...”

SCO6014 cationic amino acid transporter from Streptomyces coelicolor A3(2)
23% identity, 76% coverage

• Functional connexion of bacterioferritin in antibiotic production and morphological differentiation in Streptomyces coelicolor
  García-Martín, Microbial cell factories 2024
  • “...g io s pore m aturation cell wall hydrolase ) domain [ 126 ], and SCO6014, a putative amino acids transporter [ 127 ], were more abundant in the mutant, while SCO5207, a putative regulatory protein from cystathionine beta-synthase family [ 126 ], was less abundant....”
• Cross-Recognition of Promoters by the Nine SigB Homologues Present in Streptomyces coelicolor A3(2)
  Sevcikova, International journal of molecular sciences 2021
  • “...them may have a function in osmoprotection, for example a possible transporter for amino acids SCO6014. Furthermore, proteins involved in cell wall biogenesis (SCO0565, SCO2509, SCO3557, SCO5998) may also increase tolerance to osmotic stress. Interestingly, the rrnE operon for 16S, 23S, 5S rRNA is also partially...”
  • “...septum site determining protein, all othermembrane HP SCO5749 atypical response regulator SCO5998 putative UDP-N-acetylglucosamine transferase SCO6014 putative cationic amino acid transporter SCO6509 hydrophobic protein SCO7446 putative regulator rrnE 16S, 23S, 5S rRNA operon HP, Hypothetical protein. ijms-22-07849-t002_Table 2 Table 2 Comparison of promoters dependent on several...”
• Initial Metabolic Step of a Novel Ethanolamine Utilization Pathway and Its Regulation in Streptomyces coelicolor M145
  Krysenko, mBio 2019
  • “...in S. coelicolor M145 allowed in silico identification of two putative ethanolamine/amino acid permease genes, SCO6014 and SCO5977 , with rather low similarity to the putative ethanolamine permease target from other Streptomycetes spp. (43% to 45%). To verify whether the expression of SCO6014 and SCO5977 might...”
  • “...the presence of ethanolamine and ammonium (control) as the sole N source. Transcriptional analysis of SCO6014 and SCO5977 revealed strong expression of these genes in the presence of ammonium, whereas no expression was observed in the presence of ethanolamine under the tested conditions (see Fig.S1 in...”

CAAT1_ARATH / Q84MA5 Cationic amino acid transporter 1; Amino acid transporter 1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT4G21120 AAT1 (AMINO ACID TRANSPORTER 1); L-glutamate transmembrane transporter/ L-lysine transmembrane transporter/ arginine transmembrane transporter/ cationic amino acid transmembrane transporter from Arabidopsis thaliana
24% identity, 56% coverage

• function: High-affinity permease involved in the transport of the cationic amino acids (e.g. arginine, lysine, histidine, citrulline, valine, and glutamate). Transport mostly basic amino acids, and, to a lower extent neutral and acidic amino acids. May function as a proton symporter.
• Fine-Tuning of Arabidopsis thaliana Response to Endophytic Colonization by Gluconacetobacter diazotrophicus PAL5 Revealed by Transcriptomic Analysis
  Soares, Plants (Basel, Switzerland) 2024
  • “...one urea transporter gene (DUR3, at5g45380), and three amino acid transporter genes (CAT5, at2g34960; CAT1, at4g21120; and APP3, at1g77380) were induced. The amino acid transporter gene (APP7, at5g23810) was repressed in shoots. In the nitrogen assimilation pathway, the NIA1 gene (at1g77760), which encodes the enzyme nitrate...”
• The Root-Colonizing Endophyte Piriformospora indica Supports Nitrogen-Starved Arabidopsis thaliana Seedlings with Nitrogen Metabolites
  Scholz, International journal of molecular sciences 2023
  • “...Amino acid (CAT family) GAT1/BAT1 At1g08230 x 2.02 x X Amino acid (CAT family) CAT1/AAT1 At4g21120 1.65 3.39 x X Amino acid (CAT family) CAT5 At2g34960 x 2.18 x X Amino acid (UmamiT family) UmamiT 4 At3G18200 x 4.31 x X Amino acid (UmamiT family) UmamiT...”
• Molecular mechanisms of resistance to Myzus persicae conferred by the peach Rm2 gene: A multi-omics view
  Le, Frontiers in plant science 2022
  • “...Glutamate synthase 1 Prupe_6G054800 AT3G47340 85 Yes 4.5 1.10E-29 ASN1; Asparagine synthetase [glutamine-hydrolyzing] 1 Prupe_4G089000 AT4G21120 72 Yes 4.0 3.80E-33 CAT1; Cationic amino acid transporter 1 Prupe_3G211600 AT3G21670 74 Yes 1.4 3.70E-02 NPF6.4; Protein NRT1/PTR FAMILY 6.4 Prupe_1G052400 AT4G13510 80 Yes 1.8 2.10E-07 AMT1; Ammonium transporter...”
• Membrane nanodomains and transport functions in plant
  Martinière, Plant physiology 2021
  • “...column. Transported molecules Protein/Protein family Accessions Tissues References Amino acids Cationic amino acid transporter (CAT) AT4G21120 (CAT1) Suspension cell cultures Keinath et al., 2010 Lysine histidine transporter (LHT) AT5G40780 (LTH1) Suspension cell cultures Keinath et al., 2010 Ammonium Ammonium transporter (AMT) AT4G13510 (AMT1;1) ; AT2G38290 (AMT2)...”
• Dynamic Development of White Lupin Rootlets Along a Cluster Root
  Le, Frontiers in plant science 2021
  • “...Gene description Element Profile number Lalb_Chr20g0113031 AT2G37330 Aluminum sensitive 3 (ALS3) Aluminum Profile 5 Lalb_Chr07g0185661 AT4G21120 Amino acid transporter 1 (AAT1) Amino acid Profile 6 Lalb_Chr14g0363171 AT5G40780 Lysine histidine transporter 1 (LHT1) Amino acid Profile 6 Lalb_Chr03g0042381 AT3G09330 Amino acid transporter (AVT1G) Amino acid Profile 6...”
• Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum
  Ma, Genes 2020
  • “...only expressed in the resistant cultivars when induced by the pathogen. BnaA03g58530D is homologous to AT4G21120 , which encodes an amino acid transporter 1 (AAT1). This gene was DAS in the mock-treated and infected resistant cultivar J4 at 24 hpi, and between the susceptible and resistant...”
  • “...J4_24 h\J4_24 h vs. J4_ck BnaA09 g19610D AT3G25840 K9I22.6 73.57 Protein kinase superfamily protein BnaA03g58530D AT4G21120 90.05 Amino acid transporter 1 J2_24 h vs. J4_24 h\J4_48 h vs. J4_ck BnaC02g27060D AT4G02620 87.23 Vacuolar ATPase subunit F protein J4_24 h vs. J4_ck BnaC06g34460D AT1G73650 F25P22.29 88.66 Protein...”
• Integrated Transcriptional and Proteomic Profiling Reveals Potential Amino Acid Transporters Targeted by Nitrogen Limitation Adaptation
  Liao, International journal of molecular sciences 2020
  • “...transporter (AtLHT1) NC 18.65 0.001 At4g35180 amino acid transporter family protein (AtLHT7) NC 15.02 0.001 At4g21120 cationic amino acid transporter (AtCAT1) NC 6.21 0.002 At2g38290 high-affinity ammonium transporter 2 (AMT2) NC 3.75 0.004 At1g31830 amino acid permease family protein (AtPUT2/AtPQR2) NC 2.93 0.002 At5g63850 amino acid...”
• Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves
  Chen, International journal of molecular sciences 2017
  • “...(KAT1) K + comp69280_c0_seq1 1.332 AT3G18830 Polyol/monosaccharide transporter 5 Linear polyols; myo-inositol; monosaccharides comp7769_c0_seq1 1.787 AT4G21120 Cationic amino acid transporter 1 Lys, Arg and Glu comp10794_c0_seq1 1.790 comp13115_c0_seq1 1.429 comp8282_c0_seq1 1.398 comp25372_c0_seq1 1.911 comp32005_c0_seq2 1.502 AT1G25480 Aluminum-activated malate transporter family protein Malate comp33002_c0_seq1 1.168 AT1G77210 Sugar...”
• More
• Plasma membrane receptor-like kinases and transporters are associated with 2,4-D resistance in wild radish
  Goggin, Annals of botany 2020
  • “...* Cationic amino acid transporter 1, CAT1 (Q84MA5) Putative receptor-like kinase At5g39000 (Q9FID8) ABC transporter G family member 35, ABCG35 (Q7PC86)*...”
• Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature
  Valadares, Journal of fungi (Basel, Switzerland) 2020
  • “...Q42400, FC = 51.7 and IDQ38967, FC = 1.7), a cationic amino acid transporter (ID Q84MA5, FC = 6.7), and a lysine histidine transporter (ID Q9FKS8, FC = 4.5), all likely located on the plasma membrane, were also up-regulated in Myc roots ( Table S7 )....”

SA2109 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV2316 transport protein from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_02590 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_2265 putative amino acid permease from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL2309 amino acid permease from Staphylococcus aureus subsp. aureus COL
27% identity, 65% coverage

• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...protein sa_c3178s2725_a_at * 3.2 2.5 ND SA1765 aminotransferase, class V sa_c4460s3803_a_at * 5.8 2.5 15 SA2109 modification methylase sa_c5126s4423_a_at * 7.3 2.5 15 SA2309 amino acid permease sa_c5638s4893_a_at 6.6 2.5 30 SA2412 amino acid ABC transporter, sa_c5835s5075_a_at 3.8 2.5 ND SA2472 peptide ABC transporter sa_c5837s5079_a_at 2.2...”
  • “...putative ribosomal-protein-alanine acetyltransferase sa_c9831s8573_a_at 4.2 2.5 2.5 SA2107 phosphotyrosine phosphatase sa_c4460s3803_a_at * 3.6 2.5 2.5 SA2109 modification methylase sa_c5126s4423_a_at * 4.2 2.5 2.5 SA2309 amino acid permease sa_c5389s4662_a_at 3.6 2.5 ND SA2410 amino acid ABC transporter sa_c5638s4893_a_at * 13.9 2.5 2.5 SA2412 amino acid ABC transporter...”
• Redox-sensing regulator Rex regulates aerobic metabolism, morphological differentiation, and avermectin production in Streptomyces avermitilis
  Liu, Scientific reports 2017
  • “...protein 4460250 4460267 2.00 TTCTGAACGTGTTCAGAA 37 SAV828 putative rhamnosidase 982811 982828 3.00 CTGTGAATCGATTCACCT 137 echA7 (SAV2316 ) putative enoyl-CoA hydratase 2820643 2820660 3.00 TCGTGACGACAGTCACAA 66 SAV2652 putative regulatory protein 3252402 3252419 3.00 TTGTGCACCGCTTCACCC 288 ndh2 (SAV3529 ) putative NADH dehydrogenase (complex I) 4369478 4369495 3.00 TTGTGAAGGGGCGCACGA...”
• Copper stress induces a global stress response in Staphylococcus aureus and represses sae and agr expression and biofilm formation
  Baker, Applied and environmental microbiology 2010
  • “...tag Description Fold change Transport genes SAV0990 SAV2316 SAV0950 SAS2358 oppA potE mnhC opp-1A Oligopeptide transporter binding protein Transport protein...”
• SARS-CoV-2 Spike Protein and Mouse Coronavirus Inhibit Biofilm Formation by Streptococcus pneumoniae and Staphylococcus aureus
  Loke, International journal of molecular sciences 2022
  • “...of bPH_3 domain-containing protein (SAOUHSC_02568), ribosome maturation factor RimM, and AA_permease domain-containing proteins (SAOUHSC_01803 and SAOUHSC_02590) in S. aureus biofilm formation have not been established. From the results of this in vitro study, we propose that SARS-CoV-2 and related coronavirus infections may trigger an active dispersion...”
  • “...N D N D N - - - - - AA_permease domain-containing proteins (SAOUHSC_01803 and SAOUHSC_02590) - - - - - D N N N N bPH_3 domain-containing protein (SAOUHSC_02568) - - - - - N D N D N CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase (SAOU-HSC_01260) - - -...”
• 6S RNA-Dependent Susceptibility to RNA Polymerase Inhibitors
  Esberard, Antimicrobial agents and chemotherapy 2022 (secret)
• Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
  Kulkarni, American journal of respiratory cell and molecular biology 2016
  • “...SAUSA300_1549 SAUSA300_2456 SAUSA300_1919 SAUSA300_2533 SAUSA300_2265 SAUSA300_1283 hisG SAUSA300_2407 SAUSA300_0629 SAUSA300_0902 SAUSA300_1287 SAUSA300_1813...”
• A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome
  Becher, PloS one 2009
  • “...are involved in the transport of amino acids or oligopeptides [from left to right: SACOL2451, SACOL2309, SACOL2452, SACOL2453, SACOL0993 (OppD), SACOL0992 (OppC), SACOL0994 (OppF), SACOL0995, SACOL1963, SACOL2450, SACOL0991 (OppB)], CPS (capsular polysaccharide) biosynthesis [SACOL0151 (Cap5P), SACOL0138 (Cap5C), SACOL0143 (Cap5H), SACOL0137 (Cap5B), SACOL0136 (Cap5A), SACOL0142 (Cap5G), SACOL0150...”

Ga0059261_1577 L-glutamine and L-histidine transporter from Sphingomonas koreensis DSMZ 15582
24% identity, 85% coverage

• mutant phenotype: Specific phenotype on glutamine; also important for histidine utilization; detrimental to fitness on some other amino acids (proline, alanine) which may indicate that it likes these amino acids

SpyM3_0013 putative amino acid permease from Streptococcus pyogenes MGAS315
24% identity, 82% coverage

• Whole-genome sequencing reveals high genetic diversity of Streptococcus uberis isolated from cows with mastitis
  Silva, BMC veterinary research 2021
  • “...6 60 1 10 9 90 9 90 1 10 8 80 2 20 10 SpyM3_0013 Cationic amino acid transporter - APC Superfamily 1 11 8 89 5 56 4 44 1 11 8 89 8 89 1 11 8 89 1 11 9 psa C...”
• First Streptococcus pyogenes signature-tagged mutagenesis screen identifies novel virulence determinants
  Kizy, Infection and immunity 2009
  • “...SPyM1_0271 (96) ABC transporter substrate-binding protein D11-5 SPyM3_0013, SPyM1_0014 (97) Putative amino acid permease I 0.0011 ND F4-11 SPyM1_0275 (94)...”

ECO26_5227 arginine/agmatin antiporter AdiC from Escherichia coli O26:H11 str. 11368
26% identity, 84% coverage

• Evolution of enterohemorrhagic escherichia coli O26 based on single-nucleotide polymorphisms
  Bletz, Genome biology and evolution 2013
  • “...Nonsynonymous (Leu Phe) 90.00 ECO26_5139 lysC (1) 5206902 T C b Nonsynonymous (Val Ala) 89.17 ECO26_5227 adiC (1) 5302486 A G b Nonsynonymous (Tyr Cys) 89.17 ECO26_5302 dipZ (1) 5389233 C G b Synonymous 89.17 ECO26_5384 cysQ (1) 5467060 T G b Synonymous 89.17 a SNP...”

GOX0025 Amino acid permease from Gluconobacter oxydans 621H
24% identity, 78% coverage

• Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
  Kranz, BMC genomics 2018
  • “...2.8 170 GOX1431 hypothetical protein 2.6 336 | GOX0024 undecaprenyl pyrophosphate phosphatase 2.6 2.8 198 GOX0025 amino acid permease 2.5 142 GOX2207 methylenetetrahydrofolate reductase 2.6 2.6 547 GOX0649 sugar-proton symporter 2.6 2.6 364 GOX2378 short chain alcohol dehydrogenase 2.6 2.6 301 GOX1151 hypothetical protein 2.5 2.5...”

LBA0943 cationic amino acid transporter from Lactobacillus acidophilus NCFM
24% identity, 68% coverage

• Microarray analysis of a two-component regulatory system involved in acid resistance and proteolytic activity in Lactobacillus acidophilus
  Azcarate-Peril, Applied and environmental microbiology 2005
  • “...aspartokinase/homoserine dehydrogenase LBA0911 aminopeptidase pepC LBA0943 cationic amino acid transporter LBA1042 ABC transporter (glutamine) membrane-spanning...”

CD630_01650 APC family permease from Clostridioides difficile 630
CD0165 putative amino acid transporter from Clostridium difficile 630
25% identity, 50% coverage

• The Alternative Sigma Factor SigL Influences Clostridioides difficile Toxin Production, Sporulation, and Cell Surface Properties
  Clark, Frontiers in microbiology 2022
  • “...C. difficile strain Locus ID Name FIMO Score FIMO q -value Motif sequence CD0166-0165 630 CD630_01650 putative amino acid transporter 26.888 0.001 TGGCATAATAATTGCTTA BI-1 CDBI1_00900 amino acid permease 26.888 0.001 TGGCATAATAATTGCTTA CDC1 Not identified CD2699-CD2697 630 CD630_26970 putative peptidase, M20D family 22.888 0.007 TGGCATAAGTTTTGCTTA BI-1 CDBI1_13130...”
• Control of Clostridium difficile Physiopathology in Response to Cysteine Availability
  Dubois, Infection and immunity 2016
  • “...and CD0166) and amino acid uptake (CD2612, CD3092, and CD0165) was differentially regulated when cysteine was added to the medium (Fig. 6A). In C. difficile,...”
• Integration of metabolism and virulence by Clostridium difficile CodY
  Dineen, Journal of bacteriology 2010
  • “...4.7 18.6 leuA hisZ ilvC Transport CD0165 CD0324 (cbiM) CD0388-CD0390 (bglPAG) CD0449 CD0853-CD0857 (oppBCADF) CD0875-CD0873 CD0878-CD0876 CD0879 CD1259-CD1260...”
  • “...4.9-23.7 3.6*-10.1 4.0 6.8 5.5 7.0 6.2 CD0165 Sporulation CD0770-CD0772 (spoIIAA-AB-AC) CD3490 (spoIIE) CD3516 (spoVG) Anti-sigma F factor antagonist Stage II...”

NP_651536 genderblind, isoform A from Drosophila melanogaster
26% identity, 66% coverage

• l(2)01810 is a novel type of glutamate transporter that is responsible for megamitochondrial formation
  Shim, The Biochemical journal 2011
  • “...(NP_001024393), Drer Eaat2 (NP_956273), Mmus Eaat2 (NP_035523), Hsap Eaat2 (NP_004162), Dmel Eaat2 (NP_001162844), Dmel genderblind (NP_651536), Cele aat-1 (NP_501707), Drer SLC7a11-like (XP_001919426), Mmus xCT (NP_036120), Hsap xCT (NP_055146), Dmel l(2)01810 (NP_620115), Dmel VGLUT (NP_608681), Cele eat-4 (NP_499023), Drer SLC17a7 (NP_001092225), Hsap VGLUT1 (NP_064705), Rnor VGLUT1 (NP_446311),...”
• A glial amino-acid transporter controls synapse strength and courtship in Drosophila.
  Grosjean, Nature neuroscience 2008
  • GeneRIF: genderblind controls synapse strength and courtship in Drosophila.

PP_4495 amino acid permease from Pseudomonas putida KT2440
PP4495 aromatic amino acid transporter from Pseudomonas putida KT2440
25% identity, 76% coverage

• Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria
  Browne, BMC microbiology 2010
  • “...nd 6.3 bkdA-1 PP_4401 PP_4401 3-methyl-2-oxobutanoate dehydrogenase 3.2 1.6 phhA PP_4490 PP_4490 phenylalanine-4-hydroxylase 2.8 1.9 PP_4495 PP_4495 aromatic amino acid transport protein AroP2 2.6 nd hmgA PP_4621 PP_4621 homogentisate 1,2-dioxygenase 5.0 7.8 PP_4636 PP_4636 acetyl-CoA acetyltransferase 3.6 2.3 hupA PP_5313 PP_5313 probable DNA-binding protein 3.8 nd...”
• Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement
  Verhoef, Applied microbiology and biotechnology 2010
  • “...Amino acid transporter, AAT family PP3727 2.5 4.2 Aromatic amino acid transporter ( aroP1 ) PP4495 4.0 14.1 Branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein PP4867 0.65 2.40.1 c a Fold change in expression level of P. putida S12palB1 compared to P. putida S12...”
• Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production
  Wierckx, Journal of bacteriology 2008
  • “...(aroP1) PP0198 PP0615 PP0618 PP0619 PP0927 PP1070 PP3023 PP4495 2.1 0.6 0.4 0.5 10.7 0.5 2.1 10.5 TCA cycle Fumarate hydratase, class I Oxidoreductase,...”
  • “...directly via 4-hydroxyphenylpyruvate (Fig. 2). The aroP1 gene (PP4495) is responsible for transport of aromatic amino acids. Disruption of this gene could...”

Z4731 putative amino acid/amine transport protein from Escherichia coli O157:H7 EDL933
27% identity, 67% coverage

• Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China
  Wang, Infection and immunity 1992
  • “...IIa, IIb IIa, IIb I Z4727, Z4728, Z4729, Z4730, Z4731, Z4732, B54, B516, B236 B303 B328, B506 Z3510, Z3515 Z3771, Z3786, Z3787 Z3905, Z3909 B503, Z3917, Z3921,...”

CTR2_CHICK / B3TP03 Cationic amino acid transporter 2; CAT-2; CAT2; cCAT-2; Low affinity cationic amino acid transporter 2; Solute carrier family 7 member 2 from Gallus gallus (Chicken) (see paper)
25% identity, 59% coverage

• function: Low-affinity, high capacity permease involved in the transport of the cationic amino acids (L-arginine, L-lysine, L- ornithine and L-homoarginine).
  catalytic activity: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: L-lysine(in) = L-lysine(out) (RHEA:70935)
  catalytic activity: L-ornithine(in) = L-ornithine(out) (RHEA:71199)
  catalytic activity: L-homoarginine(in) = L-homoarginine(out) (RHEA:71203)

G1SZJ1 Solute carrier family 7 member 3 from Oryctolagus cuniculus
24% identity, 65% coverage

• Comparative Bioinformatic Analysis of the Proteomes of Rabbit and Human Sex Chromosomes
  Pinto-Pinho, Animals : an open access journal from MDPI 2024
  • “...G1T7A1 PTCHD1 Patched domain-containing 1 TM PM G1SZZ7 RS1 Retinoschisin 1 SP PM, ESPM, ES G1SZJ1 SLC7A3 Solute carrier family 7 member 3 TM PM G1T4W3 SLC9A6 Sodium/hydrogen exchanger SP+TM PM G1SLC9 SLC9A7 Sodium/hydrogen exchanger SP+TM PM G1T0T4 SRPX2 Sushi repeat containing protein X-linked 2 SP...”

KP1_1204 putative proline transporter from Klebsiella pneumoniae NTUH-K2044
22% identity, 81% coverage

• YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43
  Huang, PloS one 2013
  • “...transporter proY 3.7 KP1_1422 Permease Putative PTS permease 6.5 KP1_0760 Putative amino acid permease 4.3 KP1_1204 Amino acid biosynthesis Arginine succinyltransferase 4.5 KP1_2499 Acetylornithine transaminase 5.0 KP1_2498 Putative glutamine synthetase 3.3 KP1_2006 Energy/intermediary metabolism Succinate antiporter 6.4 KP1_2563 Succinylarginine dihydrolase 5.3 KP1_2502 Glucosamine-fructose-6-phosphate aminotransferase 6.0 KP1_0764...”

PfGW456L13_4291 L-tryptophan transporter from Pseudomonas fluorescens GW456-L13
25% identity, 74% coverage

• mutant phenotype: Specifically important for utilization of tryptophan as a carbon source.

5j4nA / P60061 Crystal structure of the l-arginine/agmatine antiporter adic in complex with agmatine at 2.6 angstroem resolution (see paper)
26% identity, 83% coverage

• Ligand: agmatine (5j4nA)

YhfM / b3370 fructoselysine/psicoselysine transporter from Escherichia coli K-12 substr. MG1655 (see 4 papers)
frlA / P45539 fructoselysine/psicoselysine transporter from Escherichia coli (strain K12) (see 4 papers)
FRLA_ECOLI / P45539 Probable fructoselysine/psicoselysine transporter FrlA from Escherichia coli (strain K12) (see paper)
b3370 putative amino acid/amine transport protein from Escherichia coli str. K-12 substr. MG1655
27% identity, 67% coverage

• function: Is likely involved in the transport of fructoselysine and psicoselysine to the cytoplasm, where they are degraded.
  catalytic activity: N(6)-(D-fructosyl)-L-lysine(in) = N(6)-(D-fructosyl)-L- lysine(out) (RHEA:28454)
  catalytic activity: N(6)-(D-psicosyl)-L-lysine(in) = N(6)-(D-psicosyl)-L- lysine(out) (RHEA:28450)
  disruption phenotype: Cells lacking this gene are unable to grow on fructoselysine or psicoselysine, where they do grow on glucose.
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...junction protein 2 3080.4 5.6 b1552 cspI Qin prophage cold shock protein CspI 6.3 5.6 b3370 frlA Fructoselysine/psicoselysine transporter 2.1 5.5 b1589 ynfG Putative oxidoreductase YnfG 87.0 5.5 b1890 motA Motility protein A 267.0 5.4 b1940 fliH Flagellar biosynthesis protein FliH 73.1 5.4 b0903 pflB Pyruvate...”
• YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
  Herzberg, Journal of bacteriology 2006
  • “...367 282 yihN yjhQ yihP uraA yhfM b3874 b4307 b3877 b2497 b3370 12.1 11.3 10.6 8.6 7.5 dcuB malK acrF artJ pheP ycfT agaD b4123 b4035 b3266 b0860 b0576 b1115...”

XP_005226082 cationic amino acid transporter 2 isoform X1 from Bos taurus
23% identity, 61% coverage

• Nitric oxide suppression of cellular proliferation depends on cationic amino acid transporter activity in cytokine-stimulated pulmonary endothelial cells.
  Chicoine, American journal of physiology. Lung cellular and molecular physiology 2011
  • GeneRIF: Lipopolysaccharide/tumor necrosis factor-alpha treatment increased the expression of iNOS, arginase II, CAT-1, and CAT-2 mRNA.

BSU37760 arginine/ornithine permease from Bacillus subtilis subsp. subtilis str. 168
22% identity, 67% coverage

• rocF affects the production of tetramethylpyrazine in fermented soybeans with Bacillus subtilis BJ3-2
  Liu, BMC biotechnology 2022
  • “...Down BSU01600 79.028 3.085 4.63 1.29E-05 1.02E-03 Down BSU40330 4924.789 203.326 4.6 4.62E-07 6.02E-05 Down BSU37760 2661.551 110.143 4.59 4.99E-07 6.28E-05 Down BSU01630 639.373 31.384 4.34 2.85E-06 3.06E-04 Down BSU40340 9319.344 465.809 4.32 2.35E-06 2.60E-04 Down BSU18310 796.701 42.378 4.23 3.91E-06 3.97E-04 Down BSU38560 1224.887 65.094...”
• Secondary structural entropy in RNA switch (Riboswitch) identification
  Manzourolajdad, BMC bioinformatics 2015
  • “...2678925 2679081 forward BSU26050 yqdB -427 0.363 12639 yqaP BSU26230 0.843 63 3875571 3875727 reverse BSU37760 rocC -130 0.3121 79 ywfA BSU37750 0.843 64 2433680 2433836 reverse BSU23340 ypuB -384 0.3885 236 ypzJ BSU23328 0.843 65 2879134 2879290 reverse BSU28190 engB -669 0.4013 79 hemA BSU28170...”
  • “...2678925 2679081 forward BSU26050 yqdB -427 0.363 12639 yqaP BSU26230 0.843 38 3875571 3875727 reverse BSU37760 rocC -130 0.3121 79 ywfA BSU37750 0.843 39 2433680 2433836 reverse BSU23340 ypuB -384 0.3885 236 ypzJ BSU23328 0.843 40 1533806 1533962 forward BSU14610 pdhD -445 0.3503 236 ykzW BSU14629...”

XF2208 cationic amino acid transporter from Xylella fastidiosa 9a5c
23% identity, 70% coverage

• Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa
  Meidanis, Microbiology and molecular biology reviews : MMBR 2002
  • “...(HME) RND (HAE1) 2.A.3.3.1 2.A.1.6.2 MHS XF2094 XF2083 XF0243 XF0866 XF0408 XF2207 XF2208 XF1462 XF1609 12 11 12 6 12 9 11 11 8 9 10 8 14 10 11 8 No. of TMSs BE...”

PP3727 amino acid transporter, AAT family from Pseudomonas putida KT2440
23% identity, 66% coverage

• Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement
  Verhoef, Applied microbiology and biotechnology 2010
  • “...protein ( aapP ) PP1300 0.56 d 3.0 0.61 2.6 Amino acid transporter, AAT family PP3727 2.5 4.2 Aromatic amino acid transporter ( aroP1 ) PP4495 4.0 14.1 Branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein PP4867 0.65 2.40.1 c a Fold change in expression...”

XP_039296825 LOW QUALITY PROTEIN: high affinity cationic amino acid transporter 1 from Nilaparvata lugens
22% identity, 65% coverage

• Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species (Nilaparvata lugens)
  Yue, Frontiers in physiology 2021
  • “...121840.4 7.37 + NlAPC15 XP_039291803 Nlug22218-TA chr9 40431699 40509646 1122 24 11 124016.4 7.73 NlAPC16 XP_039296825 Nlug17187-TA chr14 16084741 16128173 615 21 14 67035.3 8.49 + NlAPC17 XP_039296817 Nlug17189-TA chr14 15988763 16025229 611 13 15 66179.6 8.42 NlAPC18 XP_039296923 Nlug20896-TA chr14 18470291 18500414 628 10 14...”

SG0955 lysine transport protein from Sodalis glossinidius str. 'morsitans'
28% identity, 65% coverage

• Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies
  Belda, BMC genomics 2010
  • “...the dependence of extracellular L-lysine through a functional APC transporter encoded by the gene lysP (SG0955). Another important feature of the S. glossinidius metabolism refers to the different pathways for cofactor biosynthesis, which have been postulated as the driving force in the maintenance of the symbiotic...”

Dhaf_2459 amino acid permease-associated region from Desulfitobacterium hafniense DCB-2
22% identity, 79% coverage

• Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction
  Kim, BMC microbiology 2012
  • “...to indole, pyruvate, and ammonia were identified in association with two permease genes (Dhaf_1325 and Dhaf_2459). These gene sets were also observed in Y51 (DSY4041-4042 and DSY1331-1332). Complete biosynthetic pathways are present for the formation of amino acids, nucleic acid precursors, as well as fatty acids...”

Mlut_00990 amino acid permease from Micrococcus luteus NCTC 2665
26% identity, 67% coverage

• Identification of New Chromosomal Loci Involved in com Genes Expression and Natural Transformation in the Actinobacterial Model Organism Micrococcus luteus
  Torasso, Genes 2021
  • “...G103500A M27, M2 Transition Mlut_00970 < Protein of unknown function DUF88 1 G106197A M33 Transition Mlut_00990 < Amino acid transporter 3 G341241A M43, M47, M101, M1080, M42 Transition Mlut_03135 < N6-DNA Methylase 3 G341448A M96 Transition Mlut_03135 < Hypothetical protein 4 C575082T M93 Transition - -...”

PA4981 probable amino acid permease from Pseudomonas aeruginosa PAO1
22% identity, 68% coverage

• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...acid ABC transporter membrane protein PA4912 PAK branched chain amino acid ABC transporter membrane protein PA4981 PA01 amino acid APC family transporter PA5074 PAK glutamine ABC transporter ATP binding protein PA5075 PA01 glutamine ABC transporter membrane protein PA5076 PAK glutamine ABC transporter periplasmic binding protein PA5097...”
• Functional genomics enables identification of genes of the arginine transaminase pathway in Pseudomonas aeruginosa
  Yang, Journal of bacteriology 2007
  • “...PA3864 PA3865 PA4975 PA4976 PA4977 PA4978 PA4979 PA4980 PA4981 *PA5302 *PA5303 *PA5304 *PA5309 *PA5312 *PA5313 *PA5314 PA3537 PA0896 b VOL. 189, 2007 THE...”
  • “...Materials and Methods. after the 3 end of the PA4981 coding sequence in the PA4981PA4980 intergenic region. This suggested the presence of another promoter for...”
• Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress
  Muller, Applied and environmental microbiology 2007
  • “...transporter 3.0 3.5 26 h PA1230 PA3370 PA3679 PA4981 Hypothetical protein Hypothetical protein Hypothetical protein Probable amino acid permease 4.9 2.1 2.3 4.0...”

ZMO1804 amino acid permease-associated region from Zymomonas mobilis subsp. mobilis ZM4
24% identity, 87% coverage

• Transcriptome profiling of Zymomonas mobilis under ethanol stress
  He, Biotechnology for biofuels 2012
  • “...monophosphate synthase TCATTATCGCTTGCCCTTCA GAGCCGAATCAGCCAGAA 101 1.1 4.9 ZMO1802 hypothetical protein TGCTTATGCAGTGTTTGG TCAGGAAGGTGTAGAGAC 94 1.1 3.5 ZMO1804 amino acid permease-associated domain-containing protein TTTATGGATTTGATACTGTC CGCTACACCAATATAGAT 119 1.4 3.71 ZZM4_0013 P2 GpU family protein GTCACATCCATAGTAGAA TTATTGTATTGTCGTCATC 106 1.7 4.3 ZZM4_0036 protein of unknown function DUF264 CCAGAATAGTGAAGAAGG ATCAAGACCTCTAAGTTG 109 1.4...”
  • “...transport and metabolism showed significant expressed under ethanol stress, such as ZMO1180, ZMO2018, hutG (ZMO1395), ZMO1804, nrdD (ZMO1025), yfeJ (ZMO1855), ZMO1522, thiE (ZMO1425), folK (ZMO1647), ssuC (ZMO1262) and ZMO0546 (see Additional file 1 : Table S1). However, 3 ORFs related carbohydrate and coenzyme transport and metabolism...”

6li9B / P82251 Heteromeric amino acid transporter b0,+at-rbat complex bound with arginine (see paper)
26% identity, 74% coverage

• Ligand: arginine (6li9B)

S0111 aromatic amino acid transport protein from Shigella flexneri 2a str. 2457T
24% identity, 74% coverage

• Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri
  Venkatesan, Infection and immunity 2001
  • “...53.0 48.7 35.0 484 96 470 99 129 157 S0104 S0105 S0111 79222 80088 83759 78794 79450 83274 ATG GTG ATG 32.9 50.2 43.1 142 212 161 No significant homology No...”

GABP_BACSU / P46349 Gamma-aminobutyric acid permease; GABA permease; 4-aminobutyrate permease; Gamma-aminobutyrate permease; Proline transporter GabP from Bacillus subtilis (strain 168) (see 3 papers)
TC 2.A.3.1.5 / P46349 β-alanine/γ-aminobutyrate/proline/3,4-dehydroproline:H+ symporter, GabP from Bacillus subtilis (see 4 papers)
gabP / AAC44641.1 gamma-aminobutyrate permease from Bacillus subtilis (see 2 papers)
24% identity, 77% coverage

• function: Transporter for gamma-aminobutyrate (GABA) (PubMed:24142252, PubMed:8951816, PubMed:9677314). Can also transport beta-alanine (PubMed:9677314). Can translocate several open-chain GABA analogs (3- aminobutyrate, 3-aminopropanoate, cis-4-aminobutenoate) across the membrane via counterflow against GABA, but cannot transport muscimol (PubMed:9677314). Functions also as a low-affinity proline importer (PubMed:24142252).
  catalytic activity: 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) (RHEA:28915)
  catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459)
  disruption phenotype: A transposon insertion in this gene eliminates the uptake of GABA and severely inhibits the utilization of GABA as a nitrogen source (PubMed:8951816). Triple deletion of gabP, putP and opuE confers resistance to the proline analog 3,4-dehydro-DL-proline (DHP), abolishes GABA utilization and prevents use of proline as a nitrogen source (PubMed:24142252).
• substrates: 3,4-dehydroproline, 3-aminobutyrate, 3-aminopropanoate, Gamma-aminobutyrate, H+, Proline, beta-alanine, cis-4-aminobutenoate
  tcdb comment: Also transports 3-aminobutyrate, 3-aminopropanoate, cis-4-aminobutenoate (Brechtel and King 1998)
• Functional Characterization of the γ-Aminobutyric Acid Transporter from Mycobacterium smegmatis MC² 155 Reveals Sodium-Driven GABA Transport
  Pavić, Journal of bacteriology 2021
  • “...from E. coli ( P25527 ), Pseudomonas syringae ( Q87UE3 ), Bacillus subtilis GabP ( P46349 ), Streptomyces coelicolor ( Q9L202 ), and Corynebacterium glutamicum AroP ( Q46065 ), a protein characterized as an aromatic amino acid transporter. The second group has a less varied taxonomic...”

AroR / b0112 aromatic amino acid:H⁺ symporter AroP from Escherichia coli K-12 substr. MG1655 (see 5 papers)
aroP / P15993 aromatic amino acid:H⁺ symporter AroP from Escherichia coli (strain K12) (see 6 papers)
AROP_ECOLI / P15993 Aromatic amino acid transport protein AroP; Aromatic amino acid:H(+) symporter AroP; General aromatic amino acid permease; General aromatic transport system from Escherichia coli (strain K12) (see 8 papers)
TC 2.A.3.1.3 / P15993 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan from Escherichia coli (see 6 papers)
b0112 aromatic amino acid transporter from Escherichia coli str. K-12 substr. MG1655
24% identity, 74% coverage

• function: Permease that is involved in the active transport across the cytoplasmic membrane of all three aromatic amino acids, phenylalanine, tyrosine and tryptophan.
  catalytic activity: L-phenylalanine(in) + H(+)(in) = L-phenylalanine(out) + H(+)(out) (RHEA:28923)
  catalytic activity: L-tryptophan(in) + H(+)(in) = L-tryptophan(out) + H(+)(out) (RHEA:28879)
  catalytic activity: L-tyrosine(in) + H(+)(in) = L-tyrosine(out) + H(+)(out) (RHEA:28875)
  disruption phenotype: Mutants show reduced aromatic amino acids transport and are resistant to p-fluorophenylalanine, beta-2- thienylalanine and 5-methyltryptophan.
• substrates: phenylalanine, tryptophan, tyrosine
• Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae
  Van't, The FEBS journal 2020
  • “...to Lat1, Lat2, and Xct, respectively; and for bacterial, P24207 , P37460 , P25737 , P15993 , P0AAE0 , P25527 , P77610 , P39137 , and P42087 corresponding to PheP, ProY, LysP, AroP, CycA, GabP, AnsP, RocE, and HutM, respectively. This resulted in a population of...”
• The two-component system histidine kinase EnvZ contributes to Avian pathogenic Escherichia coli pathogenicity by regulating biofilm formation and stress responses
  Fu, Poultry science 2023
  • “...slp Outer membrane lipoprotein 2.21 b0565 ompT Outer membrane protein 3b (a), protease VII 2.16 b0112 aroP Aromatic amino acid transport protein AroP 1.96 b3688 yidQ Outer membrane protein 1.80 FeS cluster b4291 fecA Iron complex outer membrane receptor protein, putative iron compound receptor 7.37 b1451...”
• Stationary-phase quorum-sensing signals affect autoinducer-2 and gene expression in Escherichia coli
  Ren, Applied and environmental microbiology 2004
  • “...b1020 2.6 2.5 2.4 2.3 2.3 2.1 2.1 aroP b0112 2 flgJ pyrE b1081 b3642 2 2 Phosphate regulon regulatory protein PhoB Nucleoside permease (nucleoside-transport...”

PA2079 probable amino acid permease from Pseudomonas aeruginosa PAO1
25% identity, 69% coverage

• Adapting to the Airways: Metabolic Requirements of Pseudomonas aeruginosa during the Infection of Cystic Fibrosis Patients
  La, Metabolites 2019
  • “...acids are the main carbon sources in vivo, genes coding for amino acid permeases (PA2202, PA2079, PA2041, and PA1916) were found to be expressed at higher levels in situ compared to laboratory conditions [ 61 ]. Moreover, analysis of ex vivo samples of an explanted CF...”
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...branched chain amino acidcation symporter ( BraZ ) PA2041 PAK amino acid APC family transporter PA2079 PA01 amino acid APC family transporter PA2202 PAK amino acid ABC transporter membrane protein PA2203 PAK amino acid ABC transporter membrane protein PA2204 PA01 amino acid ABC transporter periplasmic binding...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859,...”

DagA / b4208 D-serine/alanine/glycine/:H⁺symporter from Escherichia coli K-12 substr. MG1655 (see 13 papers)
cycA / P0AAE0 D-serine/alanine/glycine:H⁺symporter from Escherichia coli (strain K12) (see 15 papers)
CYCA_ECOLI / P0AAE0 D-serine/D-alanine/glycine transporter; Amino acid carrier CycA from Escherichia coli (strain K12) (see 7 papers)
TC 2.A.3.1.7 / P0AAE0 D-Serine/D-alanine/glycine/D-cycloserine:H+ symporter from Escherichia coli (see 4 papers)
NP_418629 D-serine/alanine/glycine/:H(+)symporter from Escherichia coli str. K-12 substr. MG1655
b4208 D-alanine/D-serine/glycine transporter from Escherichia coli str. K-12 substr. MG1655
ECs5186 transport protein of D-alanine / D-serine / glycine from Escherichia coli O157:H7 str. Sakai
22% identity, 64% coverage

• function: Permease that is involved in the transport across the cytoplasmic membrane of D-alanine, D-serine, glycine and beta-alanine (PubMed:15221223, PubMed:23316042, PubMed:4574696, PubMed:4583203, PubMed:4926674). Also contributes to L-alanine uptake (PubMed:4574696, PubMed:4583203). In addition, in minimal media, transports the broad spectrum antibiotic D-cycloserine into the cell (PubMed:23316042, PubMed:4574696, PubMed:4926674). Transports D-cycloserine only in minimal media, and not in a complex medium, suggesting that CycA does not play a role in D-cycloserine transport when E.coli is grown in a complex or biologically relevant medium, probably due to competition from other CycA substrates present in the medium (PubMed:23316042).
  catalytic activity: D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) (RHEA:28903)
  catalytic activity: D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) (RHEA:70647)
  catalytic activity: glycine(in) + H(+)(in) = glycine(out) + H(+)(out) (RHEA:28899)
  catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459)
  catalytic activity: L-alanine(in) + H(+)(in) = L-alanine(out) + H(+)(out) (RHEA:29443)
  catalytic activity: D-cycloserine(in) + H(+)(in) = D-cycloserine(out) + H(+)(out) (RHEA:70703)
  disruption phenotype: Mutant exhibits increased resistance to D- cycloserine when grown in a minimal medium, but no change in D- cycloserine sensitivity compared to its parental strain when grown in a complex medium.
• substrates: D-alanine, D-cycloserine, D-serine, Glycine, H+, Serine
  tcdb comment: The system is active after growth in minimal medium but not after growth in complex medium (Baisa et al. 2013)
• CycA-Dependent Glycine Assimilation Is Connected to Novobiocin Susceptibility in Escherichia coli.
  Shi, Microbiology spectrum 2022
  • GeneRIF: CycA-Dependent Glycine Assimilation Is Connected to Novobiocin Susceptibility in Escherichia coli.
• Identification and characterization of the main beta-alanine uptake system in Escherichia coli.
  Schneider, Applied microbiology and biotechnology 2004 (PubMed)
  • GeneRIF: beta-Alanine uptake was found to be an active process catalyzed by the amino acid carrier CycA.
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...membrane 454 P0A9R7 FTSE Cell cycle control, cell division, chromosome partitioning Cell inner membrane 455 P0AAE0 CYCA Amino acid transport and metabolism Cell inner membrane 456 P0AAH8 SAPF Function unknown Cell inner membrane 457 P0ABG7 RODA Cell cycle control, cell division, chromosome partitioning Cell inner membrane...”
• A Continuous Assay Set to Screen and Characterize Novel Protein N-Acetyltransferases Unveils Rice General Control Non-repressible 5-Related N-Acetyltransferase2 Activity
  Asensio, Frontiers in plant science 2022
  • “...0.20.1 83.44.7 P0ABB0 ATPA ATP synthase subunit alpha (EC 7.1.2.2) 1 - MQLNSTEISE 0.50.3 83.69.5 P0AAE0 CYCA D-serine/D-alanine/glycine transporter 2 M VDQVKVVADD 39.8 82.71.6 P75838 YCAO Ribosomal protein S12 methylthiotransferase accessory factor YcaO 2 M TQTFIPGKDA 1.00.6 81.41.2 P0A9S3 GATD Galactitol 1-phosphate 5-dehydrogenase (EC 1.1.1.251) 1...”
• Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae
  Van't, The FEBS journal 2020
  • “...Lat2, and Xct, respectively; and for bacterial, P24207 , P37460 , P25737 , P15993 , P0AAE0 , P25527 , P77610 , P39137 , and P42087 corresponding to PheP, ProY, LysP, AroP, CycA, GabP, AnsP, RocE, and HutM, respectively. This resulted in a population of 450, 105,...”
• The Escherichia coli Amino Acid Uptake Protein CycA: Regulation of Its Synthesis and Practical Application in l-Isoleucine Production
  Hook, Microorganisms 2022
  • “...of d -serine on cell growth [ 28 ] and assumed that the gene cycA (b4208) was responsible for d -cycloserine transport in E. coli , as was earlier shown by Wargel et al. [ 29 ]. Further investigations of the amino acid transport systems expanded...”
• Genome-wide analysis of fitness data and its application to improve metabolic models
  Vitkin, BMC bioinformatics 2018
  • “...candidate (with Bayesian confidence of ~4% and unbiased confidence of ~98.97%, see Methods) is cycA (b4208), which can act as an L-alanine transporter [ 34 , 35 ]. Another example is the internal reaction CMPN (CMP nucleosidase: CMP + H2OCytosine + D-Ribose-5P ), for which the...”
• Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
  Franchini, PloS one 2015
  • “...12.5 actP f b4067 acetate permease 10.7 alsB b4088 D-allose-binding periplasmic protein -3.2 ** cycA b4208 transport of D-alanine, D-serine, and glycine 4.0 ytfQ b4227 putative D-ribose transport protein, ABC superfamily 3.6 ytfR b4228 putative ATP-binding component of a transport system 5.2 idnT f , g...”
• Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes
  Skippington, Genome biology and evolution 2012
  • “...gltL b0652 gcvB 26 Variable Incongruent No livK b3458 gcvB 27 Core Congruent No cycA b4208 gcvB 27 Core Incongruent Yes livJ b3460 gcvB 27 Core Incongruent Yes galK b0757 spf 27 Core Incongruent No Units of genetic transfer and recombination do not necessarily correspond to...”
• RNApredator: fast accessibility-based prediction of sRNA targets
  Eggenhofer, Nucleic acids research 2011
  • “...metE b3829 5(8) 120(37) NC_000913 E.c.K. FnrS sodB b1656 24(21) 615(192) NC_000913 E.c.K. GcvB cycA b4208 37(5) 41(10) NC_000913 E.c.K. IstR tisB b4405 2(NF) NF(NF) NC_000913 E.c.K. MicA phoP b1130 80(23) 57(10) NC_000913 E.c.K. MicC ompC b2215 2(5) 2(2) NC_000913 E.c.K. MicF ompF b0929 43(5) 2(2)...”
• Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
  Ren, Applied and environmental microbiology 2005
  • “...soxS b4062 1.2 0.3597 1.4 0.0069 2.1 Transport cycA dcuA b4208 b4138 1.5 0.0005 1.6 0.0074 1.4 0.0170 1.5 0.0004 b1312 bglF fhuD b1312 b3722 b0152 1.0 1.0000...”
• Microarray analysis of transposition targets in Escherichia coli: the impact of transcription
  Manna, Proceedings of the National Academy of Sciences of the United States of America 2004
  • “...b4322 b2920 b0863 b4161 b3409 b0208 b4323 b4180 b2672 b2592 b4208 b0365 Gene yidP ybjP intC artP ytfE yafB yrfD ytfF thyA yfiH dgkA yhgG yrfG uxuA ygfH artl...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b3517 b3509 b2019 b3856 b1260 b0074 b3829 b2599 b2215 b3196 b4208 b0431 b1263 b4016 b0720 b3458 0.04 0.07 0.08 0.08 0.08 0.09 0.11 0.11 0.11 0.14 0.14 0.14 0.15...”
• More
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...6: ZansP, 7: ZgabP), E.coli H7 (1: ECs0614, 2: ECs0116, 3: ECs4729, 4: ECs0452, 5: ECs5186, 6: ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398,...”

Q16N01 ABC-type polar-amino-acid transporter (EC 7.4.2.1) from Aedes aegypti (see paper)
XP_001662274 cationic amino acid transporter 3 from Aedes aegypti
24% identity, 62% coverage

• Substrate specificity and transport mechanism of amino-acid transceptor Slimfast from Aedes aegypti
  Boudko, Nature communications 2015
  • GeneRIF: Slif transports essential cationic and neutral amino acids with preference for arginine.
  • “...-histidine 23 . The Aa CAT1 paralogue, Aa Slif ( = CAT3; GenBank accession #: XP_001662274 ) is closely related to fruit fly slimfast (slif). Characterization of slif homologues in mosquito is of high interest as it may function as a mechanism combining transporter and receptor...”

AO353_12275 histidine permease from Pseudomonas fluorescens FW300-N2E3
24% identity, 65% coverage

• mutant phenotype: Specific phenotype on histidine. 86% identical to PFLU0368, which is required for histidine utilization (PMCID: PMC1950622).

LOC110863868 cationic amino acid transporter 1 from Helianthus annuus
24% identity, 57% coverage

• Dissecting the Genetic Architecture of Morphological Traits in Sunflower (Helianthus annuus L.)
  Delen, Genes 2024
  • “...10 were shared by both models. The SNP NC_035433.2-12278968 was closely located to two genes (LOC110863868 and LOC110863881) in the results of both methods. Similarly, another SNP, NC_035441.2-99824358, was closely located to two genes, LOC110875903 and LOC110875902. The genes that were identified by the MLM method...”
  • “...chromosomes 1, 9, and 10, were shared by both models. Among these genes, the gene LOC110863868 was functioning in coding cationic amino acid transporter 1, which is an amino acid transporter that plays a significant role in nitrogen distribution throughout the plant, which is necessary to...”

WP_023637659 proline-specific permease ProY from Dickeya solani
23% identity, 65% coverage

• Oxygen Availability Influences Expression of Dickeya solani Genes Associated With Virulence in Potato (Solanum tuberosum L.) and Chicory (Cichorium intybus L.)
  Lisicka, Frontiers in plant science 2018
  • “...2.0 hypoxia 1.9 6 B7 small, creamish, white, crateriform with entire margin wt decreased decreased WP_023637659; proline-specific permease ProY D. dadantii, D. dianthicola, D. zeae, D. chrysanthemi, D. paradisiaca 68.0 normoxia 1.8 7 B18 small, creamish, white, crateriform with entire margin elongated cells decreased decreased WP_022634983;...”
  • “...2.4 5.4 5 A77 WP_012883918; colicin transporter, TolR protein 6.45 0 0 1.65 6 B7 WP_023637659; proline-specific permease ProY 7.7 8.0 16.8 5.4 7 B18 WP_022634983; hypothetical protein 2.4 0 0 1.3 8 B29 WP_022634128; hypothetical protein 0 3.6 0 0 The 8 D. solani mutants...”

CNBG_5513 L-methionine transporter from Cryptococcus deuterogattii R265
25% identity, 67% coverage

• Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection
  Ferrareze, Microorganisms 2017
  • “...268.427 CNBG_4571 Gamma-aminobutyric acid transporter 61.0116 CNBG_4665 Gamma-aminobutyric acid transporter 4.20125 CNBG_4156 Choline transporter 74.1659 CNBG_5513 l -methione transporter 11.9407 CNBG_4785 General amino acid transporter (AAP2) 441.806 CNBG_1371 General amino acid transporter (AAP4) 416.72 CNBG_9416 General amino acid transporter (AAP1) 363.575 CNBG_6051 General amino acid transporter...”

PA14_65850 putative amino acid ABC transporter, permease protein from Pseudomonas aeruginosa UCBPP-PA14
22% identity, 68% coverage

• Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates
  Jeske, NPJ biofilms and microbiomes 2022
  • “...PA14_64800 vanA 2.57 PA14_20370 phnH 1.75 PA14_32100 xylY 1.50 PA14_64810 vanB 1.72 PA14_20380 phnI 1.46 PA14_65850 rocE 1.32 PA14_20390 phnJ 1.65 PA14_20400 phnK 1.35 Attachment Resistance PA14_21110 plcN 1.00 PA14_11070 cupB2 1.93 PA14_18760 mexP 1.28 PA14_21410 phoA 1.37 PA14_11080 cupB3 1.29 PA14_18780 mexQ 1.22 PA14_21620 oprP...”

TC 2.A.3.1.6 / P37460 Proline-specific permease (ProY) from Salmonella typhimurium (see 2 papers)
STM0400 putative APC family, proline transporter from Salmonella typhimurium LT2
23% identity, 88% coverage

• substrates: Proline
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937). Table 1 Results of the algorithm on the COGs...”
• Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae
  Van't, The FEBS journal 2020
  • “..., and Q9UPY5 corresponding to Lat1, Lat2, and Xct, respectively; and for bacterial, P24207 , P37460 , P25737 , P15993 , P0AAE0 , P25527 , P77610 , P39137 , and P42087 corresponding to PheP, ProY, LysP, AroP, CycA, GabP, AnsP, RocE, and HutM, respectively. This resulted...”

Q7NI34 Gll2350 protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)
26% identity, 79% coverage

• Transcriptome analysis in response to heat shock and cadmium in the aquatic fungus Blastocladiella emersonii.
  Georg, Eukaryotic cell 2007 (no snippet)

E1B761 Cationic amino acid transporter C-terminal domain-containing protein from Bos taurus
24% identity, 61% coverage

• Comparative Analysis of Erythrocyte Proteomes of Water Buffalo, Dairy Cattle, and Beef Cattle by Shotgun LC-MS/MS
  Guo, Frontiers in veterinary science 2019
  • “...65120.95 6.54 Q3ZC32 Optineurin 1 1 65237.76 5.16 A6QPL7 DDN protein 1 1 66093.01 11.11 E1B761 Uncharacterized protein 2 2 67491.08 6.67 Q5EA82 Chromosome 6 open reading frame 11 1 1 67523.59 9.86 Q6B855 Transketolase 6 5 67905.04 7.56 L8J1A5 Zinc finger protein 48 1 1...”

ACSP50_2706 amino acid permease from Actinoplanes sp. SE50/110
24% identity, 82% coverage

• A maltose-regulated large genomic region is activated by the transcriptional regulator MalT in Actinoplanes sp. SE50/110
  Droste, Applied microbiology and biotechnology 2020
  • “...Class II glutamine amidotransferase Amino acid metabolism ACSP50_6409 ACSP50_3920 Amino acid permease Amino acid metabolism ACSP50_2706 ; ACSP50_3876 ACSP50_3921 Arginine deiminase Arginine biosynthesis ACSP50_8316 ACSP50_3922 Ornithine carbamoyltransferase Arginine biosynthesis ACSP50_4060 ACSP50_3923 Carbamate kinase Arginine biosynthesis ACSP50_6398 ACSP50_3924 Cyclic nucleotidebinding protein (phosphodiesterase) Put. serine/threonine biosynthesis ACSP50_3944 Beta-Ala-His...”

LOC102626651 cationic amino acid transporter 1 from Citrus sinensis
24% identity, 56% coverage

• Hub Genes and Pathways Related to Lemon (Citrus limon) Leaf Response to Plenodomus tracheiphilus Infection and Influenced by Pseudomonas mediterranea Biocontrol Activity
  Sicilia, International journal of molecular sciences 2024
  • “...the central part of the network, including PIN (Cluster-5871.3), Cyt-p450 (Cluster-6461.16030), PHO84 (Cluster-6461.10355), ndh1 (Cluster-6461.23594), LOC102626651 (Cluster-6461.3793) and three receptor-like kinases (RLK): HERK1 (Cluster-6461.1373), CLAVATA1 (Cluster-6461.9951) and LRR (Cluster-6461.18390). Due to their high neighborhood connectivity and module membership values, they could be considered candidate hub genes...”
  • “...five associated genes in the central part of the network PIN, Cyt-p450, PHO84, SLC15A3_4, ndh1, LOC102626651 in the 3CPt vs.CK samples. It is important to mention that receptor-like kinases (RLK) are not hub genes in the 3CPt vs. CK. Moreover, these gene networks reveal that 6:...”

gabP / AAB62306.1 GabP from Bacillus subtilis (see 4 papers)
24% identity, 77% coverage

PA5097 probable amino acid permease from Pseudomonas aeruginosa PAO1
24% identity, 65% coverage

• Global transcriptome analysis of Pseudomonas aeruginosa NT06 response to potassium chloride, sodium lactate, sodium citrate, and microaerophilic conditions in a fish ecosystem
  Tomaś, FEMS microbiology letters 2024
  • “...transporter that maintains outer membrane lipid asymmetry (Ekiert et al. 2022 ). In KCl-treated cells, PA5097 (amino acid permease), PA2982 (transport of siderophores), and opdO (pyroglutamate porin), were upregulated, indicating the nutrient-limited conditions of P. aeruginosa cell growth (Tamber et al. 2006 ). DEGs involved in...”
• Iron-regulated expression of alginate production, mucoid phenotype, and biofilm formation by Pseudomonas aeruginosa
  Wiens, mBio 2014
  • “...O -acetyltransferase PA3550 algF NC 5 Alginate O -acetyltransferase PA3551 algA 2 11 Phosphomannose isomerase PA5097 hutT 3 6 -Aminobutyrate permease PA5098 hutH 2 14 Histidine ammonia-lyase PA5099 NC 47 Nucleoside transporter family PA5100 hutU 5 23 Urocanase a Change in gene expression for P ....”
  • “...One additional salient outcome from these experiments is the considerably increased levels of expression of PA5097 ( hutT ), PA5098 ( hutH ), and PA5099 ( Table2 ). Transcription of these genes, which comprise an operon, was significantly increased in the PAO1 mucA mutant under iron...”
• Regulation of the histidine utilization (hut) system in bacteria
  Bender, Microbiology and molecular biology reviews : MMBR 2012
  • “...member of the 568 mmbr.asm.org HutT (Pfl) ProY (Ppu) PA5097 (Pae) ProY (Kpn) % Amino acid sequence identity/% amino acid similarityb ProY (Ppu) PA5097 (Pae)...”
• Induction by cationic antimicrobial peptides and involvement in intrinsic polymyxin and antimicrobial peptide resistance, biofilm formation, and swarming motility of PsrA in Pseudomonas aeruginosa
  Gooderham, Journal of bacteriology 2008
  • “...PA3723 PA3877 PA3957 PA4135 PA4497 PA4599 PA4654 PA4911 PA5020 PA5097 PA5141 PA5187 PA5188 PA5234 PA5302 b 5632 GOODERHAM ET AL. J. BACTERIOL. cated a role for...”
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...PA5075 PA01 glutamine ABC transporter membrane protein PA5076 PAK glutamine ABC transporter periplasmic binding protein PA5097 PAK proline APC family transporter PA5153 PAK amino acid (lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein PA5155 PAK amino acid (lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein PA5170 PAK arginine/ornithine APC family antiporter...”
• Effects of antibiotics on quorum sensing in Pseudomonas aeruginosa
  Skindersoe, Antimicrobial agents and chemotherapy 2008
  • “...PA4211 PA4217 PA4290 PA4345 PA4377 PA4677 PA4738 PA4739 PA4876 PA4880 PA5097 PA5099 PA5212 PA5220 PA5235 PA5297 PA5480 phzA1 PA4210 glpT poxB C D C C B B D B...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...ECs4729, 4: ECs0452, 5: ECs5186, 6: ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854,...”
• Effect of metabolic imbalance on expression of type III secretion genes in Pseudomonas aeruginosa
  Rietsch, Infection and immunity 2004
  • “...by amplifying the chromosomal region carrying genes PA5097 (hutT) to PA5099 with primers 5097 3 (5-AAA AAAAGCTTCTCAGGCCGCCGTCGGTTCCGTCACA-3) and perm5 (5-G...”
  • “...bacteria to kill RAW264.7 macrophages was restored by deleting PA5097, a putative amino acid transporter gene (Fig. 3). Deletion of PA5097 in wild-type PAO1 had...”
• More

ABA1_02141 amino acid permease from Acinetobacter baumannii
23% identity, 67% coverage

• Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1
  Holt, Microbial genomics 2016
  • “...resistance, transporter TTTCTT FL NS ABA1_02065 PcaH protocatechuate 3,4-dioxygenase, subunit 144 AAAACA KT NS (2) ABA1_02141 Proline-specific permease proY 233 CCGCCA PP S (2) Transport ABA1_02431 Serine/threonine protein kinase 1 55 TTTTAT FY NS (2) ABA1_02631 ( ampC ) -Lactamase class C, ampC 341 AACACC NT...”

BAS0610 amino acid ABC transporter, permease protein from Bacillus anthracis str. Sterne
23% identity, 67% coverage

• Identification of CodY targets in Bacillus anthracis by genome-wide in vitro binding analysis
  Château, Journal of bacteriology 2013
  • “...BAS0498 BAS0518 BAS0566 (nprR)* BAS0567 (nprB) BAS0580 BAS0610 BAS0638 (inhA2) BAS0660 BAS0669 BAS0779 BAS0809 BAS0841 (sap) BAS0842 (eag) BAS0842 (eag) BAS0847...”

YPTB1621 APC family aromatic amino acid transport protein from Yersinia pseudotuberculosis IP 32953
YPO1743 aromatic amino acid transport protein from Yersinia pestis CO92
25% identity, 66% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(pepN) YPO1414 putative aminopeptidase N 1.432 (0.041) YPTB1541 (ysuJ) YPO1529 putative decarboxylase 2.092 (< 0.001) YPTB1621 (aroP) YPO1743 aromatic amino acid transport protein 1.68 (0.006) YPTB1641 (hpaF) YPO1765 5-carboxymethyl-2-hydroxymuconate delta-isomerase 1.812 (0.015) YPTB1656 (ptrB) YPO1780 oligopeptidase B 1.695 (0.006) YPTB1889 (lysA) or1363 possible diaminopimelate decarboxylase 1.621...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...putative aminopeptidase N 1.432 (0.041) YPTB1541 (ysuJ) YPO1529 putative decarboxylase 2.092 (< 0.001) YPTB1621 (aroP) YPO1743 aromatic amino acid transport protein 1.68 (0.006) YPTB1641 (hpaF) YPO1765 5-carboxymethyl-2-hydroxymuconate delta-isomerase 1.812 (0.015) YPTB1656 (ptrB) YPO1780 oligopeptidase B 1.695 (0.006) YPTB1889 (lysA) or1363 possible diaminopimelate decarboxylase 1.621 (0.01) 0.45...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937). Table 1 Results of the algorithm on the COGs database # % Pairs with score below threshold, not tested 1021764...”

y2564 aromatic amino acid permease from Yersinia pestis KIM
25% identity, 66% coverage

• Genome-wide mutant fitness profiling identifies nutritional requirements for optimal growth of Yersinia pestis in deep tissue
  Palace, mBio 2014
  • “...d -Alanine/ d -serine/glycine permease 0.709 3.50E03 pabB (y2535) para -aminobenzoate synthesis 0.690 1.00E04 aroP (y2564) Aromatic amino acid import 0.777 1.00E05 hisF (y2627) Histidine biosynthesis 0.570 6.00E04 y2739 Putative ATP-dependent protease 0.591 7.00E04 aspC (y2760) Amino acid metabolism/biosynthesis 0.706 1.00E04 aroA (y2783) Aromatic amino acid...”

A1S_3404 proline transport protein (APC family) from Acinetobacter baumannii ATCC 17978
27% identity, 58% coverage

• A corepressor participates in LexA-independent regulation of error-prone polymerases in Acinetobacter
  Peterson, Microbiology (Reading, England) 2020
  • “...putative lipoprotein precursor (RlpA-like) 2.03 yes A1S_2936 copper resistance protein A precursor 2.11 A1S_3402 A1S_3403 A1S_3404 rocF hydrolase 1.69 yes hutI imidazolonepropionase 1.65 yes proline transport protein (APC family) 1.39 yes A1S_3627 hypothetical 2.15 yes A1S_3748 hypothetical 1.24 yes A1S_3794 hypothetical 1.68 yes A1S_3858 hypothetical 1.73...”
• Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
  Rumbo-Feal, PloS one 2013
  • “...involved in amino acid metabolism and transport (such as A1S_0115, A1S_0429, A1S_1357, A1S_3134, A1S_3185, A1S_3402, A1S_3404, A1S_3405, A1S_3406, A1S_3407, or A1S_3413), or related to iron acquisition and transport (A1S_0653, A1S_0742, A1S_0980, A1S_1631, A1S_1657, A1S_2385, or A1S_2390, encoding a ferrous iron transport protein, an iron-regulated protein, a...”
  • “...dehydrogenase subunit E1 0.50 0.92 A1S_3350 hypothetical protein 0.38 0.89 A1S_3402 arginase/agmatinase/formimionoglutamate hydrolase 3.72 7.33 A1S_3404 amino acid APC transporter 3.88 4.18 A1S_3405 histidine ammonia-lyase 3.13 3.94 A1S_3406 urocanate hydratase 3.92 0.85 A1S_3407 urocanase 4.52 2.63 A1S_3413 APC family aromatic amino acid transporter 66.30 18.38 A1S_3414...”

YPO1937 L-asparagine permease from Yersinia pestis CO92
23% identity, 79% coverage

• Cell membrane is impaired, accompanied by enhanced type III secretion system expression in Yersinia pestis deficient in RovA regulator
  Yang, PloS one 2010
  • “...transporter permease 4.A Transport/binding proteins YPO4111 3.77 ----- putative periplasmic solute-binding protein 4.A Transport/binding proteins YPO1937 3.73 ansP L-asparagine permease 4.A.1 Transport/binding proteins YPO4109 4.28 ----- putative amino acid transport system permease 4.A.1 Transport/binding proteins YPO2338 3.86 ----- CorA-like Mg2+ transporter protein 4.A.2 Transport/binding proteins YPO0182...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937). Table 1 Results of the algorithm on the COGs database # % Pairs with score below threshold, not tested 1021764 44.0 Pairs with score above threshold 1298435 66.0 Non-orthologous pairs...”

AO353_05930 L-tryptophan transporter from Pseudomonas fluorescens FW300-N2E3
24% identity, 69% coverage

• mutant phenotype: Specifically important for utilization of tryptophan as a nitrogen source.

PA1819 probable amino acid permease from Pseudomonas aeruginosa PAO1
24% identity, 81% coverage

• Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
  Salvà-Serra, Frontiers in microbiology 2022
  • “...PA1809 NppB/OppC NppB 7 17 1.00 0.96 1.10 0.28 1.61 0.01 Down 1.18 0.14 WP_003087965.1 PA1819 YjdE Probable amino acid permease 3 7 1.09 0.06 1.25 0.00 4.78 0.00 Down 1.35 0.00 WP_003088303.1 PA1948 RbsC Membrane protein component of ABC ribose transporter 3 14 1.05 0.43...”
  • “...protein, CmpX protein 6 22 1.02 0.19 1.29 0.00 1.55 0.00 Down 1.48 0.00 WP_023464637.1 PA1819 YjdE Probable amino acid permease 4 6 1.00 0.90 1.16 0.04 1.72 0.00 Down 1.18 0.02 WP_003088303.1 PA1948 RbsC Membrane protein component of ABC ribose transporter 3 14 1.10 0.19...”
• [In vitro activity of ceftazidime-avibactam combined with colistin against extensively drug-resistant Pseudomonas aeruginosa]
  Mei, Zhonghua wei zhong bing ji jiu yi xue 2019 (PubMed)
  • “...more than 6 log CFU/L when these two drugs were used together, and number of PA1819 planktonic bacteria decreased more than 5.1 log CFU/L compared with monotherapy group. Viable quantity in biofilm (A490) of normal saline group, CAZ-AVI group, COL group and CAZ-AVI-COL group were 0.665 0.068,...”
• A Novel Subfamily of Bacterial AAT-Fold Basic Amino Acid Decarboxylases and Functional Characterization of Its First Representative: Pseudomonas aeruginosa LdcA
  Carriel, Genome biology and evolution 2018
  • “...cluster with a gene coding for a homologue of the CadB antiporter, although cadB ( PA1819 in P. aeruginosa ) appears downstream, and not upstream, of the lysine decarboxylase-encoding gene. The presence of a dedicated Lys/Cad transporter could be important from a physiological standpoint because CadB...”
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...APC family transporter PA1590 PAK branched chain amino acid sodium ion symporter ( BraB ) PA1819 PAK amino acid APC family transporter PA1958 PAK nicotinamide mononucleotide transporter PA1971 PA01 branched chain amino acidcation symporter ( BraZ ) PA2041 PAK amino acid APC family transporter PA2079 PA01...”
• Transcriptome analysis of the ArgR regulon in Pseudomonas aeruginosa
  Lu, Journal of bacteriology 2004
  • “...members of the ArgR regulon include PA1818 and PA1819. These two genes encode a putative arginine/ornithine/lysine decarboxylase and an amino acid/ amine...”
  • “...observed arginine activation effect, we propose that PA1818 and PA1819 be designated adcA and adcB for their possible roles in the ADC pathway of P. aeruginosa....”

ECs0116 aromatic amino acid transport protein from Escherichia coli O157:H7 str. Sakai
24% identity, 74% coverage

• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...3: ZyifK, 4: ZproY, 5: ZcycA, 6: ZansP, 7: ZgabP), E.coli H7 (1: ECs0614, 2: ECs0116, 3: ECs4729, 4: ECs0452, 5: ECs5186, 6: ECs2057, 7: ECs3524), P.aeruginosa (2a: PA3000, 2b: PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150,...”

XP_039288773 high affinity cationic amino acid transporter 1 from Nilaparvata lugens
23% identity, 65% coverage

• Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species (Nilaparvata lugens)
  Yue, Frontiers in physiology 2021
  • “...7.43 + NlAPC10 XP_039288486 Nlug07560-TA chr7 31287561 31321892 586 10 12 63325.7 6.96 + NlAPC11 XP_039288773 Nlug13938-TA chr7 43966644 43979867 602 11 14 65792.0 8.66 + NlAPC12 XP_039290058 Nlug00063-TA chr8 17493916 17510991 495 12 12 54414.6 6.96 NlAPC13 XP_039289667 Nlug11217-TA chr8 2510817 2535142 1062 13 11...”

Q4V799 Similar to solute carrier family 7 (Cationic amino acid transporter, y+ system), member 3 from Rattus norvegicus
24% identity, 61% coverage

• ITRAQ Based Proteomics Reveals the Potential Mechanism of Placental Injury Induced by Prenatal Stress.
  Li, International journal of molecular sciences 2024
  • “...(Lamc1) Q99MZ8 LIM and SH3 domain protein 1 (Lasp1) G3V8L3 Lamin A, isoform CRA_b (Lmna) Q4V799 Similar to solute carrier family 7 (Cationic amino acid transporter, y+ system), member 3 (LOC292543) A0A0G2JYK0 Protein LOC299282 (LOC299282) A0A0G2JU68 Protein LOC304903 (LOC680415) Q5BK33 p55 protein (LOC691642) A0A0G2JYI0 Protein Lrba...”

XP_001346314 large neutral amino acids transporter small subunit 2 from Danio rerio
27% identity, 80% coverage

• The developmental effects of pentachlorophenol on zebrafish embryos during segmentation: A systematic view
  Xu, Scientific reports 2016
  • “...(membrane) aminopeptidase b ANPEP 128.30 5 mespaa NM_131551 mesoderm posterior aa MESP2 99.29 6 slc7a8b XP_001346314 solute carrier family 7 (amino acid transporter light chain, L system) SLC7A8 94.66 7 tbx16 NM_131058 T-box 16 TBX6 85.61 8 msgn1 NM_182882 mesogenin 1 MSGN1 80.36 9 six7 NM_131354...”
  • “...signaling 9 binding protein RGS9BP 22.17 3 her1 NM_131078 hairy-related 1 HES7 17.74 4 slc7a8b XP_001346314 solute carrier family 7 (amino acid transporter light chain, L system) SLC7A8 17.35 5 LOC100334535 XP_005164589 ubl carboxyl-terminal hydrolase 18-like USP18 14.46 6 ftr07 XP_698750 finTRIM family, member 7 TRIM25...”

PA4628 lysine-specific permease from Pseudomonas aeruginosa PAO1
26% identity, 66% coverage

• Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
  Salvà-Serra, Frontiers in microbiology 2022
  • “...c4-dicarboxylate-binding protein 3 4 1.45 0.03 1.14 0.37 5.36 0.00 Up 5.55 0.00 Lower WP_003094922.1 PA4628 LysP lysine-specific permease 4 9 1.01 0.93 1.22 0.07 2.00 0.00 Up 1.22 0.03 WP_003121056.1 PA4688 HitB iron (III)-transport system permease HitB 2 5 1.20 0.18 1.21 0.15 1.71 0.01...”
• Additive Effects of Quorum Sensing Anti-Activators on Pseudomonas aeruginosa Virulence Traits and Transcriptome
  Asfahl, Frontiers in microbiology 2017
  • “...1.7 NC NC NC PA4569 ispB octaprenyl-diphosphate synthase ( cel ) 1.8 NC NC 1.9 PA4628 lysP lysine-specific permease 1.7 NC NC NC PA4630 hypothetical protein 2.0 1.6 2.6 2.5 PA4672 peptidyl-tRNA hydrolase ( pth ) 2.1 NC NC NC PA4757 conserved hypothetical protein ( yeaS...”
• Gene expression in Pseudomonas aeruginosa swarming motility
  Tremblay, BMC genomics 2010
  • “...ATP-binding component of ABC transporter 1.5 PA3188 gltG probable permease of ABC sugar transporter 2.0 PA4628 lysP lysine-specific permease 1.7 PA5479 gltP proton-glutamate symporter 1.6 PA0782 3 putA proline dehydrogenase 1.8 PA0783 1 putP sodium/proline symporter PutP 1.6 PA4770 1 lldP L-lactate permease 1.5 Translation, post-translational...”
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...membrane protein PA4195 PAK amino acid ABC transporter periplasmic binding protein PA4233 PA01 MFS transporter PA4628 PAK lysine APC family transporter PA4804 PAK amino acid APC family transporter PA4909 PA01 branched chain amino acid ABC transporter ATP binding protein PA4910 PAK branched chain amino acid ABC...”
• Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment
  Wagner, Journal of bacteriology 2003
  • “...PA3877 PA3911 PA3912 PA3913 PA3914 PA3916 PA3917 PA3918 PA4587 PA4628 PA4918 ig 29233662922568 nirN exaB ptxS cobJ nosR nosZ nosD nosF nosY nosL moaA1 narI narJ...”

VK055_1734 amino acid permease from Klebsiella pneumoniae subsp. pneumoniae
25% identity, 65% coverage

• Urine-mediated suppression of Klebsiella pneumoniae mucoidy is counteracted by spontaneous Wzc variants altering capsule chain length
  Khadka, mSphere 2023
  • “...VK055_5017_wzc G1709T G569V 5 B4 Tn insertion unknown 0.137 + + VK055_5017_wzc G1709T VK055_0186_vgrG2 G2248A VK055_1734 A212C VK055_5017_wzc WT VK055_5017_wzc G1709T WT G569V 6 B4 Tn insertion unknown 0.054 0 WT None reported VK055_1828 0.06 + 0.0587 7 C8 VK055_1828 0.055 0 WT VK055_5031 T406A 8...”

CTR3_MOUSE / P70423 Cationic amino acid transporter 3; CAT-3; CAT3; Cationic amino acid transporter y+; Solute carrier family 7 member 3 from Mus musculus (Mouse) (see paper)
TC 2.A.3.3.5 / P70423 The brain L-cationic (Arg, Lys, Orn, 2,4-diamino-n-butyrate) transporter, CAT3 (capacity of trans-stimulation by internal Arg) from Mus musculus (Mouse) (see 4 papers)
Slc7a3 / GI|123218479 Cationic amino acid transporter 3 from Mus musculus (see paper)
XP_011245815 cationic amino acid transporter 3 isoform X1 from Mus musculus
23% identity, 62% coverage

• function: Uniporter that mediates the uptake of cationic L-amino acids such as L-arginine, L-lysine and L-ornithine (PubMed:9334265). The transport is sodium ions- and pH-independent, moderately trans- stimulated and is mediated by passive diffusion (PubMed:9334265).
  catalytic activity: L-arginine(in) = L-arginine(out) (RHEA:32143)
  catalytic activity: L-lysine(in) = L-lysine(out) (RHEA:70935)
  catalytic activity: L-ornithine(in) = L-ornithine(out) (RHEA:71199)
• substrates: 2,4-diamino-n-butyrate, Argnine, Ornithine, lysine
• Identification of Sec23ip, Part of 14-3-3γ Protein Network, as a Regulator of Acute Steroidogenesis in MA-10 Leydig Cells.
  Aghazadeh, Endocrinology 2020
• 2D DIGE proteomic analysis reveals fasting-induced protein remodeling through organ-specific transcription factor(s) in mice
  Kamata, FEBS open bio 2018
  • “...diphosphate kinase B Q01768 Nme2 Mm.1260 62 59% 7/32 17466 6.97 65 1.22 0.023 Catalase P70423 Cat Mm.4215 115 22% 12/21 60043 7.72 66 1.21 0.039 Cytoplasmic aconitate hydratase P28271 Aco1 Mm.331547 223 52% 37/77 98691 7.23 67 1.20 0.009 Peroxiredoxin1 P35700 Prdx1 Mm.30929 90 47%...”
• Extracellular arginine is required but the arginine transporter CAT3 (Slc7a3) is dispensable for mouse normal and malignant hematopoiesis.
  Yan, Scientific reports 2022
  • GeneRIF: Extracellular arginine is required but the arginine transporter CAT3 (Slc7a3) is dispensable for mouse normal and malignant hematopoiesis.
• p53 Promotes Cancer Cell Adaptation to Glutamine Deprivation by Upregulating Slc7a3 to Increase Arginine Uptake.
  Lowman, Cell reports 2019
  • GeneRIF: Slc7a3 expression is significantly induced by p53 upon glutamine deprivation.
• Genetic ablation of solute carrier family 7a3a leads to hepatic steatosis in zebrafish during fasting.
  Gu, Hepatology (Baltimore, Md.) 2014 (PubMed)
  • GeneRIF: knockdown impaired AMPK-PPAR-alpha signaling and resulted in lipid accumulation under fasting
• Y+ and y+ L arginine transporters in neuronal cells expressing tyrosine hydroxylase.
  Bae, Biochimica et biophysica acta 2005 (PubMed)
  • GeneRIF: In a neuronal cell model, y+,L and y+ transport systems are the predominant form of arginine uptake mechanisms and the transport of arginine is altered by membrane potential and redox factors.

7nf6B / A0A6P3EL78 Ovine b0,+at-rbat heterodimer (see paper)
26% identity, 74% coverage

• Ligands: cholesterol; 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (7nf6B)

RR42_RS33495 L-phenylalanine:H+ symporter AroP from Cupriavidus basilensis FW507-4G11
23% identity, 80% coverage

• mutant phenotype: Specifically important for utliization of phenylalanine as the nitrogen source.

SF5M90T_4187 D-serine/D-alanine/glycine transporter from Shigella flexneri 5a str. M90T
22% identity, 64% coverage

• RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
  Vergara-Irigaray, BMC genomics 2014
  • “...lysC aspartokinase III, lysine sensitive -1.33 1.37 1.14 SF5M90T_1253 trpE anthranilate synthase component I -1.57 SF5M90T_4187 cycA transport of D-alanine, D-serine, and glycine -1.69 SF5M90T_1946 yedA putative transmembrane subunit -1.79 SF5M90T_3626 yifK putative amino acid/amine transport protein -1.94 SF5M90T_3385 livJ Leu/Ile/Val-binding protein precursor -1.95 SF5M90T_2843 lysA...”

B1745_06875 APC family permease from Lactobacillus amylolyticus
23% identity, 76% coverage

• Adaptive mechanism of Lactobacillus amylolyticus L6 in soymilk environment based on metabolism of nutrients and related gene-expression profiles
  Fei, Food science & nutrition 2022
  • “...glnM glutamine ABC transporter permease 1.60 B1745_02545 pepX dipeptidylpeptidase 1.56 B1745_02045 dacD DalanylDalanine carboxypeptidase 1.44 B1745_06875 amino acid permease 1.44 B1745_00945 oppD peptide ABC transporter ATPbinding protein 1.43 B1745_RS07280 lysC aspartate kinase 1.41 B1745_06870 att amino acid permease 1.40 B1745_04855 atpA haloacid dehalogenase 1.40 B1745_00955 pepC...”
  • “...under soymilk environment (Wang etal., 2012 ). Meanwhile, many uncharacterized amino acid permease genes (B1745_03105, B1745_06875, B1745_06870, and B1745_06860) were upregulated, while two amino acid permease genes (B1745_04680 and B1745_03815) were downregulated in the logarithmic and stationary phase. Interestingly, two genes livB and brnQ coding for...”

STM4398 APC family, D-alanine/D-serine/glycine transport protein from Salmonella typhimurium LT2
22% identity, 64% coverage

• The coenzyme B₁₂ precursor 5,6-dimethylbenzimidazole is a flavin antagonist in Salmonella
  Malalasekara, Microbial cell (Graz, Austria) 2023
  • “...DNA Technologies, Inc. (IDT, Coralville, IA]), and are listed Table 3 . Genes cycA ( stm4398 ), dctA ( stm3614 ), and tcuC ( stm0689 ) glpF ( stm4087 ) and rbsACB ( stm3882-4 ) were amplified using Phusion high fidelity polymerase (Thermo Fisher Scientific). PCR...”
• Repression of Salmonella enterica phoP expression by small molecules from physiological bile
  Antunes, Journal of bacteriology 2012
  • “...hybD feoB hypO cutC yhgI yhfA feoA STM2378 STM4398 STM0600 STM3218 STM2389 PSLT052 STM1231 STM4159 STM3557 STM0734 STM0662 ORF01131 STM1238 STM1712 STM0549...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937). Table 1 Results of the algorithm on the COGs database #...”

LOC11435913 cationic amino acid transporter 4, vacuolar from Medicago truncatula
23% identity, 61% coverage

• Genome-wide association analysis for drought tolerance and associated traits in faba bean (Vicia faba L.)
  Gutiérrez, Frontiers in plant science 2023
  • “...2.3 VF1L LOC11430458 - MTR_5g083560 Cation/H(+) antiporter 14 Chr5: 37,260,367 - 37,261,590 AX-181483294 1.9 VF5 LOC11435913 - MTR_7g086510 Cationic amino acid transporter 4, vacuolar Chr7: 40,354,298 - 40,361,570 AX-416771643 0.9 VF1L LOC11426550 - MTR_5g082490 Protein yippee-like Chr5: 36,649,198 - 36,652,967 AX-416761080 0.8 VF6 LOC25492837 - MTR_4g074390...”

CAC3164 Lysine-specific permease from Clostridium acetobutylicum ATCC 824
25% identity, 66% coverage

• Meta-analysis and functional validation of nutritional requirements of solventogenic Clostridia growing under butanol stress conditions and coutilization of D-glucose and D-xylose
  Heluane, Applied and environmental microbiology 2011
  • “...0.000250975 0.003281643 0.002038606 0.000640894 E E E CAC3164 CAC3348 CAC3618 0.003458938 0.000180346 0.000132942 E CAC3619 0.006894683 a The meta-analysis...”
  • “...CAC2388 CAC2389 CAC2390 CAC2634 CAC2708 CAC2711 CAC2712 CAC3164 CAC3170 CAC3348 CAC3462 CAC3596 CAC3680 CAC3681 0.40506 1.51803 1.07553 1.7949 2.70695 0.54094...”
• A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing
  Borden, Metabolic engineering 2010
  • “...and CAC2338 [19% identity]) and adiC (CAC0727 [22% identity], CAC0852 [20% identity], CAC2719 [20% identity], CAC3164 [21% identity], and CAC3347 [22% identity]). An emerging mechanism of acid tolerance has been investigated in Streptococcus mutans ( Gutierrez et al., 1999 ; Kremer et al., 2001 ), and...”

XP_039290058 large neutral amino acids transporter small subunit 1 from Nilaparvata lugens
22% identity, 79% coverage

• Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species (Nilaparvata lugens)
  Yue, Frontiers in physiology 2021
  • “...6.96 + NlAPC11 XP_039288773 Nlug13938-TA chr7 43966644 43979867 602 11 14 65792.0 8.66 + NlAPC12 XP_039290058 Nlug00063-TA chr8 17493916 17510991 495 12 12 54414.6 6.96 NlAPC13 XP_039289667 Nlug11217-TA chr8 2510817 2535142 1062 13 11 117217.1 7.38 + NlAPC14 XP_039291870 Nlug19381-TA chr9 43515190 43580863 1098 20 13...”

STM14_0180 aromatic amino acid transporter AroP from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM0150 APC family, aromatic amino acid transporter from Salmonella typhimurium LT2
25% identity, 73% coverage

• Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress
  Zhang, Microbiology spectrum 2023
  • “...protein STM14_0076 STM14_0177 0.76 0.046 Putative cytoplasmic protein STM14_0178 0.84 0.017 Na + /galactoside symporter STM14_0180 aroP 0.84 0.017 Aromatic amino acid transporter STM14_1053 0.90 0.014 Hypothetical protein STM14_1053 STM14_1388 ycfR 0.68 0.05 Putative outer membrane protein STM14_2212 manX 0.82 0.024 Mannose-specific enzyme IIAB STM14_2213 manY...”
• Transcriptomic Responses of Salmonella enterica Serovars Enteritidis in Sodium Hypochlorite
  Wang, Frontiers in cellular and infection microbiology 2022
  • “...C STM0705 kdpB 3.6 potassium-transporting ATPase subunit KdpB STM0704 kdpA 3.7 potassium-transporting ATPase subunit A STM0150 aroP 3.5 aromatic amino acid transporter AroP STM0399 brnQ 1.4 branched-chain amino acid transporter carrier protein BrnQ STM3560 livF 1.7 branched-chain amino acid ABC transporter ATP-binding protein LivF Carbohydrate and...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...PA0866, 4a: PA5097, 4b: PA0789, 7: PA0129, out: PA2079), Salmonella typhimurium LT2 (1: STM0568, 2: STM0150, 3: STM3930, 4: STM0400, 5: STM4398, 6: STM1584, 7: STM2793), Y.pestis (2a: YPO3421, 2b: YPO1743, 3: YPO3854, 4a: YPO3201, 4b: YPO4015, 5: YPO1859, 6: YPO1937). Table 1 Results of the...”

8wntB / Q9NS82 Cryo em map of slc7a10 with l-alanine substrate (see paper)
28% identity, 57% coverage

• Ligand: alanine (8wntB)

New Search

Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.