PaperBLAST
PaperBLAST Hits for SwissProt::P30145 Sodium/proton-dependent alanine carrier protein (Bacillus sp. (strain PS3)) (445 a.a., MIRLVTMGKS...)
Show query sequence
>SwissProt::P30145 Sodium/proton-dependent alanine carrier protein (Bacillus sp. (strain PS3))
MIRLVTMGKSSEAGVSSFQALTMSLSGRIGVGNVAGTATGIAYGGPGAVFWMWVITFIGA
ATAYVESTWRKFIKRNKTDNTVAVRRSTLKKALAGNGLRCSRAAIILSMAVLMPGIQANS
IADSFSNAFGIPKLVTGIFVIAVLGFTIFGGVKRIAKTAEIVVPFMAVGYLFVAIAIIAA
NIEKVPDVFGLIFKSAFGADQVFGGILGSAVMWGVKRGLYANEAGQGTGAHPAAAAEVSH
PAKQGLVQAFSIYLDVFLVVTATALMILFTGQYNVINEKTGETIVEHLKGVEPGAGYTQA
AVDTLFPGFGSAFIAIALFFFAFTTMYAYYYIAETNLAYLVRSEKRGTAFFALKLVFLAA
TFYGTVKTATTAWAMGDIGLGIMVWLNLIAILLLFKPAYMALKDYEEQLKQGKDPEFNAS
KYGIKNAKFWENGYKRWEEKKGKAL
Running BLASTp...
Found 126 similar proteins in the literature:
ALCP_BACP3 / P30145 Sodium/proton-dependent alanine carrier protein from Bacillus sp. (strain PS3) (see paper)
TC 2.A.25.1.2 / P30145 Alanine:Na+ (or H+) symporter (see paper)
100% identity, 100% coverage
- function: Mediates the active transport of alanine, driven by either an H(+) or Na(+) gradient.
- substrates: Alanine, H+, Na+
tcdb comment: The sequence as reported appears to lack the first 45 aas and the first two tMSs, probably because of incorrect initiation codon selection
BAS0605 sodium/alanine symporter family protein from Bacillus anthracis str. Sterne
57% identity, 91% coverage
- A genetic approach for the identification of exosporium assembly determinants of Bacillus anthracis
Spreng, Journal of microbiological methods 2013 - “...compared to the wild-type parent by flow cytometry. Representative examples (Tn 916 inactivated bas0389 , bas0605 , bas1726 , and bas1747 ) are shown in Fig. 2 . Each mutant exhibited a reduced level of DsRed fluorescence compared to wild-type levels. The results confirmed the fluorescence...”
- “...were selected for further study. Two of these, BAS0389 and BAS1747, are of unknown function. BAS0605 was annotated as a sodium/alanine symporter family protein. 3.2 bas0389 The bas0389 determinant harbored the Tn 916 element 501 bp into the open reading frame. This determinant is the penultimate...”
NP_390659 sodium/proton-dependent alanine transporter from Bacillus subtilis subsp. subtilis str. 168
60% identity, 91% coverage
SO3063 sodium:alanine symporter family protein from Shewanella oneidensis MR-1
55% identity, 87% coverage
- SO2426 is a positive regulator of siderophore expression in Shewanella oneidensis MR-1
Henne, BMC microbiology 2011 - “...protein, putative CCGGATCAGCAAAA + -284 1.46E-05 SO3033 ferric alcaligin siderophore receptor ATCAAACAGCCAAA + -112 3.20E-06 SO3063 sodium:alanine symporter family protein CAAAAACAACAGAA + -18 1.09E-06 SO4150 transporter, putative AAAAAACTGCAGAA + +16 7.64E-06 SO4516 ferric vibriobactin receptor ( viuA ) CAGTAGCAGAAGAA + -249 1.62E-05 SO4743 TonB-dependent receptor, putative...”
- “...of the SO2426 regulon proposed here, namely, so1188, so1190, so3025, so3030 - 3031 - 3032, so3063 , and so4743 [ 14 ]. All of these genes, including so2426 , were up-regulated under iron-depleted growth conditions compared to iron-replete conditions. Additionally, so3030 was up-regulated almost 14-fold in...”
- Snapshot of iron response in Shewanella oneidensis by gene network reconstruction
Yang, BMC genomics 2009 - “...reductase protein (AlcE) 1.07 1.02 1.60 3.76 5.51 5.25 0.65 1.01 0.50 0.15 0.18 0.11 SO3063 sodium:alanine symporter family protein 1.04 1.67 2.11 4.10 4.38 4.68 0.85 0.54 0.23 0.41 0.54 0.29 SO3065 colicin V production protein -- -- 0.33 0.35 0.37 0.42 2.16 -- 1.29...”
- Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge
Chourey, BMC genomics 2008 - “...0.25 0.14 0.06 0.73* SO3033 Ferric alcaligin siderophore receptor 0.73 0.34 0.29 0.17 0.07 0.77* SO3063 Sodium:alanine symporter family protein 0.26 0.18 0.12 0.15 0.18 0.34 SO4150 Transporter, putative 0.07 0.12 0.11 0.34 0.27 0.3 SO4516 Ferric vibriobactin receptor ( viuA ) 0.59 0.54 0.37 0.21...”
- “...putative siderophore biosynthesis proteins encoded immediately downstream of alcA ), so3033 (ferric alcaligin siderophore receptor), so3063 (sodium:alanine symporter family protein), so4150 (putative transporter), viuA (ferric vibriobactin receptor), so4712 (putative ABC transporter, ATP-binding protein), and so4743 (putative TonB-dependent receptor). In contrast to the TonB-dependent receptor genes so1580...”
- Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response
Yang, BMC genomics 2008 - “...(1.0E-04) SO3032 siderophore biosynthesis protein, putative 9.14 (1.4E-04) SO3033 ferric alcaligin siderophore receptor 10.86 (1.2E-04) SO3063 sodium: alanine symporter family protein 4.16 (1.6E-05) SO3914 TonB-dependent receptor, putative 3.63 (0.002) SO4743 TonB-dependent receptor, putative 3.82 (4.7E-04) TonB1 TonB1 protein 21.92 (1.7E-05) ViuA ferric vibriobactin receptor 5.73 (2.9E-04)...”
- Cellular response of Shewanella oneidensis to strontium stress
Brown, Applied and environmental microbiology 2006 - “...cellular detoxification processes, and a sodium:alanine symporter gene (SO3063) showed temporal mean expression ratios of 4.7 (5 min), 2.6 (30 min), 5.2 (60...”
BAS2639 sodium/alanine symporter family protein from Bacillus anthracis str. Sterne
BA2830 sodium/alanine symporter family protein from Bacillus anthracis str. Ames
52% identity, 89% coverage
HD73_3147 alanine/glycine:cation symporter family protein from Bacillus thuringiensis serovar kurstaki str. HD73
54% identity, 89% coverage
- Sox transcription in sarcosine utilization is controlled by Sigma(54) and SoxR in Bacillus thuringiensis HD73
Peng, Scientific reports 2016 - “...focused on the organization and regulation of the sarcosine oxidase gene and nearby genes ( HD73_3147 - HD73_3138 ) in B. thuringiensis subsp. kurstaki strain HD73 (Bt HD73) 26 . The HD73_3147 - HD73_3138 genes of the sox locus were separately designated as soxI , soxH...”
- “...encodes ten proteins, which have been annotated as amino acid carrier protein ( soxI , HD73_3147), aldehyde dehydrogenase ( soxH , HD73_3146), dihydrodipicolinate synthase ( soxG , HD73_3145), proline racemase ( soxE , HD73_3143), sarcosine oxidase, subunit ( soxB , HD73_3142), Sigma 54 -dependent transcriptional activator...”
- Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis
Peng, Frontiers in microbiology 2015 - “...Proline racemase 35.278 HD73_3144 Hypothetical protein 31.999 HD73_3145 Dihydrodipicolinate synthase 34.853 HD73_3146 Aldehyde dehydrogenase 28.844 HD73_3147 Amino acid carrier protein 37.362 HD73_3213 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha 25.424 HD73_3214 TPP-dependent acetoin dehydrogenase E1 alpha-subunit 19.979 HD73_3215 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit beta 9.610 HD73_3216 Dihydrolipoyllysine-residue acetyltransferase component of acetoin...”
VP0622 alanine/glycine:cation symporter family protein from Vibrio parahaemolyticus RIMD 2210633
51% identity, 86% coverage
A0QRB1 Amino acid carrier protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_1052 amino acid carrier protein from Mycobacterium smegmatis str. MC2 155
MSMEG_2332 amino acid carrier protein from Mycobacterium smegmatis str. MC2 155
MSMEG_1052, MSMEG_2332 alanine/glycine:cation symporter family protein from Mycolicibacterium smegmatis MC2 155
49% identity, 84% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...translocase subunit SecA 1 0.07 0.06 0.04 0.05 A0QXF3 MSMEG_3280, MSMEI_3196 Polyamine-binding lipoprotein 0.06 0.03 A0QRB1 MSMEG_1052, MSMEG_2332 Amino acid carrier protein 0.13 0.13 0.1 0.07 A0QYK4 MSMEG_3689, MSMEI_3602 Sodium:solute symporter 0.05 0.03 0.1 0.03 A0R261 MSMEG_4999, MSMEI_4871 Bacterial extracellular solute-binding protein, family protein 5 0.05...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...subunit SecA 1 0.07 0.06 0.04 0.05 A0QXF3 MSMEG_3280, MSMEI_3196 Polyamine-binding lipoprotein 0.06 0.03 A0QRB1 MSMEG_1052, MSMEG_2332 Amino acid carrier protein 0.13 0.13 0.1 0.07 A0QYK4 MSMEG_3689, MSMEI_3602 Sodium:solute symporter 0.05 0.03 0.1 0.03 A0R261 MSMEG_4999, MSMEI_4871 Bacterial extracellular solute-binding protein, family protein 5 0.05 0.03...”
- Nitrogen starvation-induced transcriptome alterations and influence of transcription regulator mutants in Mycobacterium smegmatis
Jeßberger, BMC research notes 2013 - “...example the nirBD gene cluster ( msmeg_0427-0428 ) coding for nitrite reductase subunits, msmeg_0781 , msmeg_1052 , msmeg_2184 and msmeg_6735 , encoding different putative permeases and transporter subunits involved in amino acid uptake, msmeg_1293 , msmeg_2748 , msmeg_4011 , msmeg_5730 and msmeg_6660 , encoding proteins putatively...”
- “...10.75 Permease, cytosine-purines, uracil, thiamine, allantoin family msmeg_6817 11.34 RNA polymerase sigma factor, sigma-70 family msmeg_1052 11.63 Amino acid carrier protein msmeg_6259 11.67 Ammonium transporter ( amt1 ) msmeg_6881 11.75 Transcriptional regulator, GntR family msmeg_2185 12.81 Conserved hypothetical protein msmeg_2525 14.19 Amino acid permease superfamily msmeg_1293...”
- Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis
Roxas, International journal of clinical and experimental medicine 2009 (secret) - Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...SecA 1 0.07 0.06 0.04 0.05 A0QXF3 MSMEG_3280, MSMEI_3196 Polyamine-binding lipoprotein 0.06 0.03 A0QRB1 MSMEG_1052, MSMEG_2332 Amino acid carrier protein 0.13 0.13 0.1 0.07 A0QYK4 MSMEG_3689, MSMEI_3602 Sodium:solute symporter 0.05 0.03 0.1 0.03 A0R261 MSMEG_4999, MSMEI_4871 Bacterial extracellular solute-binding protein, family protein 5 0.05 0.03 A0QWJ3...”
WP_047131695 alanine/glycine:cation symporter family protein from Staphylococcus condimenti
48% identity, 80% coverage
SXYL_01919 alanine/glycine:cation symporter family protein from Staphylococcus xylosus
47% identity, 84% coverage
VIBR0546_18581 alanine/glycine:cation symporter family protein from Vibrio brasiliensis LMG 20546
50% identity, 87% coverage
- Effects of NaCl Concentration on the Behavior of Vibrio brasiliensis and Transcriptome Analysis
Hu, Foods (Basel, Switzerland) 2022 - “...1.984 4.35 10 11 down VIBR0546_05877 OmpA family protein 0.293 1.772 1.04 10 10 down VIBR0546_18581 sodium/alanine symporter 0.383 1.385 8.86 10 9 down VIBR0546_13282 outer membrane protein 0.396 1.338 1.58 10 6 down VIBR0546_03420 putative outer membrane protein 0.370 1.434 2.10 10 5 down VIBR0546_02985...”
- “...3.32 10 37 down VIBR0546_00505 putative anti-sigma regulatory factor 0.030 5.066 5.08 10 36 down VIBR0546_18581 sodium/alanine symporter 0.171 2.552 1.12 10 19 down VIBR0546_09929 universal stress protein family 8 0.160 2.647 3.93 10 19 down VIBR0546_00270 universal stress protein UspE 0.221 2.179 3.5 10 15...”
VC0784 sodium/alanine symporter from Vibrio cholerae O1 biovar eltor str. N16961
50% identity, 86% coverage
SA0871 hypothetical protein from Staphylococcus aureus subsp. aureus N315
47% identity, 88% coverage
NWMN_0883 Na+/alanine symporter family protein from Staphylococcus aureus subsp. aureus str. Newman
47% identity, 82% coverage
SAUSA300_0914 sodium:alanine symporter family protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL1018 sodium:alanine symporter family protein from Staphylococcus aureus subsp. aureus COL
47% identity, 85% coverage
- Identification of the main glutamine and glutamate transporters in Staphylococcus aureus and their impact on c-di-AMP production
Zeden, Molecular microbiology 2020 - “...YrbD (evalue: e117) and YflA (evalue: 2e72). Also in S. aureus, a second AlsT homologue, SAUSA300_0914 (evalue 9e108), could be identified (Figure S2 ), which is encoded at a different chromosomal region. AlsT is annotated in B. subtilis as a potential glutamine sodium symporter (Zhu &...”
- “...all strains were grown and processed at the same time 2.3 Investigating the contribution of SAUSA300_0914 and GlnQ to glutamine and glutamate transport in S. aureus S. aureus SAUSA300_0914 codes for a predicted amino acid symporter, which shows 41% identity to the S. aureus AlsT protein....”
- Differential gene expression in Staphylococcus aureus exposed to Orange II and Sudan III azo dyes
Pan, Journal of industrial microbiology & biotechnology 2015 - “...SAUSA300_0846 (argG) SAUSA300_1808 SAUSA300_0914 GTGGCGCAGCATAAGGAT GGGCATGGAGTCGTGAAG GTGGCGCAGCATAAGGAT ACTGCGATGTATGCACAAGC CAGTGCAACAAACGCCTTAAT...”
- “...SAUSA300_1231 SAUSA300_0864 SAUSA300_2538 SAUSA300_1808 SAUSA300_1916 SAUSA300_0914 SAUSA300_2006 ilvD EG Amino acid permease family protein Amino acid...”
- Identification of Staphylococcus aureus Cellular Pathways Affected by the Stilbenoid Lead Drug SK-03-92 Using a Microarray
Schwan, Antibiotics (Basel, Switzerland) 2017 - “...2.6 ascorbate-specific PTS system subunit IIC ( ulaA ) SACOL0454 2.3 sodium:dicarboxylate symporter family protein SACOL1018 2.3 sodium:alanine symporter family protein SACOL1872 3.0 epidermin immunity protein F ( epiE ) SACOL2146 2.7 PTS system, mannitol-specific IIBC components ( mtlA ) SACOL2333 2.8 YnfA family protein SACOL2573...”
- In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
Sadaka, PloS one 2014 - “...Oligopeptide ABC transporter ATP-binding protein 7.9 (1.2) SACOL0995 Oligopeptide ABC transporter oligopeptide-binding protein 8.3 (1.2) SACOL1018 Sodium:alanine symporter family protein 21.9 (1.2) 9.9 (3.4) 15.7 (1.7) ig_SACOL1018-9 Intergenic region betweenSACOL1018 and SACOL1019 12.3 (1.7) 21.9 (3.7) SACOL1019 Hypothetical protein 6.1 (1.1) SACOL1033 Hypothetical protein 8.9 (1.5)...”
- Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung
Chaffin, PloS one 2012 - “...fold upregulated in fresh LB compared to stationary phase cells. Significantly increased in vivo were SACOL1018, a sodium:alanine symporter, and SACOL2619 and SACOL0630, two cation/H + :amino acid symporters of unknown specificity. Several operons coding for branched-chain amino acid (BCAA) transport and responsible for transport of...”
SAFDA_0883 alanine/glycine:cation symporter family protein from Staphylococcus aureus
47% identity, 85% coverage
SAOUHSC_00949 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
47% identity, 85% coverage
- Clemastine Inhibits the Biofilm and Hemolytic of Staphylococcus aureus through the GdpP Protein
Shang, Microbiology spectrum 2022 - “...0.48 Uncharacterized protein SAOUHSC_00618 2.55 Uncharacterized protein SAOUHSC_00660 0.27 Uncharacterized protein SAOUHSC_00890 3.78 Uncharacterized protein SAOUHSC_00949 0.50 Uncharacterized protein SAOUHSC_01073 2.19 Uncharacterized protein SAOUHSC_01130 2.93 Uncharacterized protein SAOUHSC_01761 3.86 Uncharacterized protein SAOUHSC_01872 0.28 Uncharacterized protein SAOUHSC_02376 2.13 Uncharacterized protein SAOUHSC_02604 0.46 Uncharacterized protein SAOUHSC_02755 0.38 Uncharacterized...”
GBAA5301 sodium/alanine symporter family protein from Bacillus anthracis str. 'Ames Ancestor'
GBAA_5301 alanine/glycine:cation symporter family protein from Bacillus anthracis str. 'Ames Ancestor'
41% identity, 92% coverage
- Global gene expression by Bacillus anthracis during growth in mammalian blood
Carlson, Pathogens and disease 2015 - “...Top 25 induced genes. GBAA # GBAA0802 GBAA5301 GBAA0831 GBAA4879 GBAA4376 GBAA4375 GBAA4880 GBAA4374 GBAA4355 GBAA4354 GBAA4662 GBAA3451 GBAA4352 GBAA4790...”
- AtxA-Controlled Small RNAs of Bacillus anthracis Virulence Plasmid pXO1 Regulate Gene Expression in trans
Corsi, Frontiers in microbiology 2020 - “...CCUCu UUUCUACCG-AUagCGa 92 72 GBAA_4468 GGAG-GGAGAUGGC aUG gaGC 14 +7 13.21 0.003 uAUACCUCUUUUCUaCCg 96 79 GBAA_5301 uUAUGGAGAAAAGGaGG 27 11 14.83 0.001 aUACCUCUUUucUACc 95 80 GBAA_0656 gGUGGAGAAGuu AUG a 12 +4 11.58 0.01 Seed region # 3 aUUCCCUCAAUcAAUAUu 177 160 GBAA_3451 aGGGGGAGUUA-UUAU Au 15 +2 14.81 0.001...”
- “...that XrrA may block the RBS of hutU to inhibit translation. The remaining two transcripts, GBAA_5301 and asnO2 , are predicted to base-pair with XrrA further upstream in their respective 5UTRs. Such interactions could affect secondary structure and stability of the transcripts, resulting in changes to...”
BCE_5200 sodium/alanine symporter family protein from Bacillus cereus ATCC 10987
39% identity, 90% coverage
VC2356 sodium/alanine symporter from Vibrio cholerae O1 biovar eltor str. N16961
41% identity, 91% coverage
U876_05745 alanine/glycine:cation symporter family protein from Aeromonas hydrophila NJ-35
42% identity, 88% coverage
GLNT_BACSU / O31464 Probable sodium/glutamine symporter GlnT from Bacillus subtilis (strain 168) (see paper)
U712_01235 alanine/glycine:cation symporter family protein from Bacillus subtilis PY79
BSU02420 glutamine transporter from Bacillus subtilis subsp. subtilis str. 168
40% identity, 93% coverage
NGO1787 putative amino-acid transport protein from Neisseria gonorrhoeae FA 1090
40% identity, 88% coverage
NMA0073 putative amino-acid transport protein from Neisseria meningitidis Z2491
40% identity, 88% coverage
HMPREF0389_01064 alanine/glycine:cation symporter family protein from Filifactor alocis ATCC 35896
38% identity, 91% coverage
- Proteome variation among Filifactor alocis strains
Aruni, Proteomics 2012 - “...55/54.8 41/0.29 4 3.927 C 0.964 M M20 peptidase D domain 0.41 Nonsecretory protein 14. HMPREF0389_01064 Amino acid carrier protein 50.8/50.2 125/0.09 18 4.789 M Nine TMMH domainsSodium: alanine symporter family domain 0.98 Nonsecretory protein 15. HMPREF0389_01173 Dehydrogenase/methenyl tetrahydrofolate cyclohydrolase Bifunctional protein GlmU 49/49.5 42/0.10 9...”
PMI1601 sodium:alanine symporter from Proteus mirabilis HI4320
39% identity, 85% coverage
GYO_2182 alanine/glycine:cation symporter family protein from Bacillus spizizenii TU-B-10
38% identity, 93% coverage
- Disparate Effects of Two Clerodane Diterpenes of Giant Goldenrod (Solidago gigantea Ait.) on Bacillus spizizenii
Bozsó, International journal of molecular sciences 2024 - “...down-regulated transporters are amino acid transporters such as glutamate and aspartate (GYO_1320, gltT ), glutamine (GYO_2182, alsT ), lysine (GYO_3644, yvsH ), serine/threonine (GYO_1603, stet ) and isoleucine and valine (GYO_3206, braB ). On the one hand, a decrease in the availability of these amino acids...”
PP0496 sodium/alanine symporter from Pseudomonas putida KT2440
38% identity, 85% coverage
SE1038 amino acid carrier protein from Staphylococcus epidermidis ATCC 12228
36% identity, 86% coverage
- The evolution of resistance to synergistic multi-drug combinations is more complex than evolving resistance to each individual drug component
Lozano-Huntelman, Evolutionary applications 2023 - “...SE1292 PIP: 1, 38 Missense 429 181G>A Asp61Asn PIP: 1, 38 Missense 545 65T>C Val22Ala SE1038 PIP: 35, 8 Frameshift/Del 272012 451delC Leu151fs PIP: 67 Missense 272162 302G>A Gly101Asp Doxycycline SE0623 DOX: 25, 8 Missense 326421 104G>A Gly35Asp YbeC DOX: 25, 8 Missense 107568 603G>C Met201Ile...”
- “..., Figure S1 G). Here, we detected conserved frameshift deletion and missense mutations in the SE1038 gene, encoding the putative amino acid transporter (Table 4 ). Similar Asp61Asn and Val22Ala missense mutations from the IS200 transposase family member encoding SE1292 gene were also detected here. TABLE...”
TC 2.A.25.1.5 / Q45068 Amino-acid carrier protein, AlsT from Bacillus subtilis (strain 168) (see 4 papers)
37% identity, 93% coverage
PLES_13941 putative amino acid permease from Pseudomonas aeruginosa LESB58
PA3641 probable amino acid permease from Pseudomonas aeruginosa PAO1
37% identity, 92% coverage
- Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Moore, Microbial genomics 2021 - “...included genes encoding the regulatory protein NosR, a predicted two-component regulatory protein (PLES_28161), transport proteins (PLES_13941 and PLES_44581), a ring cleavage dioxygenase (PLES_44361), a putative hydroxylase (PLES_48951) and DNA gyrase ( gyrB ). loss-of-function mutations in genes encoding two other regulatory proteins (FleR and GltR) were...”
- 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 - “...HasR precursor 3 6 1.04 0.71 1.39 0.02 3.69 0.00 Down 3.04 0.00 Higher WP_003092370.1 PA3641 - Probable amino acid permease 4 19 1.12 0.02 1.07 0.11 1.80 0.00 Up 1.44 0.00 WP_003092547.1 PA3709 - Probable major facilitator superfamily (MFS) transporter 6 22 1.14 0.11 1.43...”
- “...- Hypothetical protein 8 13 1.00 0.98 1.29 0.00 1.80 0.00 Down 1.20 0.01 WP_003092370.1 PA3641 - Probable amino acid permease 5 25 1.04 0.26 1.40 0.00 1.51 0.00 Down 0.91 0.10 WP_031636628.1 PA3709 - Probable major facilitator s superfamily (MFS) transporter 6 19 1.10 0.01...”
- Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa
Fraser-Pitt, Frontiers in cellular and infection microbiology 2021 - “...protein PA3819 Rick_17kDa_Anti domain-containing protein NP_251263.1 chemotaxis transducer PA2573 Signal transduction NP_252331.1 amino acid permease PA3641 Sodium/alanine symporter NP_253795.1 hypothetical protein PA5108 Uncharacterised NP_249700.1 hypothetical protein PA1009 Uncharacterised NP_249342.1 indole-3-glycerol phosphate synthase PA0651 trpC Tryptophan biosynthesis/metabolism NP_253323.1 chemotaxis transducer PA4633 Signal transduction NP_253619.1 50S ribosomal protein...”
- A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa
Glanville, mSystems 2021 - “...a predicted GB transporter, and (iii) two genes encoding predicted glycine transporters ( PA2252 and PA3641 ) ( TableS1A and Fig.S4 ). Taken together, the plethora of Tn insertions identified by Met-Seq within the GB/choline uptake and catabolism genes are consistent with the literature, which has...”
- Seawater salt-trapped Pseudomonas aeruginosa survives for years and gets primed for salinity tolerance
Elabed, BMC microbiology 2019 - “...PA5530* 2.67 0.00011 Sulfate transport protein CysT 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...”
- “...all 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...”
- High-throughput detection of RNA processing in bacteria
Gill, BMC genomics 2018 - “...identified None 4 1 4,536,5414,536,848 PA4055.1 308 pant373 Not identified PA2728, mfd , chpA , PA3641 3 2 5,080,4505,080,630 PA4539.1 181 pant415 Not identified wzz 2 10 5,207,8985,208,463 PA4639.1 566 pant428 PA14sr_139 PA5156, PA2502, PA4510, aruI , PA0475, PA0558, PA1025 5 n/a 5,224,5685,224,795 PA4656.1 228 pant430...”
- Analysis of Pseudomonas aeruginosa cell envelope proteome by capture of surface-exposed proteins on activated magnetic nanoparticles
Vecchietti, PloS one 2012 - “...PA4309 Chemotactic transducer PctA 1 IM,3 + PA4431 Putative Ubiquinol-cytochrome c reductase 3 IM,3 + PA3641 Putative amino acid permease 3 IM,3 PA4423 f Putative uncharacterized protein 4 IM,3 - P,1 fimV PA3115 Motility protein FimV 1 U,3 + PA4639 f Putative uncharacterized protein 4 U,3...”
- “...hook-associated protein) were detected as NP-CbP. Instead, an interesting result was that MexE, PctA, PA4431, PA3641 and PA4423 were predicted to localize in IM, but were bound directly by NPs. This may suggest that these proteins localize in an envelope district wider than IM and extending...”
- High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
Johnson, PLoS genetics 2008 - “...phosphotransferase system transporter enzyme I ( FruI ) PA3597 PAK amino acid APC family transporter PA3641 PAK alanine/sodium symporter PA3760 PAK N-Acetyl-D-Glucosamine acphosphotransferase system transporter PA3761 PAK N-Acetyl-D-Glucosamine phosphotransferase system transporter PA3865 PAK arginine/ornithine ABC transporter periplasmic binding protein PA3889 PAK glycine ABC transporter periplasmic binding...”
WP_047131152 alanine/glycine:cation symporter family protein from Staphylococcus condimenti
36% identity, 89% coverage
HI0183 amino acid carrier protein, putative from Haemophilus influenzae Rd KW20
36% identity, 89% coverage
FN1398 Amino acid carrier protein alsT from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
35% identity, 90% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...FN1136, FN1166, FN1167, FN1187, FN1190, FN1198, FN1256, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1362, FN1363, FN1398, FN1420, FN1432, FN1480, FN1525, FN1701, FN1734, FN1735, FN1737, FN1738, FN1739, FN1740, FN1741, FN1797, FN1798, FN1801, FN1811, FN1833, FN1834, FN1858, FN1860, FN1898, FN1989, FN2008, FN2009, FN2102, FN2105, FN2106. 2 Covers FN0130,...”
- “...FN1080, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1701,FN2102. 3 Covers FN0660, FN0793, FN0800, FN0801, FN1187, FN1398, FN1432, FN1801. 4 Covers FN0192, FN0396, FN0397, FN0399, FN0400, FN0998, FN1111, FN1359, FN1362, FN1363, FN1523, FN1525. 5 Covers FN0308, FN0309, FN0310, FN0375, FN0376, FN0377. In contrast to FnSg, FnPg and...”
PA14_35460 putative sodium/alanine symporter from Pseudomonas aeruginosa UCBPP-PA14
37% identity, 85% coverage
PA2252 probable AGCS sodium/alanine/glycine symporter from Pseudomonas aeruginosa PAO1
37% identity, 85% coverage
- Distinct transcriptome and traits of freshly dispersed <i>Pseudomonas aeruginosa</i> cells
Kalia, mSphere 2024 - “...Upregulated 0.691559 PA1984 exaC Upregulated 0.803372 Upregulated 0.446629 PA2147 katE-catalase HPII Upregulated 0.960918 Upregulated 0.105907 PA2252 Probable AGCS sodium/alanine/glycine symporter Upregulated 1.003606 Upregulated 0.372598 PA2567 Hypothetical protein Upregulated 1.437009 Upregulated 1.697091 PA2624 Isocitrate dehydrogenase Upregulated 0.834501 Upregulated 0.710761 PA2638 nuoB-NADH dehydrogenase Upregulated 1.339827 Upregulated 1.053319 PA2639...”
- Structural genome variants of Pseudomonas aeruginosa clone C and PA14 strains
Klockgether, Frontiers in microbiology 2023 - “...4 C4 CF sputum (1988) 6.847 1.424 3,287,154ff. SpA SpF 12.7 kbp transposon * Symporter (PA2252) disrupted 4,698.4744,711,181 SpU SpA 12.7 kbp transposon Part of PAGI-4/RGP7 C8 CF sputum (1992) 6.896 0.228 5,401,061ff. SpL SpI IS 6100 * warA (PA4379) disrupted 5,628,2255,629,105 SpAB SpI IS 6100...”
- “...C12 CF throat swab (1989) 6.847 1.424 3,287,154ff. SpA SpF 12.7 kbp transposon * Symporter (PA2252) disrupted 4,698.4744,711,181 SpU SpA 12.7 kbp transposon Part of PAGI-4/RGP7 3.061 2,854,3542,857,225 SpK SpX 2.9 kbp of RGP26 Duplication of part of RGP26 Before 5,912,212 SpC SpC 2.9 kbp of...”
- 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 - “...superfamily (MFS) transporter 3 6 1.04 0.56 1.02 0.76 6.45 0.00 Down 1.06 0.55 WP_003089254.1 PA2252 - Probable AGCS sodium/alanine/glycine symporter 2 5 1.04 0.66 1.23 0.02 3.57 0.00 Up 2.73 0.00 Lower WP_003089429.1 PA2328 - Hypothetical protein 3 6 1.15 0.08 2.72 0.00 Down 3.33...”
- “...ribose transporter 3 14 1.10 0.19 1.10 0.22 1.81 0.00 Down 1.66 0.00 Higher WP_023464954.1 PA2252 - Probable AGCS sodium/alanine/glycine symporter 3 5 1.08 0.40 1.07 0.40 1.88 0.00 Up 0.99 0.84 WP_003116900.1 PA2431 - Hypothetical protein 2 4 1.10 0.05 1.13 0.15 2.40 0.00 Down...”
- The AhR ligand phthiocol and vitamin K analogs as Pseudomonas aeruginosa quorum sensing inhibitors
Jia, Frontiers in microbiology 2022 - “...protein 0.80 PA2526 Probable Resistance-Nodulation-Cell Division (RND) efflux transporter 0.79 PA1655 Probable glutathione S-transferase 0.79 PA2252 Probable AGCS sodium/alanine/glycine symporter 0.78 pilO Type IV pilus inner membrane component PilO 0.77 phnA Anthranilate synthase component 1, pyocyanin specific 0.76 PA1654 Probable aminotransferase 0.76 wspC Probable biofilm formation...”
- Utilization of L-glutamate as a preferred or sole nutrient in Pseudomonas aeruginosa PAO1 depends on genes encoding for the enhancer-binding protein AauR, the sigma factor RpoN and the transporter complex AatJQMP
Lundgren, BMC microbiology 2021 - “...L-asparagine was shown to induce expression of two transporter-gene lacZ fusions, PA5530 - lacZ and PA2252 - lacZ [ 29 ]. The PA2252 gene encodes for a putative sodium-amino acid symporter and potentially forms an operon with the ansA gene, encoding for a cytoplasmic glutaminase-asparaginase. The...”
- “...positively regulated by both RpoN and L-asparagine [ 13 , 29 ]. In contrast, the PA2252 - ansA genes, which have also been associated with L-asparagine utilization [ 29 ], are neither predicted nor experimentally-proven targets of RpoN regulation in P. aeruginosa . The growth deficiencies...”
- The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa
Kotecka, International journal of molecular sciences 2021 - “...showed increased expression relatively to WT cells, while the two other tested genes PA1270 and PA2252 exhibited the decreased expression ( Figure 5 C). Importantly, for all tested genes, the opposite effect of change of their expression than those observed under conditions of PA3458 excess tested...”
- A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa
Glanville, mSystems 2021 - “...which encodes a predicted GB transporter, and (iii) two genes encoding predicted glycine transporters ( PA2252 and PA3641 ) ( TableS1A and Fig.S4 ). Taken together, the plethora of Tn insertions identified by Met-Seq within the GB/choline uptake and catabolism genes are consistent with the literature,...”
- Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
Thöming, NPJ biofilms and microbiomes 2020 - “...PA2385 pvdQ 3.3 PA14_68430 PA5180 fdhD 2.9 PA14_35430 PA2254 pvcA 2.7 PA14_68440 PA5181 2.5 PA14_35460 PA2252 2.9 PA2958.1 PA2958.1 rgsA 3.7 PA14_35980 2.9 PA3964-PA3965 PA3964-PA3965 P24 3.6 PA14_37380 PA2097 2.4 PA4704.1 PA4704.1 prrF1 3.3 PA14_38210 PA2034 2.6 PA4704.2 PA4704.2 prrF2 2.8 PA14_38220 PA2033 2.6 PA4704-PA4705 PA4704-PA4705...”
- More
SACOL1392 sodium:alanine symporter family protein from Staphylococcus aureus subsp. aureus COL
38% identity, 85% coverage
- Transcriptomic and Metabolomic Analysis of a Fusidic Acid-Selected fusA Mutant of Staphylococcus aureus
Gupta, Antibiotics (Basel, Switzerland) 2022 - “...encoding amino acid permeases and uptake systems ( aapA , brnQ3 , gltT , SACOL1367, SACOL1392, SAR1419, SAS2274, and SAV1380) and oligopeptide transporters (SAV0727, SAV1380, and SAV1381) were upregulated in SH10001st-2, 8 other genes in this category (SACOL1476, SACOL2453, SAR2503, SAV0722, SAS0283, SAV2412, opuCA , and...”
- Investigating the genetic regulation of the ECF sigma factor σS in Staphylococcus aureus
Burda, BMC microbiology 2014 - “...NE1292 Na+/H+antiporter, MnhE component, putative 2 1 SACOL1319 NE1580 Glycerol uptake facilitator protein 5 1 SACOL1392 NE142 Sodium:alanine symporter family protein 3 1 SACOL1414 NE1609 Peptide ABC transporter, ATP-binding protein 4 1 Amino acid biosynthesis SACOL0168 NE595 Glutamate N-acetyltransferase/amino-acid acetyltransferase argJ 2 1 SACOL1349 NE809 Threonine...”
SATW20_13570 alanine/glycine:cation symporter family protein from Staphylococcus aureus subsp. aureus TW20
SAV1356 amino acid carrier protein from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_01354 sodium:alanine symporter family protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1252 amino acid carrier protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1269 sodium:alanine symporter family protein from Staphylococcus aureus subsp. aureus str. Newman
38% identity, 86% coverage
- Mutations upstream of fabI in triclosan resistant Staphylococcus aureus strains are associated with elevated fabI gene expression
Grandgirard, BMC genomics 2015 - “...4.7 3.9 SAV0944 / SATW20_09440 / thioesterase superfamily protein 3.6 2.6 8.9 2.0 SAV1356 / SATW20_13570 / sodium:alanine symporter family protein 2.1 2.3 2.9 4.3 SAV1573 / SATW20_15690 / putative exported protein 3.0 2.2 4.6 5.5 SAV1853 / SATW20_18470 / putative membrane protein 2.7 2.5 3.0...”
- Mutations upstream of fabI in triclosan resistant Staphylococcus aureus strains are associated with elevated fabI gene expression
Grandgirard, BMC genomics 2015 - “...2.5 2.6 4.7 3.9 SAV0944 / SATW20_09440 / thioesterase superfamily protein 3.6 2.6 8.9 2.0 SAV1356 / SATW20_13570 / sodium:alanine symporter family protein 2.1 2.3 2.9 4.3 SAV1573 / SATW20_15690 / putative exported protein 3.0 2.2 4.6 5.5 SAV1853 / SATW20_18470 / putative membrane protein 2.7...”
- Genome-wide screen for genes involved in eDNA release during biofilm formation by Staphylococcus aureus
DeFrancesco, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...Locus tag Gene Product Log2-FC SAOUHSC_01354 SAOUHSC_01028 SAOUHSC_01029 SAOUHSC_00420 SAOUHSC_00880 SAOUHSC_02699 SAOUHSC_00670 SAOUHSC_03037 SAOUHSC_00636...”
- Identification of the main glutamine and glutamate transporters in Staphylococcus aureus and their impact on c-di-AMP production
Zeden, Molecular microbiology 2020 - “...main glycine betaine transporter OpuD (SAUSA300_1245) as well as the predicted amino acid transporter AlsT (SAUSA300_1252) allows an S. aureus dacA mutant to grow in rich medium in the absence of cdiAMP (Zeden et al., 2018 ). In several other Firmicutes, including B. subtilis, Lactococcus lactis,...”
- “...opuD ( SAUSA300_1245 ) coding for the main glycine betaine osmolyte transporter and alsT ( SAUSA300_1252 ) coding for a predicted amino acid sodium symporter, rescue the growth defect observed for the cdiAMP negative S. aureus strain LAC* dacA::kan in the rich medium TSB (Zeden et...”
- Cyclic di-adenosine monophosphate (c-di-AMP) is required for osmotic regulation in Staphylococcus aureus but dispensable for viability in anaerobic conditions
Zeden, The Journal of biological chemistry 2018 - “...1 ). More specifically, mutations were identified in opuD ( SAUSA300_1245 ) and alsT ( SAUSA300_1252 ) coding for the predicted glycinebetaine transporter OpuD and the predicted alanineproton symporter AlsT, respectively ( Fig. 3 B ). In addition, several strains contained mutations in hepS ( SAUSA300_1359...”
- Novel Pathways for Ameliorating the Fitness Cost of Gentamicin Resistant Small Colony Variants
Vestergaard, Frontiers in microbiology 2016 - “...): JE2 hemB ::N (NE1845), JE2 menD ::N (NE1345), JE2 rpoF ::N (NE1109) and JE2 SAUSA300_1252 ::N (NE142). Strains were grown in TSB at 37C with shaking at 200 rpm or on TSA agar plates with or without addition of gentamicin (Sigma). Minimal inhibitory concentrations (MICs)...”
- “...g/ml) (Sigma) or hemin (1 g/ml) (Sigma). Construction of MV118 rpoF ::N (MV216) and MV118 SAUSA300_1252 ::N (MV218) mutants was performed by transduction with bacteriophage 11, selecting for transductants on erythromycin plates (5 g/ml) ( Fey et al., 2013 ). Table 1 Strains used in this...”
- 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_0435 rplL SAUSA300_0437 SAUSA300_2321 SAUSA300_1252 SAUSA300_0215 SAUSA300_0798 SAUSA300_1675 SAUSA300_0436 SAUSA300_2565 SAUSA300_0354 SAUSA300_0848...”
- “...SAUSA300_1936 SAUSA300_1935 SAUSA300_1934 SAUSA300_1395 SAUSA300_1252 SAUSA300_1052 SAUSA300_1029 SAUSA300_0987 SAUSA300_0986 SAUSA300_0883 SAUSA300_0798...”
- Conditions and mutations affecting Staphylococcus aureus L-form formation
Han, Microbiology (Reading, England) 2015 (PubMed)- “...glpF, glpK, NWMN_0623, NWMN_0843, NWMN_0333, NWMN_0872 and NWMN_1269 were preferentially expressed in L-forms as compared with normal cell-walled form (P,0.05)....”
- “...glpF mutant glpK mutant NWMN_0872 gntK mutant NWMN_1269 NWMN_0623 NWMN_0333 NWMN_0843 RN4220 Plasmids pBursa pFA545 mutant mutant mutant mutant mutant Relevant...”
- Glycerol uptake is important for L-form formation and persistence in Staphylococcus aureus
Han, PloS one 2014 - “...glpK , 1 mapped to gluconate kinase ( gntK ), NWMN_0623 , NWMN_0872 (GTP pyrophosphokinase), NWMN_1269 (sodium:alanine symporter family protein), 2 mapped to hypothetical proteins NWMN_0333 and NWMN_0843 of unknown function, 3 mapped to intergenic region. Because we found 4 mutants (3 in glpF and 1...”
BMEII0783 NA(+)-LINKED D-ALANINE GLYCINE PERMEASE from Brucella melitensis 16M
40% identity, 87% coverage
NMB1647 putative amino acid symporter from Neisseria meningitidis MC58
37% identity, 88% coverage
PM0529 unknown from Pasteurella multocida subsp. multocida str. Pm70
35% identity, 86% coverage
PBPRA1278 hypothetical amino acid carrier protein(sodium/alanine symporter) from Photobacterium profundum SS9
34% identity, 90% coverage
CJJ81176_0912 amino acid carrier protein from Campylobacter jejuni subsp. jejuni 81-176
35% identity, 86% coverage
Cj0903c putative amino-acid transport protein from Campylobacter jejuni subsp. jejuni NCTC 11168
CJSA_0849 alanine/glycine:cation symporter family protein from Campylobacter jejuni subsp. jejuni IA3902
36% identity, 85% coverage
- Proteomics of Campylobacter jejuni Growth in Deoxycholate Reveals Cj0025c as a Cystine Transport Protein Required for Wild-type Human Infection Phenotypes
Man, Molecular & cellular proteomics : MCP 2020 - “...measure citrate (Cj0203 [2.35-fold/2.40-fold]). Increased intracellular levels of alanine (Ala, hypothesized to be transported by Cj0903c [1.97-fold/1.49-fold]), Glu (associated with the Peb cluster Cj0920c-Cj0922c [Cj0920c, 1.70-fold/2.18-fold; Cj0921c, down-regulated at 0.34-fold/0.13-fold; and Cj0922c, no change in abundance), Asn and Gln were detected, whereas carbon sources with unknown...”
- The Anti-Campylobacter Activity and Mechanisms of Pinocembrin Action
Klančnik, Microorganisms 2019 - “...], the Cj0073c gene, which is important for NAD-independent respiratory lactate dehydrogenase activity, and the Cj0903c gene, which is a gene for putative amino-acid transporters with homology to members of the sodium:alanine symporter family with unknown substrate specificity [ 45 ]. The down-regulation of ribosomal proteins...”
- Proteomics Reveals Multiple Phenotypes Associated with N-linked Glycosylation in Campylobacter jejuni
Cain, Molecular & cellular proteomics : MCP 2019 (secret) - Characterization of antimicrobial resistance patterns and detection of virulence genes in Campylobacter isolates in Italy
Di, Sensors (Basel, Switzerland) 2014 - “...acetyltransferase [ 45 ] docB Probable methyl;accepting chemotaxis domain singal transduction protein [ 45 ] Cj0903c Probable amino acid transport protein [ 45 ] Cj0618c Unknown identity [ 45 ] Cj0454c Probable membrane protein [ 45 ] Cj0456c Unknown identity [ 45 ] aas Probable 2-acylglycerophosphoethanolamine...”
- Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
Hofreuter, Frontiers in cellular and infection microbiology 2014 - “...amino acid transporters are present within the sequenced genomes of C. jejuni . For example, Cj0903c with homology to members of the sodium:alanine symporter family and SstT (Cj1097), the putative sodium/serine-threonine symporter, are conserved in C. jejuni and future studies are needed to elucidate their substrate...”
- “...experiments with a C. jejuni transposon mutant library that identified the putative amino acid transporter Cj0903c and the periplasmic binding protein LivJ of the LIV branched-chain amino acid ABC transporter as colonization factors of C. jejuni (Hendrixson and DiRita, 2004 ). Additionally, inactivation of the periplasmic...”
- Colonization factors of Campylobacter jejuni in the chicken gut
Hermans, Veterinary research 2011 - “...operon fdhABCD operon oorDABC (12) nuo genes nrfA napAGHBLD operon ccoNOQP operon sdaA cj0415 livJ cj0903c peb1A ggt fumarate reductase aspartate ammonia-lyase hydrogenase formate dehydrogenase 2-oxoglutarate:acceptor oxidoreductase NADH:ubiquinone oxidoreductase (complex I) nitrite reductase nitrate reductase cbb 3 -type cytochrome c oxidoreductase L-serine dehydratase putative oxidoreductase subunit...”
- “...one of two genes probably involved in amino acid transportation in C. jejuni, livJ and cj0903c , resulted in a marked colonization defect in chicks [ 32 ]. Due to an observed reduction in adhesion to and invasion in cultured epithelial cells the PEB1a protein has...”
- Identification of Campylobacter jejuni genes contributing to acid adaptation by transcriptional profiling and genome-wide mutagenesis
Reid, Applied and environmental microbiology 2008 - “...genes encoding putative amino acid transport proteins (Cj0903c and Cj0934c). The gene encoding the -ketoglutarate permease (kgtP), which imports a tricarboxylic...”
- In vitro transposition system for efficient generation of random mutants of Campylobacter jejuni
Colegio, Journal of bacteriology 2001 - “...R2 R3 21,949 1,032,893 842,931 CjaE Intergenic region Cj0903c Putative membrane protein R4 R5 R6 5,188 1,489,676 1,043,086 Intergenic region Cj1555c Cj1109...”
- Direct interaction of small non-coding RNAs CjNC140 and CjNC110 optimizes expression of key pathogenic phenotypes of Campylobacter jejuni
Ruddell, mBio 2023 - “...glnA CJSA_1180 CJSA_0396 CJSA_0397 CJSA_0395 gltB CJSA_0165 CJSA_0930 CJSA_0040 CJSA_0037 trxB flgI flgH CJSA_1562 CJSA_0008 CJSA_0849 CJSA_0195 flgD CJSA_1387 CJSA_0041 flgL flgB flgG2 flgE flgE2 flgG CJSA_1388 CJSA_1131 CJSA_0521 pseB CJSA_0969 CJSA_0352 CJSA_1374 CJSA_0929 CJSA_0818 gltD CJSA_pVir0041 CJSA_1328 CJSA_0389 acs cmeA CJSA_1456 CJSA_0412 peb3 modA CJSA_0392...”
NMA1901 putative sodium:alanine symporter from Neisseria meningitidis Z2491
36% identity, 88% coverage
NGO1290 putative amino-acid transporter, sodium/alanine symporter from Neisseria gonorrhoeae FA 1090
36% identity, 88% coverage
- Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
McClure, mSystems 2020 - “...have high betweenness values. Instead, high betweenness genes included NGO1132, a phage-associated gene, two transporters, NGO1290 and NGO0446, a number of ribosomal protein genes, NGO1834 ( rpsS ), NGO1835 ( rplB ), and NGO1838 ( rplC ), and several hypothetical proteins. These hypothetical proteins include NGO0672,...”
- Fur-mediated activation of gene transcription in the human pathogen Neisseria gonorrhoeae
Yu, Journal of bacteriology 2012 - “...the iron-upregulated genes we examined, NGO0376, NGO0432, NGO1290, NGO1789, and NGO1957 showed increased transcription in the fur mutant strain (Fur-repressed...”
- “...NGO1205 NGO1207-NGO1209 NGO1275 NGO1276 NGO1282 NGO1290 NGO1317 NGO1430 NGO1685 NGO1751-NGO1747 NGO1788 NGO1789 NGO1842-NGO1841 NGO1850 NGO1851 NGO1859...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...-5.6 -9.1 ABC-type sulfate transporter, ATP-binding protein Lrp sbp NGO0877 -4.8 -25.0 ABC-related sulfate-binding protein NGO1290 -3.8 -3.3 Putative sodium/alanine symport protein hemO NGO1318 -7.1 -12.5 Heme oxygenase/iron starvation protein Fur lldP NGO1361 -9.1 -8.3 L-lactate permease (partial only) exbD NGO1377 -3.4 -3.6 Membrane bound biopolymer...”
SXYL_01528 alanine/glycine:cation symporter family protein from Staphylococcus xylosus
34% identity, 90% coverage
DV527_RS07535 alanine/glycine:cation symporter family protein from Staphylococcus saprophyticus
36% identity, 90% coverage
A1S_2793 putative amino-acid transport protein from Acinetobacter baumannii ATCC 17978
37% identity, 93% coverage
AbA118F_2024 alanine/glycine:cation symporter family protein from Acinetobacter baumannii
ABAYE0689 putative amino-acid transport protein from Acinetobacter baumannii AYE
37% identity, 84% coverage
TDE1259 amino acid carrier family protein from Treponema denticola ATCC 35405
37% identity, 87% coverage
- Investigation of the potential regulator proteins associated with the expression of major surface protein and dentilisin in Treponema denticola
Arai, Journal of oral microbiology 2020 - “...Type I restriction-modification system, S subunit 2.08 TDE1817 Hypothetical protein 2.07 TDE0439 Hypothetical protein 2.06 TDE1259 Amino acid carrier 2.04 TDE0175 Pyrrolidone-carboxylate peptidase 2.03 TDE0443 Hypothetical protein 2.03 TDE0132 Hypothetical protein 2.01 TDE1640 3-Dehydroquinate dehydratase 2.00 The expression of the genes was 2-fold lower than that...”
- Porphyromonas gingivalis and Treponema denticola exhibit metabolic symbioses
Tan, PLoS pathogens 2014 - “...sample. Primers for the validation gene set TDE1624 , TDE1625 , TDE1626 , TDE1627 , TDE1259 , TDE2119 , TDE2120 , TDE0405 , TDE0762 , TDE1669 , TDE0387 , TDE0627 and TDE0832 were designed using Primer3 [39] ( Table S1 ). Scanning electron microscopy Co-cultures from...”
- “...Conversion of acetyl-phosphate to acetate TDE0933 Acetate kinase 1.2 1 ND Alanine/Glycine cation symporter (AGCS) TDE1259 Na+/Alanine-glycine symporter 1.4 1 1.8 1 1 represents fold change with adjusted p <0.05. 2 Not determined. The COG category with the most differentially expressed genes was O (posttranslational modification,...”
BP951000_1860 alanine/glycine:cation symporter family protein from Brachyspira pilosicoli 95/1000
38% identity, 84% coverage
- Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity
Mappley, BMC genomics 2012 - “...(B2904_orf1811; wesB_0925) and a peptidase (B2904_orf863; wesB_1557). The glycine reductase complex locus of 95/1000 (BP951000_1852 BP951000_1860) and B. murdochii 56-150 T (Bmur_2720 Bmur_2728) [ 28 ] was identified in B2904 (B2904_orf665 B2904_orf673) and WesB (wesB_0746 wesB_0754), but with an additional ATP-binding cassette (ABC)-type glycine betaine transport...”
- The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes
Wanchanthuek, PloS one 2010 - “..., BP951000_1857 and BP951000_1858), and two copies for a sodiumalanine symporter family protein (BP951000_1859 and BP951000_1860). In B.murdochii , the locus consisted of genes encoding putative glycine reductase complex component ( grdX , 4083292.C42.orf00552) thioredoxin reductase ( trxB , 4083292.C42.orf00553), glycine/sarcosine/betaine reductase component B alpha/beta subunit...”
cg0254 amino acid carrier protein (sodium/alanine symporter) from Corynebacterium glutamicum ATCC 13032
36% identity, 85% coverage
FN0328 Na(+)-linked D-alanine glycine permease from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
37% identity, 84% coverage
TP0998 sodium/proton-dependent alanine transporter from Treponema pallidum subsp. pallidum str. Nichols
34% identity, 81% coverage
- Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen
Radolf, Nature reviews. Microbiology 2016 - “...are putative symporters for aspartate and glutamate (TP0555 and TP0934), alanine and glycine (TP0414 and TP0998) and branched chain amino acids (TP0265). In addition, TP0144 functions as the SBP for a thiamine ABC transporter (TbpAPQ(TP0142-0144)) 95 . BioMNY (TP0226-0228), a putative biotin importer, seems to be...”
- Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons
Häse, Microbiology and molecular biology reviews : MMBR 2001 - “...predicted the Na/ alanine symporters TP0414 and TP0998, the Na/branchedchain amino acid symporter TP0265, the Na/phosphate symporter TP0771, and the Ca2/Na...”
STM0006 putative AGCS family, alanine/glycine transport protein from Salmonella typhimurium LT2
33% identity, 86% coverage
t0006 putative amino-acid transport protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
33% identity, 86% coverage
BP951000_1859 alanine/glycine:cation symporter family protein from Brachyspira pilosicoli 95/1000
37% identity, 87% coverage
AGCS_METMP / Q6LX42 Sodium/alanine symporter AgcS; Alanine permease; Alanine/glycine:cation symporter from Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL) (see 2 papers)
TC 2.A.25.1.3 / Q6LX42 Alanine:Na+ symporter, AgcS from Methanococcus maripaludis (see paper)
MMP1511 Sodium:alanine symporter from Methanococcus maripaludis S2
36% identity, 89% coverage
- function: Catalyzes the sodium-dependent uptake of extracellular D- alanine and L-alanine (PubMed:15659675, PubMed:30659158). Can also transport glycine (PubMed:30659158). Binds glycine and both enantiomers of alanine, while strictly excluding other amino acids (PubMed:30659158).
catalytic activity: D-alanine(in) + Na(+)(in) = D-alanine(out) + Na(+)(out) (RHEA:71447)
catalytic activity: L-alanine(in) + Na(+)(in) = L-alanine(out) + Na(+)(out) (RHEA:29283)
catalytic activity: glycine(in) + Na(+)(in) = glycine(out) + Na(+)(out) (RHEA:68228)
disruption phenotype: No growth on L- or D-alanine. - substrates: Alanine, Na+
- They all rock: A systematic comparison of conformational movements in LeuT-fold transporters.
Licht, bioRxiv : the preprint server for biology 2024 - “...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 5OQT (A) I op alanine X-ray 2.86 C _BasC A8UCQ5...”
- Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
Paparoditis, Biochimica et biophysica acta 2014 - “...9 amino acids amino acid Q7UV95 11 2.A.25 Alanine or Glycine:Cation Symporter (AGCS) Family 2.A.25.1.3 Q6LX42 11 amino acids alanine:Na+ symporter Q7UKE2 12 2.A.27 Glutamate:Na+Symporter (ESS) Family 2.A.27.2.1 B1XKD9 11 amino acids glutamate:sodium Q7UGS6 12 2.A.33 NhaA Na+:H+Antiporter (NhaA) Family 2.A.33.1.2 Q56725 10 cations Na +...”
- Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions
Turkarslan, The ISME journal 2021 - “...G-score mutations DVU0799, DVU0597, DVU0797) and Mm (harboring dominant mutations in MMP1255, MMP1611, MMP1362, and MMP1511) clones disappeared (Fig. 3E ). At the same time a new Dv clone with mutations in DVU2394, DVU2451, DVU1862, and intergenic region IG_184033, and a new Mm clone with mutations...”
- “...dependencies that are costly [ 47 , 65 ]. One high G-score mutation in Mm (MMP1511) could reflect the evolution of a new costly dependency. Alanine was earlier shown to be exchanged between the two interacting partners during syntrophic growth, likely at a cost to the...”
- Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis
Sarmiento, Proceedings of the National Academy of Sciences of the United States of America 2013 - “...increase in the number of reads in one specific gene (MMP1511) as discussed below. from differences in the gene conversion rates as well as the growth rates of...”
- “...other insertions, the abundance of reads in the gene MMP1511, which encodes an alanine/sodium symporter, increased from 0.6% of the total reads in the T0...”
- Functional responses of methanogenic archaea to syntrophic growth
Walker, The ISME journal 2012 - “...2 ). The associated alanine transport gene, annotated as a sodium:alanine symporter ( alsT , Mmp1511), exhibited a significant downregulation at the transcript level that may have resulted from repression by the nrpR nitrogen-regulation gene ( Xia et al. , 2009 ). AlsT was not identified...”
- “...Leigh, 2008 Mm1002 ald Mmp1513 Alanine dehydrogenase deletion mutant Moore and Leigh, 2005 Mm1018 agcS Mmp1511 Sodium:alanine symporter deletion mutant Moore and Leigh, 2005 Desulfovibrio vulgaris strain Hildenborough (=ATCC 29579) NA NA Wild-type strain ATCC Abbreviations: NA, not applicable. Table 2 Expression ratios of selected genes...”
- Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis
Xia, BMC microbiology 2009 - “...molybdate transporter operons (MMP02050207 and MMP05040507), and a gene encoding a Na + -alanine symporter (MMP1511). (The Na + -alanine symporter may function in nitrogen assimilation since alanine is a nitrogen source for M. maripaludis , [ 11 ].) Data presented above suggest for all of...”
- “...[ 8 ]. Alanine transporter- lacZ fusion The promoter of the Na + -alanine symporter (MMP1511) gene was PCR-amplified from M. maripaludis S2 [ 31 ] genomic DNA using primers 5'AAACTAGTAATCAAGTATTTAAATCCGTTAC3' (forward) and 5' ACCATGCATCCACTCCAAATTTTTTTGG (reverse). Herculase (Stratagene) was used and conditions were 94C for 2...”
- Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR
Xia, Molecular & cellular proteomics : MCP 2006 - “...Transport/regulation Mmp0165 Mmp0166 Mmp0167 Mmp0168 Mmp1510 Mmp1511 Mmp1512a Mmp1513 Translation Mmp1319 Mmp1320 Mmp1321 Mmp1322 Mmp1323 Mmp1324 Mmp1325...”
- Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease
Moore, Journal of bacteriology 2005 - “...follows: hpt, Mmp0145; ald, Mmp1513; alr, Mmp1512; agcS, Mmp1511; upt, Mmp0680. Homologs were found with Blastp in NCBI-Blast2 at the European Bioinformatics...”
- Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
Hendrickson, Journal of bacteriology 2004 - “...(Mmp1513), an alanine racemase (Mmp1512), and an alanine permease (Mmp1511) account for the unusual ability of M. maripaludis to use L- and D-alanine (Moore and...”
- “...transporters (Mmp0065 and Mmp0068) and an alanine-cation symporter (Mmp1511) are encoded. M. maripaludis strains have been reported to take up a variety of...”
6cseM / Q6LX42 Crystal structure of sodium/alanine symporter agcs with l-alanine bound (see paper)
36% identity, 92% coverage
- Ligands: sodium ion; alanine (6cseM)
PH0781 alanine transport protein from Pyrococcus horikoshii OT3
31% identity, 77% coverage
PF0514 d-alanine glycine permease from Pyrococcus furiosus DSM 3638
31% identity, 74% coverage
APL_1127 predicted Na+/alanine symporter from Actinobacillus pleuropneumoniae L20
35% identity, 89% coverage
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...cysA Sulfate/thiosulfate import ATP-binding protein cysA 2.401 APL_1843 cysJ Sulfite reductase [NADPH] flavoprotein alpha-component 2.757 APL_1127 APL_1127 Predicted Na+/alanine symporter 3.402 Hypothetical/unknown/unclassified APL_1100 APL_1100 Hypothetical protein 3.395 APL_0920 APL_0920 Hypothetical protein 2.835 APL_1882 APL_1882 Hypothetical protein 2.776 APL_1856 APL_1856 Hypothetical protein 2.775 APL_1855 APL_1855 Hypothetical protein...”
APJL_1146 Na+/alanine symporter from Actinobacillus pleuropneumoniae serovar 3 str. JL03
35% identity, 85% coverage
HI0883 amino acid carrier protein, putative from Haemophilus influenzae Rd KW20
35% identity, 88% coverage
- Characterization of nontypable Haemophilus influenzae isolates recovered from adult patients with underlying chronic lung disease reveals genotypic and phenotypic traits associated with persistent infection
Garmendia, PloS one 2014 - “...Hi0888 (98) NTHI1052 (98) Phosphoribosylamine-glycine ligase 1146 G 0 0 1 T A 2 457 Hi0883 (99) NTHI1046 (99) Na+/alanine symporter 1153 A 0 0 1 E K 395 404 obgE HI0877 (95) NTHI1040 (96) GTPase 1155 G 0 1 1 G G 223 435 pepB...”
- Extensive cotransformation of natural variation into chromosomes of naturally competent Haemophilus influenzae
Mell, G3 (Bethesda, Md.) 2014 - “...43 2 LysArg 839,913 Spc R HI0778 ( rplD ) GC 65 2 GlyAla 935,046 HI0883 (unk) AC 356 3 Gly Gly 1,344,100 a Nal R HI1264 ( gyrA ) CA 88 1 AspTyr SNVs detected in MAP7 reads against the Rd reference that were also...”
- Pasteurella multocida gene expression in response to iron limitation
Paustian, Infection and immunity 2001 - “...ABC transporter Hypothetical E. coli protein Hypothetical HI0883 protein Hypothetical Hl0379 protein Unknown Putative ABC transporter, ATP-binding protein Skp,...”
- Topology prediction for helical transmembrane proteins at 86% accuracy
Rost, Protein science : a publication of the Protein Society 1996 - “...HI 1586 out 13 MLSVLSINYR HI0772 in 12 MISRVSRFMT HI0883 out 11 MTIESILSAI HI1154 in 11 MLLVNLAIFI HI0687 in 10 MNNENMVRVF HI1241 HI0359 HI0392 HI0407 HI0825...”
Z0007 inner membrane transport protein from Escherichia coli O157:H7 EDL933
33% identity, 87% coverage
- Genome mining of novel rubiginones from Streptomyces sp. CB02414 and characterization of the post-PKS modification steps in rubiginone biosynthesis
Zhang, Microbial cell factories 2021 - “...into the respective gene-deletion mutants for complementation, to generate mutant strains Z0006 (for rubN1 complementation), Z0007 (for rubN2 complementation), and Z0009 (for rubM4 complementation). The Z0004 mutant produced compounds 3 , 4 , 5 , and 6 , and the production of compounds 1 , 2...”
- “...L, and N) that have the C-4 hydroxyl group was abolished. The rubN2 complementation strain Z0007 was able to produce all the eight rubiginones. Therefore, RubN2 catalyzes the C-4 oxidation step to form a hydroxyl group with an -configuration (Fig. 6 ). Fig. 6 HPLC analysis...”
YaaJ / b0007 putative transporter YaaJ from Escherichia coli K-12 substr. MG1655 (see 4 papers)
P30143 Uncharacterized transporter YaaJ from Escherichia coli (strain K12)
b0007 predicted transporter from Escherichia coli str. K-12 substr. MG1655
33% identity, 87% coverage
NTHI1046 predicted Na+/alanine symporter from Haemophilus influenzae 86-028NP
35% identity, 88% coverage
PMI2114 sodium:alanine symporter from Proteus mirabilis HI4320
35% identity, 88% coverage
DEFDS_1601 sodium:alanine symporter from Deferribacter desulfuricans SSM1
36% identity, 86% coverage
PAP_09570 alanine/glycine:cation symporter family protein from Palaeococcus pacificus DY20341
31% identity, 88% coverage
NMB0177 putative sodium/alanine symporter from Neisseria meningitidis MC58
33% identity, 88% coverage
- The Hfq regulon of Neisseria meningitidis
Huis, FEBS open bio 2017 - “...Function b Pathway or Biological role b LCMS E c SDS/PAGE/MS d Microarray e Upregulated NMB0177 Sodium/alanine symporter Membrane components 13.1 4.0 NMB0227 Mn 2+ iron transporter Membrane components 3.3 2.4 NMB0317 queF 7cyano7deazaguanine reductase tRNA modification 4.5 4.5 NMB0325 rplU 50S ribosomal protein L21 Ribosomal...”
- Metabolism and virulence in Neisseria meningitidis
Schoen, Frontiers in cellular and infection microbiology 2014 - “...comprised aspC encoding an aromatic amino acid aminotransferase, a gene for a putative sodium/alanine symporter (NMB0177), the aspartate kinase genes lysC as well as genes involved in glycine metabolism ( gcvT , gcvH and metF ) and the glutamate dehydrogenase ( gdhA ). Of note, differences...”
- Role of Hfq in iron-dependent and -independent gene regulation in Neisseria meningitidis
Mellin, Microbiology (Reading, England) 2010 - “...Alcohol dehydrogenase 1.71 3.09 1.15 1.09 NMB1572 acnB Aconitate hydratase 2.71 2.97 1.11 1.19 Transport: NMB0177 Sodium/alanine symporter 13.07 10.65 1.14 1.14 NMB0402 putp Sodium/proline symporter 2.94 1.58 1.27 1.70 NMB2136 Peptide transporter 3.65 2.54 1.51 1.51 Unclassified: NMB0432 Putative membrane protein 5.86 4.11 1.36 1.65...”
- Transcriptome analysis of Neisseria meningitidis during infection
Dietrich, Journal of bacteriology 2003 - “...NMB0889 NMB1415/NMB0585 NMB1429 NMB1651 NMB1730 NMB1809 NMB1810 NMB0177 NMB0633 NMB0787 Serogroup B ORF no.a NMB1887 NMB1940 NMB2154 NMB2155 Translation NMB0124...”
- “...in both studies: NMB0124, NMB0129, NMB0159, NMB0167, NMB0177, NMB0328, NMB0517, NMB0617, NMB0700, NMB0787, NMB0788, NMB0880, NMB0881, NMB0977, NMB0994, NMB0995,...”
SAG1145 sodium:alanine symporter family protein from Streptococcus agalactiae 2603V/R
33% identity, 92% coverage
gbs1212 Unknown from Streptococcus agalactiae NEM316
33% identity, 92% coverage
- Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae
Rosinski-Chupin, BMC genomics 2015 - “...sequence consensus [ 44 ]. An inverse behavior was observed for the glycine riboswitch upstream gbs1212 encoding a putative alanine/glycine cation symporter. While transcription predominantly terminated at the rho-independent terminator at neutral pH, the shift to a lower pH was associated with an increased transcription of...”
- “...A. The yybP/ykoY leader located upstream gbs0560 encoding a cation-transporting P-ATPase. B. The glycine-riboswitch upstream gbs1212 encoding a putative amino acid transporter. Left panels: dRNA-seq (TAP+ and TAP- samples) and RNA-seq data from exponentially growing bacteria submitted or not to a 20min-acid stress (pH5.2) are visualized...”
NMA0091 putative amino-acid transporter from Neisseria meningitidis Z2491
33% identity, 88% coverage
NGFG_01721 alanine/glycine:cation symporter family protein from Neisseria gonorrhoeae MS11
NGO1807 putative amino-acid transporter from Neisseria gonorrhoeae FA 1090
33% identity, 88% coverage
- Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae
Steiner, mBio 2023 - “...the NgncR_162/163 target genes validated previously by real-time quantitative PCR (qRT-PCR) ( 19 ), the NGFG_01721 and NGFG_02049 genes, prpC , ack , and gltA were detected by RNA-seq ( Fig.1b ), whereas prpB , gdhR , fumC , and sucC did not meet the applied...”
- “...phosphate (NGFG_01353), as well as NGFG_01722, whose gene is cotranscribed with the putative alanine symporter NGFG_01721 gene and encodes d -alanine dehydrogenase ( dadA ). Furthermore, differential expression of lactate permease (NGFG_01471) showing a ratio slightly above the applied cutoff in RNA-seq (0.765779; q =0.0191) could...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...NGO1688 -2.6 -3.7 Putative iron uptake protein FNR yaaJ NGO1787 -3.3 -4.3 Sodium/alanine symport protein NGO1807 -2.7 -3.8 Amino-acid symport protein gltS NGO1890 -3.1 -5.0 Sodium/glutamate symport protein MtrR NGO1954 -3.6 -6.3 Di- and tri-peptide permease, PRT2 sstT NGO1957 -4.5 -11.1 Sodium/serine symport protein glnM NGO2011...”
- “...associated protein NGO1688 -3.1 3.7 Conserved hypothetical protein folA NGO1694 3.3 -2.0 Dihydrofolate reductase (FolA) NGO1807 -3.3 -3.0 Amino-acid transporter dadA NGO1808 -4.4 -2.9 D-amino acid dehydrogenase small subunit (DadA) yhhF NGO1860 3.9 2.2 Probable DNA methylase Symport protein (possible sodium/dicarboxylate NGO1957 -7.8 -2.0 symporter) NGO2023...”
SPD_0372 sodium:alanine symporter family protein from Streptococcus pneumoniae D39
spr0369 D-alanine glycine permease from Streptococcus pneumoniae R6
33% identity, 91% coverage
- Dynamic Pneumococcal Genetic Adaptations Support Bacterial Growth and Inflammation during Coinfection with Influenza
Smith, Infection and immunity 2021 - “...PurH SPD_0058 purD Phosphoribosylamine-glycine ligase SPD_0059 purE Phosphoribosylaminoimidazole carboxylase, catalytic subunit SPD_0182 Conserved hypothetical protein SPD_0372 Sodium:alanine symporter SPD_0395 efp Translation elongation factor P SPD_0723 rpiA Ribose 5-phosphate isomerase A SPD_0822 proB Glutamate 5-kinase SPD_0823 proA Gamma-glutamyl phosphate reductase SPD_0824 proC Pyrroline-5-carboxylate reductase SPD_0907 hemK HemK...”
- Redefining the Small Regulatory RNA Transcriptome in Streptococcus pneumoniae Serotype 2 Strain D39
Sinha, Journal of bacteriology 2019 - “...uppS spd_0266, spd_0265 spd_0288, spd_0287 spd_0371, spd_0372 Spd_sr29 381067-381205 () spd_0376, serS Spd_sr31b Spd_sr32b Spd_sr33 Spd_sr34 Spd_sr35b Spd_sr36b...”
- Characterization of central carbon metabolism of Streptococcus pneumoniae by isotopologue profiling
Härtel, The Journal of biological chemistry 2012 - “...It is plausible that the sodium:alanine symporter (SPD_0372) of pneumococci mediates Ala uptake. The [U-13C3]PEP is converted into [U-13C3]pyruvate by...”
- Reactive Oxygen Species Contribute to the Bactericidal Effects of the Fluoroquinolone Moxifloxacin in Streptococcus pneumoniae
Ferrándiz, Antimicrobial agents and chemotherapy 2016 - “...(rplL)d spr1871 spr1943c-1944 (rpmFG)d spr0327 (aliA)d spr0369 (dagA) spr0524 spr0535c-0532 spr1704c-1703 (amiEF) spr0648 spr0063 spr0875 (pmrA) spr1203...”
- Functionally cloned pdrM from Streptococcus pneumoniae encodes a Na(+) coupled multidrug efflux pump
Hashimoto, PloS one 2013 - “...a coupling ion based on the genome information of S. pneumoniae R6. They are spr1598, spr0369, and spr0648. Among them, we could not find any reports relating to spr0648. spr1598 is presumed to encode a serine transporter because of its high similarity (90%) to SstT from...”
- Comparative transcriptomic analysis of streptococcus pseudopneumoniae with viridans group streptococci
Park, BMC microbiology 2012 - “...- - spr1862 Competence protein 1 - - spr0469 Conserved hypothetical protein - - 4 spr0369 D-alanine glycine permease - - 1 spr1563 Degenerate transposase 1 2 11 spr0227 DEOR-type transcriptional regulator 1 - - spr0347 DNA alkylation repair enzyme, truncation 1 - - spr1144 DNA...”
- Pneumococcal gene complex involved in resistance to extracellular oxidative stress
Andisi, Infection and immunity 2012 - “...spd0642 spd0864 spd0953 spd1029 spd1158 spd1328 spr0266 spr0369 spr0374 spr0426 spr0427 spr0576 spr0648 spr0880 spr0974 spr1052 spr1181 spr1353 NP_357860.1...”
BH4033 amino acid transporter from Bacillus halodurans C-125
32% identity, 88% coverage
NSU_2100 alanine/glycine:cation symporter family protein from Novosphingobium pentaromativorans US6-1
32% identity, 75% coverage
PP1Y_AT4545 alanine/glycine:cation symporter family protein from Novosphingobium sp. PP1Y
32% identity, 75% coverage
STACADC2_0872 alanine/glycine:cation symporter family protein from Streptococcus thermophilus
33% identity, 91% coverage
- The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2
Alexandraki, Standards in genomic sciences 2017 - “...polar amino acid ABC transporters (STACADC2_0780-0782, STACADC2_0992-0995, STACADC2_1355-1358, STACADC2_1431-1433), two symporters for branched-chain amino acids (STACADC2_0872, STACADC2_1160), and two glutamine ABC transporters (STACADC2_0547-0548, STACADC2_1281-1282). Strain ACA-DC 2 lacks a cell wall-associated proteinase (PrtS). Although this gene may be important for optimal growth of S. thermophilus in...”
AWO_RS12525, Awo_c24340 alanine/glycine:cation symporter family protein from Acetobacterium woodii DSM 1030
31% identity, 80% coverage
- Redirecting electron flow in Acetobacterium woodii enables growth on CO and improves growth on formate
Moon, Nature communications 2024 - “...ATA) acsB1 acetyl CoA synthase catalytic subunit AcsB 2,849,933 AT 34.9% intergenic (79/+265) nifJ / Awo_c24340 pyruvate:ferredoxin oxidoreductase NifJ/hypothetical protein 2,884,514 GA 44.6% 39.3% L264F (CTTTTT) fliG flagellar motor switch protein FliG 2,884,844 GA 30.1% 42.3% R154W (CGGTGG) fliG flagellar motor switch protein FliG 2,939,053 (ATGGCTCTTT)...”
- A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii
Moon, Environmental microbiology reports 2023 - “...CarD 1220 52 4.55 Awo_c15740 Electron transfer flavoprotein alpha subunit apoprotein CarE 2209 125 4.14 Awo_c24340 Alanine or glycine:cation symporter Alanine metabolism 453 123 1.84 Awo_c24350 Alanine dehydrogenase 9213 863 3.39 Awo_c24360 AsnC family transcriptional regulator AldR 1660 218 2.91 Awo_c25770 CoAdependent propionaldehyde dehydrogenase PduP Alcohol...”
- Defining Genomic and Predicted Metabolic Features of the Acetobacterium Genus
Ross, mSystems 2020 - “...degradation pathway consists of a pyruvate:ferredoxin (flavodoxin) oxidoreductase (PFO) (AWO_RS12520), a sodium:alanine symporter family protein (AWO_RS12525), alanine dehydrogenase (AWO_RS12530), and the Lrp/AsaC family transcriptional regulator (AWO_RS12535). Examination of this operon revealed it was well conserved across the Acetobacterium genus, with the exception of A. fimetarium ,...”
- Alanine, a Novel Growth Substrate for the Acetogenic Bacterium Acetobacterium woodii
Dönig, Applied and environmental microbiology 2018 (secret)
TC 2.A.25.1.9 / W0WFC6 Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS from Pseudomonas aeruginosa MH38
PA2533 probable sodium:alanine symporter from Pseudomonas aeruginosa PAO1
31% identity, 90% coverage
- substrates: Alanine, Asparagine, Glutamine, Glycine
- 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 - “...protein 3 6 1.15 0.08 2.72 0.00 Down 3.33 0.00 Down 1.93 0.00 Lower WP_003089954.1 PA2533 - Probable sodium:alanine symporter 2 8 1.01 0.90 1.07 0.78 2.17 0.01 Down 1.06 0.68 WP_003090842.1 PA2777 YfdC Conserved hypothetical protein 3 7 1.13 0.28 1.76 0.00 Down 3.81 0.00...”
- “...- Hypothetical protein 2 4 1.10 0.05 1.13 0.15 2.40 0.00 Down 1.36 0.00 WP_023464768.1 PA2533 - Probable sodium:alanine symporter 2 5 1.08 0.26 1.39 0.00 1.57 0.00 Down 1.45 0.00 WP_023464848.1 PA2777 YfdC Conserved hypothetical protein 3 5 1.15 0.03 1.04 0.66 2.28 0.00 Down...”
- Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa
Sonnleitner, PloS one 2012 - “...subunit) PA2249 bkdB 2,48 3,22 branched-chain alpha-keto acid dehydrogenase PA2250 lpdV 2,62 3,07 lipoamide dehydrogenase-Val PA2533 2,13 probable sodium:alanine symporter AACAAGAAUAA (20 to 10) PA3038 4,13 16,75 2,11 probable porin AAUAACAA (7 to +1) PA3190 7,43 7,81 probable binding protein component ofABC sugar transporter AAUAACAA (24...”
- The Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression
Liang, Journal of bacteriology 2012 - “...189 190 298 292 373 78 309 305 100 103 82 hcnC PA2477 PA2533 cif PA3133 PA3471 ygbP 352 34 183 329 378 132 239 335 17 166 312 361 115 222 PA4090 mexH 301 375...”
- High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
Johnson, PLoS genetics 2008 - “...transporter periplasmic binding protein PA2252 PA01 alanine/glycine/sodium symporter PA2307 PAK nitrate/sulfonate/taurine ABC transporter membrane protein PA2533 PAK alanine/glycine/sodium symporter PA2923 PAK histidine ABC transporter periplasmic binding protein ( HisJ ) PA2924 PAK histidine ABC transporter membrane protein ( HisQ ) PA2925 PAK histidine ABC transporter membrane...”
Spy49_1008 Putative amino acid symporter from Streptococcus pyogenes NZ131
33% identity, 91% coverage
PM0091 unknown from Pasteurella multocida subsp. multocida str. Pm70
PmVP161_1144 alanine/glycine:cation symporter family protein from Pasteurella multocida
32% identity, 90% coverage
BC2317 Na(+)-linked D-alanine glycine permease from Bacillus cereus ATCC 14579
34% identity, 84% coverage
SPy1270, SPy_1270 putative amino acid symporter from Streptococcus pyogenes M1 GAS
33% identity, 91% coverage
ABO_0618 sodium/alanine symporter from Alcanivorax borkumensis SK2
32% identity, 84% coverage
CD2276 putative sodium:solute symporter from Clostridium difficile 630
33% identity, 88% coverage
Pro1538, SS120_15671 Na+/alanine symporter from Prochlorococcus marinus str. SS120
34% identity, 85% coverage
- Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
Kettler, PLoS genetics 2007 - “...of these seven additional genes in SS120 are transporters: SS120_12271, an iron or manganese transporter; SS120_15671, a sodum/alanine symporter; and SS120_0683106851, three genes encoding an ABC-type amino acid transporter. The other two, sdhA and sdhB , are putatively responsible for the conversion of fumarate to succinate...”
- Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome
Dufresne, Proceedings of the National Academy of Sciences of the United States of America 2003 - “...proline symporter PutP (Pro1635), Naalanine symporter AlsT (Pro1538), Na glutamate symporter GltS (Pro0784), Nagalactoside symporter MelB (Pro1404), and two...”
Pcar_2492 sodium/alanine symporter from Pelobacter carbinolicus str. DSM 2380
33% identity, 85% coverage
VIBR0546_12742 alanine/glycine:cation symporter family protein from Vibrio brasiliensis LMG 20546
31% identity, 87% coverage
HP0942 D-alanine glycine permease (dagA) from Helicobacter pylori 26695
30% identity, 88% coverage
Elen_1016 amino acid carrier protein from Eggerthella lenta DSM 2243
30% identity, 87% coverage
- Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities
Martinelli, Gut microbes 2024 - “...metabolic pathway. Clostridium scindenss CLOSCI_00522 and CLOSCI_01264 , respectively ortholog of E. lentas Elen_108 and Elen_1016 gene, have been suggested to be renamed baiO and baiP . 69 In a subsequent comparative genomics analysis, the gene has been identified in 33/5,451 microbial genomes, spanning 18 species,...”
- Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
Heinken, Microbiome 2019 - “...S3). Additionally, these genes were co-localized with a gene encoding for a probable transporter ( Elen_1016 ) in the genomes of E. lenta and Eggerthella sp. HGA1. Hence, the gene Elen_1016 was assumed to encode a transporter for the products of the bai pathway and was...”
VP1741 sodium/alanine symporter from Vibrio parahaemolyticus RIMD 2210633
30% identity, 89% coverage
- Bacteriostatic effects of benzyl isothiocyanate on Vibrio parahaemolyticus: Transcriptomic analysis and morphological verification
Liu, BMC biotechnology 2021 - “...4 ). Three genes VP0295, VPA1128, and VPA1735 were upregulated, while eight genes VP1092, VP1256, VP1741, nhaB, VP2351, VP2545, VP2778, and VP2826 were downregulated in sodium ion transport of biological processes. They regulated multiple proteins related to sodium ion transport, such as sodium/sulfate symporter, acyl-CoA carboxylase...”
- QseC Inhibition as a Novel Antivirulence Strategy for the Prevention of Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus
Yang, Frontiers in cellular and infection microbiology 2020 - “...transcriptional regulator VP1470 1.536542 0.003818 Uncharacterized peptidase YqjE 2 VP1740 2.30968 1.75E-15 FIG01199787: hypothetical protein VP1741 2.394921 2.28E-17 Chromosome segregation ATPase VP1742 2.438215 1.55E-05 hypothetical protein 3 VP1043 1.70837 3.81E-10 hypothetical protein VP1044 1.889812 7.64E-08 hypothetical protein VP1045 1.791027 1.62E-11 Chromosome partition protein MukB VP1046 1.945746...”
BSU07750 putative aminoacid transporter from Bacillus subtilis subsp. subtilis str. 168
36% identity, 61% coverage
- Secondary structural entropy in RNA switch (Riboswitch) identification
Manzourolajdad, BMC bioinformatics 2015 - “...3648264 3648420 reverse BSU35530 tagO -311 0.363 1806 degS BSU35500 0.818 74 850053 850209 forward BSU07750 yflA -3789 0.3694 236 treP BSU07800 0.817 75 255279 255435 forward BSU02330 ybfQ -1718 0.2994 2434 ybgA BSU02370 0.816 76 1541729 1541885 forward BSU14680 ykzC -2958 0.3376 79 ylaA BSU14710...”
- “...-44.60 - 0.2600 124.4599991 - 0.4300 202 yokD BSU21630 0.9058990479 200 nt 850067 850266 forward BSU07750 yflA -3783 -57.20 - 0.4000 124.1029968 - 0.3800 202 treP BSU07800 0.9058393836 200 nt 1466905 1467104 forward BSU13960 ykwC -207 -56.93 - 0.3900 123.7220001 - 0.4200 802 pbpH BSU13980 0.9029595852...”
SO0858 sodium:alanine symporter family protein from Shewanella oneidensis MR-1
34% identity, 84% coverage
jhp0877 putative SODIUM/ALANINE SYMPORTER from Helicobacter pylori J99
30% identity, 88% coverage
VC1422 sodium/alanine symporter from Vibrio cholerae O1 biovar eltor str. N16961
30% identity, 89% coverage
- Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism
Tan, Research (Washington, D.C.) 2022 - “...fermentation [ 24 ]. A glycine-on riboswitch, which was from the upstream nucleotide sequences of VC1422 gene of Vibrio cholerae [ 25 ], was used to detect the glycine concentrations in the cell and subsequently combined with fluorescence-activated cell sorting (FACS) to develop a high-throughput screening...”
- Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets
Pavlova, Antibiotics (Basel, Switzerland) 2022 - “...II, have been identified. They are represented by the regions architecture immediately upstream of the VC1422 gene, which encodes putative sodium and the alanine symporter. The gcvT is an aminomethyltransferase called glycine cleavage system protein T and catalyzes the reaction: (6S)-5,6,7,8-tetrahydrofolate + (R)-N 6 -(S 8...”
- Discovery of a Structurally Unique Small Molecule that Inhibits Protein Synthesis
Thakral, The Yale journal of biology and medicine 2017 - “...incubated at 37C for 2.0 hours. Transcription Inhibition Counterscreen. A plasmid containing the Vibrio cholera VC1422 glycine riboswitch [ 21 ] for use as a test transcription product was linearized by restriction digest and in vitro transcribed by run-off transcription as described above but with the...”
- Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy
Ruff, RNA (New York, N.Y.) 2014 - “...of this study (see Supplemetal Material for full sequence). This particular glycine riboswitch controls the VC1422 gene, which encodes a sodium/alanine- or glycine-symporter. It was the initial glycine riboswitch characterized ( Mandal et al. 2004 ) and has served as the prototype for subsequent biochemical study...”
- “...further purification. Glycine and other chemicals were obtained from Sigma. DNA constructs The V. cholerae VC1422 glycine riboswitch (VC1-2 WT) and single-aptamer constructs were made by adding the seven base leader sequence to previously reported plasmids using a PCR reaction with corresponding primers ( Erion and...”
- Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches
Baird, RNA (New York, N.Y.) 2013 - “...dual aptamer glycine riboswitches from the V. cholerae VC1422, B. subtilis gcvT, and F. nucleatum FN0328 genes were generated by PCR of overlapping synthetic...”
- Riboswitch structure in the ligand-free state
Liberman, Wiley interdisciplinary reviews. RNA 2012 - “...of transcription 27 . Further analysis on a pair of homologous aptamers upstream of the VC1422 gene from Vibrio cholerae showed that the type I (designated VCI) and II (designated VCII) riboswitches actually compose a single riboswitch with tandem aptamers and a single expression platform. Each...”
- Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch
Erion, RNA (New York, N.Y.) 2011 - “...obtained from Sigma. DNA constructs The Vibrio cholera VC1422 glycine riboswitch (VC12-WT) and single aptamer glycine riboswitch (VC1, VC2) constructs were made...”
- Structural basis of cooperative ligand binding by the glycine riboswitch
Butler, Chemistry & biology 2011 - “...C-G base pair) to a U G in the Vibrio cholerae glycine riboswitch of the VC1422 gene resulted in loss of cooperativity, presumably by disrupting the formation of the type I A minor interaction ( Kwon and Strobel, 2008 ). The interaction is thematically similar but...”
- More
SPO2370 sodium:alanine symporter family protein from Silicibacter pomeroyi DSS-3
31% identity, 77% coverage
- Ecological genomics of marine Roseobacters
Moran, Applied and environmental microbiology 2007 - “...other compounds (likely amino acids; SPO1810 and SPO2370), and a respiratory sodium pump (SPOA0030; a component of a multigene NADH:ubiquinone oxidoreductase)...”
SPO2370 alanine/glycine:cation symporter family protein from Ruegeria pomeroyi DSS-3
31% identity, 80% coverage
- Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda
Ferrer-González, ISME communications 2023 - “...isethionate TRAP transporter, small permease iseL SPO2358* AAV95619.1 9.3 isethionate TRAP transporter, substrate-binding protein iseK SPO2370 AAV95630.1 3 sodium:alanine symporter family protein SPO2699 AAV95944.1 5.4 opine/polyamine ABC transporter, permease SPO2700 AAV95945.1 3.2 opine/polyamine ABC transporter, permease SPO2701 AAV95946.1 3.1 opine/polyamine ABC transporter, substrate binding protein SPO2702...”
- Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy
Olofsson, ISME communications 2022 - “...Lactic acid transporter SPO1017-1021 Glycolate SPOA0143 Glycerol-3-phosphate transporter SPO0239, 0240 Glycerol transporter SPO0608-0612 Alanine symporter SPO2370 Trimethylamine transporter SPO1551, 1552, 1562 Amino acid transporter SPO1516 Sugar transporter SPO0608-0612 Acetate SPO2963 Polaribacter dokdonensis Hypothetical protein PUL2 MED152_00445 MFS transporter (fucose) PUL3 MED152_05095 Glycosyl hydrolase family 17 PUL2...”
- Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium
Chan, Frontiers in microbiology 2012 - “...ABC transporter, permease protein 4.6 SPO1807 DNA polymerase III epsilon subunit family exonuclease 3.7 1.0 SPO2370 Sodium:alanine symporter family protein 3.4 SPO3291 Branched-chain amino acid ABC transporter, periplasmic binding protein, putative 5.5 4.0 SPO3461 Flagellar protein FlgJ, putative 8.5 SPO3783 Sugar ABC transporter, ATP-binding protein 8.0...”
- “...0.5 SPO2301 OsmC-like family protein 5.2 SPO2306 Hypothetical protein 3.4 SPO2325 serS Seryl-tRNA synthetase 3.2 SPO2370 Sodium:alanine symporter family protein 3.4 SPO2371 Universal stress protein family protein 4.4 1.8 SPO2422 d -isomer specific 2-hydroxyacid dehydrogenase family protein 6.4 SPO2644 VWA domain CoxE-like family protein 11.3 SPO2647...”
SMU_1175 alanine/glycine:cation symporter family protein from Streptococcus mutans UA159
31% identity, 92% coverage
DVU0724 sodium/alanine symporter family protein from Desulfovibrio vulgaris Hildenborough
33% identity, 82% coverage
FN1747 Cysteine permease from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
30% identity, 80% coverage
- Annotation-based inference of transporter function
Lee, Bioinformatics (Oxford, England) 2008 - “...annotation, the annotation substrates are used, thereby overriding TransportDB. For example, the protein for gene FN1747 in F.nucleatum is annotated as cysteine permease but its primary substrate is identified as alanine in TransportDB; cysteine is used in the standard. In the absence of conflicting or non-specific...”
IL1268 Na(+)-linked D-alanine and glycine permease from Idiomarina loihiensis L2TR
35% identity, 47% coverage
DAGA_PSEHA / P30144 Na(+)-linked D-alanine glycine permease; Sodium/alanine symporter from Pseudoalteromonas haloplanktis (Alteromonas haloplanktis) (see 2 papers)
TC 2.A.25.1.1 / P30144 Alanine (or glycine):Na+ symporter from Alteromonas haloplanktis (see paper)
34% identity, 49% coverage
- function: Catalyzes the sodium-dependent uptake of extracellular D- alanine and glycine.
catalytic activity: D-alanine(in) + Na(+)(in) = D-alanine(out) + Na(+)(out) (RHEA:71447)
catalytic activity: glycine(in) + Na(+)(in) = glycine(out) + Na(+)(out) (RHEA:68228) - substrates: Alanine, Glycine, Na+
Q7UKE2 Na(+)-linked D-alanine glycine permease from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
31% identity, 72% coverage
CLOSCI_01264 hypothetical protein from Clostridium scindens ATCC 35704
31% identity, 86% coverage
CLOSCI_01264 alanine/glycine:cation symporter family protein from [Clostridium] scindens ATCC 35704
31% identity, 88% coverage
TP0414 D-alanine glycine permease (dagA) from Treponema pallidum subsp. pallidum str. Nichols
31% identity, 88% coverage
- Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen
Radolf, Nature reviews. Microbiology 2016 - “...acid requirements are putative symporters for aspartate and glutamate (TP0555 and TP0934), alanine and glycine (TP0414 and TP0998) and branched chain amino acids (TP0265). In addition, TP0144 functions as the SBP for a thiamine ABC transporter (TbpAPQ(TP0142-0144)) 95 . BioMNY (TP0226-0228), a putative biotin importer, seems...”
- Comparative investigation of the genomic regions involved in antigenic variation of the TprK antigen among treponemal species, subspecies, and strains
Giacani, Journal of bacteriology 2012 - “...TP0312 TP0312 IGR236 TP0326 TP0334 TP0345 TP0346 TP0408 TP0414 TP0438 TP0456 TP0456 TP0458 IGR335 TP0488 IGR364 IGR483 TP0685 TP0711 TP0733 IGR549 TP0856 TP0859...”
- Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons
Häse, Microbiology and molecular biology reviews : MMBR 2001 - “...group includes predicted the Na/ alanine symporters TP0414 and TP0998, the Na/branchedchain amino acid symporter TP0265, the Na/phosphate symporter TP0771, and...”
pc0622 putative D-alanine/glycine transport protein, sodium-dependent from Parachlamydia sp. UWE25
29% identity, 86% coverage
AMK26_RS14790 alanine/glycine:cation symporter family protein from Streptomyces sp. CB03234
28% identity, 81% coverage
Wbm0424 Na+/alanine symporter from Wolbachia endosymbiont strain TRS of Brugia malayi
26% identity, 88% coverage
CT735 D-Ala/Gly Permease from Chlamydia trachomatis D/UW-3/CX
25% identity, 88% coverage
SEN0907 putative ion:amino acid symporter from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
26% identity, 85% coverage
CPn0536 D-Ala/Gly Permease from Chlamydophila pneumoniae CWL029
26% identity, 62% coverage
- Growth of Chlamydia pneumoniae Is Enhanced in Cells with Impaired Mitochondrial Function
Käding, Frontiers in cellular and infection microbiology 2017 - “...ABC transporter ATPase 934 1,470 Cpn0290 Na-dependent transporter 215 395 Cpn0486 proline permease 208 665 Cpn0536 dagA_1 D-Ala%2FGly permease 717 1,143 Cpn0604 fliY amino acid ABC transporter substrate-binding protein 2,852 4,541 Cpn0614 adt_2 ADP/ATP translocase 1,418 2,137 Gene coverage was normalized using RPKM conversion. Ranking of...”
HMPREF0389_01240 alanine/glycine:cation symporter family protein from Filifactor alocis ATCC 35896
31% identity, 53% coverage
- Proteome variation among Filifactor alocis strains
Aruni, Proteomics 2012 - “...determining protein MinD 29/29.5 55/0.11 3 0.126 M Membrane-associated ATPase domain 0.56 Nonsecretory protein 38. HMPREF0389_01240 3-Oxy acyl carrier protein Amino acid carrier protein 27.5/28 341/1.23 19 0.747 M Eight TMMH domains 0.45 Uncleavable N terminal signal sequence 39. HMPREF0389_00128 GTP sensing transcriptional pleotropic repressor CodY...”
CT409 Amino acid permease from Chlamydia trachomatis D/UW-3/CX
24% identity, 83% coverage
pc1598 putative D-alanine/glycine transport protein, sodium-dependent from Parachlamydia sp. UWE25
26% identity, 83% coverage
STM14_1138, STMMW_10141 alanine/glycine:cation symporter family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM1003 putative transcriptional regulator, Lrp family from Salmonella typhimurium LT2
26% identity, 85% coverage
- Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
Fong, Microbial genomics 2023 - “...chain P125109_00774 SEN0689 D7795_00799 STMMW_07961 STM0739 1.35 SEN0907 Putative ion:amino acid symporter P125109_01022 SEN0907 D7795_01047 STMMW_10141 STM1003 1.01 yedD Putative lipoprotein P125109_01175 SEN1044 D7795_01257 STMMW_19441 STM1964 3.78 cheZ Chemotaxis protein CheZ P125109_01224 SEN1088 D7795_01307 STMMW_18981 STM1915 1.81 lrhA NADH dehydrogenase operon transcriptional regulator P125109_02623 SEN2312 D7795_02672...”
- Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis
Fong, 2022 - Genetic Determinants in Salmonella enterica Serotype Typhimurium Required for Overcoming In Vitro Stressors in the Mimicking Host Environment
Mandal, Microbiology spectrum 2021 - “..., barA , hscA , rfaQ , rfbI , and the genes encoding putative proteins STM14_1138, STM14_3334, STM14_4825, and STM_5184) that have compelling potential for the development of vaccines and antibacterial drugs to curb Salmonella infection. IMPORTANCE Salmonella enterica serotype Typhimurium is a major human bacterial...”
- “...is required for fitness at pH 3, including csgF and csgG . Additionally, putative proteins STM14_1138, STM14_1486, STM14_1981, and STM14_3333 and STM14_4826, STM14_4828, STM14_5184, and STM14_5185 (hypothetical protein) were required for fitness in vitro under acidic and osmotic stress, respectively, and enteric infection in the three...”
- Genetic determinants inSalmonella entericaserotype Typhimurium required for overcoming stressors in the host environment
Mandal, 2019 - Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
Fong, Microbial genomics 2023 - “...P125109_00774 SEN0689 D7795_00799 STMMW_07961 STM0739 1.35 SEN0907 Putative ion:amino acid symporter P125109_01022 SEN0907 D7795_01047 STMMW_10141 STM1003 1.01 yedD Putative lipoprotein P125109_01175 SEN1044 D7795_01257 STMMW_19441 STM1964 3.78 cheZ Chemotaxis protein CheZ P125109_01224 SEN1088 D7795_01307 STMMW_18981 STM1915 1.81 lrhA NADH dehydrogenase operon transcriptional regulator P125109_02623 SEN2312 D7795_02672 STMMW_23521...”
- Adaptation of multilocus sequencing for studying variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium
Hu, Genetics 2006 - “...knownd (d) 1096650-1096833 4 bp (dp) IG (STM1003, pncB) 1766735-1766881 8 bp (dp) IG (STM1672, STM1673) 3062413-3062595 (Ec) 791460 456364 720484-720485...”
- Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar typhimurium reveals phage-type- specific markers and potential for microarray typing
Hu, Journal of clinical microbiology 2002 - “...5-GGTA-3, respectively, in an intergenic region between STM1003 and the pncB gene (nicotinate phosphoribosyltransferase [38]) at serovar Typhimurium LT2 genome...”
SEET0819_11930 alanine/glycine:cation symporter family protein from Salmonella enterica subsp. enterica serovar Tennessee str.
27% identity, 81% coverage
Wbm0197 Na+/alanine symporter from Wolbachia endosymbiont strain TRS of Brugia malayi
25% identity, 89% coverage
AM882 hypothetical protein from Anaplasma marginale str. St. Maries
26% identity, 85% coverage
EHF_0383 alanine:cation symporter family protein from Ehrlichia japonica
23% identity, 89% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
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.
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.
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.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory