PaperBLAST
PaperBLAST Hits for sp|Q2IH94|GATA_ANADE Glutamyl-tRNA(Gln) amidotransferase subunit A OS=Anaeromyxobacter dehalogenans (strain 2CP-C) OX=290397 GN=gatA PE=3 SV=1 (492 a.a., MSTPAKELCR...)
Show query sequence
>sp|Q2IH94|GATA_ANADE Glutamyl-tRNA(Gln) amidotransferase subunit A OS=Anaeromyxobacter dehalogenans (strain 2CP-C) OX=290397 GN=gatA PE=3 SV=1
MSTPAKELCRLGLREAGAGVAAKAISSTELVEASLARIQATDGKLGAFLAVCADRARAAA
KAADARAARGERRSELDGVPVAVKDLFVTKGVPTTAGSRILEGYLPPYDATVVERLEAAG
AVIVGKLNMDEFAMGSSNENSAYKPCHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTDT
GGSIREPAAFCGVVGVKPTYGRVSRYGVVAFASSLDQVGPLAREVGDAALVLRTIAGHDP
RDMTSSTRPVDDYLGPLEEGARGLRVGVPREWLSGGLDAGVEAAIRAALDTYRRLGATLV
DVSLPHSKYGIGAYYLIAPAEASSNLARYDGVRYGLRAEGAKGLKEMYAESREQGLGAEP
KRRIMLGTYALSSGYYDAYYLRAQKVRTLIRRDFDEAFRGCDVIAGPVTPSVAFALGERT
GDPLQMYLADIFTITCNLAALPGLSVPCGLEAASGLPVGLQLVGRPFDEATLFRAARALE
RELGPLPAPPEP
Running BLASTp...
Found 251 similar proteins in the literature:
Q88XP7 Glutamyl-tRNA(Gln) amidotransferase subunit A from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
53% identity, 95% coverage
gatA / O06491 glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7) from Bacillus subtilis (strain 168) (see paper)
GATA_BACSU / O06491 Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 from Bacillus subtilis (strain 168) (see 2 papers)
BSU06680 aspartyl/glutamyl-tRNA amidotransferase subunit A from Bacillus subtilis subsp. subtilis str. 168
57% identity, 96% coverage
GSU3381 glutamyl-tRNA(Gln) amidotransferase, A subunit from Geobacter sulfurreducens PCA
60% identity, 97% coverage
Gmet_0075 Glutamyl-tRNA(Gln) amidotransferase A subunit from Geobacter metallireducens GS-15
59% identity, 97% coverage
BAB2_0646 Amidase:Glutamyl-tRNA(Gln) amidotransferase A subunit from Brucella melitensis biovar Abortus 2308
55% identity, 97% coverage
cce_1710 glutamyl-tRNA (Gln) amidotransferase subunit A from Cyanothece sp. ATCC 51142
55% identity, 95% coverage
FUT48_26015 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Pseudomonas sp. JG-B
56% identity, 96% coverage
LSEI_1058 Asp-tRNA-Asn/Glu-tRNA-Gln amidotransferase A subunit from Lactobacillus casei ATCC 334
55% identity, 95% coverage
SSA_0570 Glutamyl-tRNA(Gln) amidotransferase subunit A, putative from Streptococcus sanguinis SK36
52% identity, 94% coverage
- Involvement of signal peptidase I in Streptococcus sanguinis biofilm formation
Aynapudi, Microbiology (Reading, England) 2017 - “...No SSA_1498 0.12 12.34 50S ribosomal protein L20 No SSA_2107 0.17 10.71 Glutaminefructose-6-phosphate aminotransferase No SSA_0570 0.23 5.46 Glutamyl-tRNA(Gln) amidotransferase subunit A No SSA_0291 0.31 5.53 Short-chain dehydrogenase Yes SSA_1012 0.42 5.99 Phosphoenolpyruvateprotein phosphotransferase No SSA_2342 0.57 5.12 VTC domain protein No SSA_2359 0.63 10.02 tRNA...”
- “...of protein SSA_0371, involved in glutamate biosynthesis, implied a deficiency of glutamine. Another related protein, SSA_0570, is needed for the addition of glutamine to the elongating peptides during translation. Moreover, the enzymes (SSA_2107 and SSA_2183) involved in the synthesis of peptidoglycan (glucosamine 6-phosphate) were also reduced....”
NE2072 Amidase:Glutamyl-tRNA(Gln) amidotransferase A subunit from Nitrosomonas europaea ATCC 19718
53% identity, 93% coverage
PA4483 glutamyl-tRNA amidotransferase subunit A from Pseudomonas aeruginosa PAO1
55% identity, 96% coverage
- The Breadth and Molecular Basis of Hcp-Driven Type VI Secretion System Effector Delivery
Howard, mBio 2021 - “...PtsN 4 1.30 Nitrogen regulatory protein 16.7 PA2015 LiuA 4 2.25 Putative isovaleryl-CoA dehydrogenase 42.2 PA4483 GatA 3.9 1.39 Glutamyl-tRNA(Gln) amidotransferase subunit A 51.9 PA3183 Zwf 3.9 2.06 Glucose-6-phosphate 1-dehydrogenase 55.6 PA3635 Eno 3.8 2.99 Enolase 45.2 PA4560 IleS 3.7 2.99 Isoleucine-tRNA ligase 105.5 PA2624 Idh...”
- Comparative genome analysis of ciprofloxacin-resistant Pseudomonas aeruginosa reveals genes within newly identified high variability regions associated with drug resistance development
Su, Microbial drug resistance (Larchmont, N.Y.) 2013 - “...PA5045 PA5146 PA5160 PA5231 PA5248 PA5262 PA2407 PA4483 PA5365 Hypothetical protein Helix destabilizing protein of bacteriophage Pf1 Probable coat protein A...”
- Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria
Deng, Cell host & microbe 2013 - “...GyrB, DNA gyrase subunit B LADC*QEK 0.23 PA3149 WbpH, probable glycosyltransferase EIVEGSNCGICVDPLS PAAIAEAIDYLVSNP C*EAAALGR 0.23 PA4483 GatA, glutamyl-tRNA(Gln) amidotransferase TAEDC*ALMLGVMA GFDPK 0.23 PA1609 FabB, beta-ketoacyl-ACP synthase I WITGLGIVSC*LGN DK 0.24 PA0266 b GabT, 4-aminobutyrate aminotransferase LSHTC*FQVLAYEPYI ELAEEIAK 0.24 PA3155 b WbpE, probable aminotransferase AIIPVSLYGQC*ADFD AINAIASK 0.24...”
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
Lecoutere, MicrobiologyOpen 2012 - “...0.152 130 PA4458 Conserved hypothetical protein R C 19.3 18 5.52 5.48 0.601 0.012 131 PA4483 gatA Glu tRNA amidotransferase J U 51.9 52 5.52 5.45 0.638 0.119 132 PA4483 gatA Glu tRNA amidotransferase J U 51.9 51 5.52 5.32 0.638 0.119 133 PA4495 Hypothetical protein...”
lmo1755 glutamyl-tRNA(Gln) amidotransferase (subunit A) from Listeria monocytogenes EGD-e
53% identity, 97% coverage
Q81IN3 Glutamyl-tRNA(Gln) amidotransferase subunit A from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
55% identity, 93% coverage
CBO3266 glutamyl-tRNA amidotransferase subunit A from Clostridium botulinum A str. ATCC 3502
49% identity, 97% coverage
- Gene expression profiling of Clostridium botulinum under heat shock stress
Liang, BioMed research international 2013 - “...(by 12.1-, 9.2-, and 5.6-fold, resp.). In addition, gatB (CBO3265, aspartyl/glutamyl-tRNA amidotransferase subunit B1), gatA (CBO3266, glutamyl-tRNA amidotransferase subunit A), and gatC (CBO3267, glutamyl-tRNA amidotransferase subunit C) compose an operon and were downregulated by heat shock stress. Moreover, proS2 (CBO3503, prolyl-tRNA synthetase), aspS (CBO1019, aspartyl-tRNA synthetase),...”
FORC47_RS01880 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Bacillus cereus
54% identity, 95% coverage
NP_385418 PUTATIVE GLUTAMYL-TRNA AMIDOTRANSFERASE SUBUNIT A PROTEIN from Sinorhizobium meliloti 1021
54% identity, 98% coverage
Bd0059 glutamyl-tRNA(Gln) amidotransferase, A subunit from Bdellovibrio bacteriovorus HD100
53% identity, 96% coverage
RPA3107 Glu-tRNA(Gln) amidotransferase subunit A from Rhodopseudomonas palustris CGA009
55% identity, 97% coverage
DVU0808 glutamyl-tRNA(Gln) amidotransferase, A subunit from Desulfovibrio vulgaris Hildenborough
59% identity, 96% coverage
LGG_01019 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Lacticaseibacillus rhamnosus GG
LGG_01019 aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit A (Adt) from Lactobacillus rhamnosus GG
55% identity, 93% coverage
CBU_1474 glutamyl-tRNA amidotransferase subunit A from Coxiella burnetii RSA 493
53% identity, 93% coverage
- Coxiella burnetii replicates in Galleria mellonella hemocytes and transcriptome mapping reveals in vivo regulated genes
Kovacs-Simon, Virulence 2020 - “...synthesis [ 42 , 43 , 54 ] and genes involved in translation (CBU_0569, CBU_1430, CBU_1474, CBU_1817, and CBU_1842). Of these, CBU_0844 has homology to CBU_0677, and CBU_1655 has homology to the CBU_0678 gene. These genes and their products are discussed in more detail above. Table...”
- “...hypothetical cytosolic protein CBU_1430 truB tRNA pseudouridine synthase B CBU_1435 nuoN NADH-quinone oxidoreductase chain N CBU_1474 gatA aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A CBU_1477 ahpC peroxiredoxin CBU_1478 ahpD peroxiredoxin reductase (NAD(P)H) CBU_1580 ATPase CBU_1655 rfaE D-glycero-D-manno-heptose-7-phosphate 1-kinase CBU_1685 hypothetical protein CBU_1696 rnfB electron transport complex protein CBU_1697 Nth...”
RHE_RS09475 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Rhizobium etli CFN 42
53% identity, 97% coverage
BCAL0484 glutamyl-tRNA amidotransferase subunit A from Burkholderia cenocepacia J2315
56% identity, 95% coverage
Q1BSL2 Glutamyl-tRNA(Gln) amidotransferase subunit A from Burkholderia orbicola (strain AU 1054)
56% identity, 95% coverage
FN0754 Glutamyl-tRNA(Gln) amidotransferase subunit A from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
49% identity, 98% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...Covers FN0040, FN0054, FN0067, FN0069, FN0070, FN0110, FN0298, FN0299, FN0405, FN0466, FN0506, FN0611, FN0697, FN0753, FN0754, FN0755, FN1268, FN1340, FN1489, FN1517, FN1579, FN1597, FN1658, FN1977, FN2011, FN2122, FN2123. Ribosomal proteins are noted to correlate with growth rates (Nomura etal. 1984 ). However, the cells were not...”
SERP1438 glutamyl-tRNA(Gln) amidotransferase, A subunit from Staphylococcus epidermidis RP62A
52% identity, 94% coverage
P63488 glutaminyl-tRNA synthase (glutamine-hydrolysing) (subunit 2/2) (EC 6.3.5.7) from Staphylococcus aureus (see paper)
2dqnA / P63488 Structure of tRNA-dependent amidotransferase gatcab complexed with asn (see paper)
SAV1900 glutamyl-tRNAGln amidotransferase subunit A from Staphylococcus aureus subsp. aureus Mu50
SA1716 glutamyl-tRNAGln amidotransferase subunit A from Staphylococcus aureus subsp. aureus N315
52% identity, 94% coverage
- Ligand: asparagine (2dqnA)
- Gap-com: general model selection criterion for sparse undirected gene networks with nontrivial community structure
Kuismin, G3 (Bethesda, Md.) 2022 - “...124 SAV1192 1,462 SAV0014 893 SAV0069 124 SAV2071 1,442 SAV1892 890 SACOL0041 123 SAV2347 1,442 SAV1900 890 SACOL0054 122 SAV0602 1,438 SAV0654 889 SAV0400 121 SAV0390 1,432 SAV2071 871 SAV0407 120 SAV2221 1,425 The graph selected with StARS is left out because all nodes in the...”
- The ORFeome of Staphylococcus aureus v 1.1
Brandner, BMC genomics 2008 - “...Transcription termination factor Rho 438 AA [ 40 ] SAV1576 Putative 2-methylthioadenine synthetase 448 AA SAV1900 Glutamyl-tRNA(Gln) amidotransferase subunit A 485 AA SAV2081 Probable DEAD-box ATP-dependent RNA helicase 506 AA SAV0205 Oligopeptide transport ATP-binding protein 530 AA SAV2029 60 kDa chaperonin 538 AA [ 41 ]...”
- Transcriptional profiling analysis of the global regulator NorG, a GntR-like protein of Staphylococcus aureus
Truong-Bolduc, Journal of bacteriology 2011 - “...and metabolism SA0946 SA2011 SA2138 SA2265 SA2266 SA2272 SA1716 SA1717 SA1718 SA1887 SA1888 SA1889 SA2173 Na/H antiporter family protein Sodium transport family...”
- walK and clpP mutations confer reduced vancomycin susceptibility in Staphylococcus aureus
Shoji, Antimicrobial agents and chemotherapy 2011 - “...SA1446 SA1456 SA1457 SA1488 SA1506 SA1550 SA1563 SA1579 SA1715 SA1716 SA1717 serS metS lysS gltX cysS argS trpS pheS pheT ileS proS asnC alaS aspS hisS valS...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...acid dehydratase sa_c2992s2549_a_at 4.2 2.5 2.5 hemC SA1717 porphobilinogen deaminase sa_c2990s2545_a_at 3.1 2.5 2.5 hemD SA1716 uroporphyrinogen-III synthase sa_c3585s3067_a_at 2.8 2.5 2.5 hemE SA1889 uroporphyrinogen decarboxylase sa_c3577s3059_a_at 4.1 2.5 2.5 hemG SA1887 protoporphyrinogen oxidase sa_c3584s3063_a_at 2.8 2.5 2.5 hemH SA1888 ferrochelatase sa_c2984s2541_a_at 2.7 2.5 5 hemL...”
DLJ56_RS04105 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Staphylococcus aureus
52% identity, 94% coverage
- Limited Adaptation of Staphylococcus aureus during Transition from Colonization to Invasive Infection
Räz, Microbiology spectrum 2023 - “...Ala306_ Gly309del DLJ56_RS12685 PTS sucrose transporter subunit IIBC CI2025 NZ_CP029629 796734 SNP 167A>G Gln56Arg gatA DLJ56_RS04105 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA CI2016 NZ_CP029629 17890 SNP 85T>C Phe29Leu gdpP DLJ56_RS00075 Cyclic-di-AMP phosphodiesterase GdpP CI2025 NZ_CP029629 2321375 SNP 766T>C Ser256Pro DLJ56_RS12045 Efflux RND transporter permease subunit CI2016 NZ_CP029629 471537...”
A6QIC8 Glutamyl-tRNA(Gln) amidotransferase subunit A from Staphylococcus aureus (strain Newman)
SAUSA300_1881 Aspartyl/glutamyl-tRNA amidotransferase subunit A from Staphylococcus aureus subsp. aureus USA300_FPR3757
52% identity, 94% coverage
- Trapping and identification of cellular substrates of the Staphylococcus aureus ClpC chaperone
Graham, Journal of bacteriology 2013 - “...23 53 A6QG79 A6QEJ0 A6QH25 A6QGD8 A6QHQ3 A6QIC8 5.0/4.0 18.0/18.5 29.0/20.8 8.0/6.4 65.0/50.2 40.0/65.3 0.0/1.5 7.0/6.4 13.0/9.8 4.0/2.0 22.0/33.9 6.0/16.2...”
- Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...CysE 2.08 Amino acid biosynthesis SAUSA300_0963 QoxA 2.05 Energy metabolism SAUSA300_2573 IsaB 2.00 Unknown function SAUSA300_1881 GatA 0.50 Protein synthesis SAUSA300_0691 SaeR 0.49 Regulatory functions SAUSA300_2469 SdaAA 0.49 Energy metabolism SAUSA300_0386 Xpt 0.48 Purines, pyrimidines, nucleosides, and nucleotides SAUSA300_1258 0.48 Energy metabolism SAUSA300_1293 LysA 0.48 Amino...”
- “...dehydrogenase, decarboxylating SAUSA300_0496 LysS 3 Lysine--tRNA ligase SAUSA300_0716 NrdE Ribonucleoside-diphosphate reductase SAUSA300_2251 Dehydrogenase family protein SAUSA300_1881 GatA Glutamyl-tRNA (Gln) amidotransferase subunit A SAUSA300_1586 AspS Aspartate--tRNA ligase SAUSA300_1167 Pnp Polyribonucleotide nucleotidyltransferase SAUSA300_0009 SerS Serine--tRNA ligase SAUSA300_1629 ThrS Threonine--tRNA ligase SAUSA300_2214 FemX Lipid II:glycine glycyltransferase 1 Fold change...”
SAR1992 glutamyl-tRNA amidotransferase subunit A from Staphylococcus aureus subsp. aureus MRSA252
52% identity, 94% coverage
LSA1547 Glutamyl-tRNA amidotransferase, subunit A from Lactobacillus sakei subsp. sakei 23K
51% identity, 95% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...-0.7 Protein synthesis LSA0377 tgt Queuine tRNA-ribosyltransferase -0.6 LSA1546 gatB Glutamyl-tRNA amidotransferase, subunit B -0.5 LSA1547 gatA Glutamyl-tRNA amidotransferase, subunit A -0.5 -0.5 RNA restriction and modification LSA0437 lsa0437 Hypothetical protein with an RNA-binding domain -0.7 LSA0443 lsa0443 Putative single-stranded mRNA endoribonuclease 2.7 1.9 LSA0738 dtd...”
gbs1712 Unknown from Streptococcus agalactiae NEM316
51% identity, 94% coverage
- The transcriptional regulator RovS controls the attachment of Streptococcus agalactiae to human epithelial cells and the expression of virulence genes
Samen, Infection and immunity 2006 - “...transcriptional apparatus (gbs0094, gbs0425, gbs1381, gbs1509, and gbs1712), four code for putative transporters (gbs0119, gbs1332, gbs2007, and gbs2017), and...”
SMU_RS08345 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Streptococcus mutans UA159
50% identity, 93% coverage
3h0lA / O66610 Structure of tRNA-dependent amidotransferase gatcab from aquifex aeolicus (see paper)
51% identity, 97% coverage
- Ligand: asparagine (3h0lA)
Cbei_2128 aspartyl/glutamyl-tRNA amidotransferase subunit A from Clostridium beijerincki NCIMB 8052
49% identity, 96% coverage
NMY233_1266 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Neisseria meningitidis NM233
49% identity, 96% coverage
NMA1568 Glu-tRNA(Gln) amidotransferase subunit A from Neisseria meningitidis Z2491
49% identity, 96% coverage
ZMO0783 aspartyl/glutamyl-tRNA amidotransferase subunit A from Zymomonas mobilis subsp. mobilis ZM4
50% identity, 98% coverage
- Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development
Li, Biotechnology for biofuels 2021 - “...ZMO0689 ), glutamate, histidine, and cysteine synthesis-related genes ( ZMO1117 , ZMO0457 , ZMO1964 , ZMO0783 , ZMO0782 , ZMO0784 ; ZMO0480 , ZMO1105 , ZMO1962 , ZMO0752 , ZMO1508 ; ZMO0005 , ZMO0007 , and ZMO0008 ), as well as ribosome protein-related genes ( ZMO0884...”
BL0403 glutamyl-tRNA amidotransferase subunit A from Bifidobacterium longum NCC2705
53% identity, 90% coverage
SP_0437 aspartyl/glutamyl-tRNA amidotransferase subunit A from Streptococcus pneumoniae TIGR4
50% identity, 95% coverage
PP0931 glutamyl-tRNA(Gln) amidotransferase, A subunit from Pseudomonas putida KT2440
53% identity, 96% coverage
PSYRMG_11680 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Pseudomonas syringae UMAF0158
52% identity, 96% coverage
ACIAD0823 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A from Acinetobacter sp. ADP1
51% identity, 97% coverage
Rv3011c glutamyl-tRNA amidotransferase subunit A from Mycobacterium tuberculosis H37Rv
55% identity, 95% coverage
- The efflux pumps Rv1877 and Rv0191 play differential roles in the protection of Mycobacterium tuberculosis against chemical stress
Sao, Frontiers in microbiology 2024 - “...al., 2020 ), rv0013 encoding a glutamine amido-transferase ( Bashiri et al., 2015 ) and rv3011c encoding a glutamyl-tRNA(GLN) amidotransferase-subunit A which were downregulated in the rv1877 and rv1878 mutants ( Supplementary Tables S3, S4 ). Moreover, few other genes involved in nitrogen metabolism were differentially...”
- Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex
Brenner, BMC medical genomics 2023 - “...Rv2922c Smc Probable chromosome partition protein Smc n/a 3,371,365 0 1 4100 2250 9 3 Rv3011c GatA Probable glutamyl-tRNA(GLN) amidotransferase (subunit A) GatA (Glu-ADT subunit A) In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Sassetti 2003; Griffin 2011) 3,534,980 0 1 4100 2250 9...”
- “...9 9 Rv2997 Possible alanine rich dehydrogenase Cys107Ser 3,371,365 0 0.998 4100 2250 9 3 Rv3011c GatA Probable glutamyl-tRNA(GLN) amidotransferase (subunit A) GatA (Glu-ADT subunit A) In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017; Minato 2019) Ala24Thr 3,388,682 0 0.951 4100 2100 161 1 Rv3029c...”
- Telacebec Interferes with Virulence Lipid Biosynthesis Protein Expression and Sensitizes to Other Antibiotics
Zhou, Microorganisms 2023 - “...0.01681 2.480604421 Rv1072 NA Transmembrane protein 0.0353 1.432802446 Rv1849 UreB Urease subunit beta 0.00076 0.150994385 Rv3011c GatA Glutamyl-tRNA amidotransferase subunit A 0.04319 0.738761056 Rv3290c Lat L-lysine-epsilon aminotransferase; catalytic activity: L-lysine + 2-oxoglutarate = 2-aminoadipate 6-semialdehyde + L-glutamate 0.04644 2.83040088 NA: not applicable. microorganisms-11-02469-t002_Table 2 Table 2...”
- Deficiency of D-alanyl-D-alanine ligase A attenuated cell division and greatly altered the proteome of Mycobacterium smegmatis
Chen, MicrobiologyOpen 2019 - “...Rv0768 51884.1 4.9 16 169 100 1509 0.19 Aspartyl/glutamyltRNA amidotransferase subunit A WP_003893733 .1 MSMEG_2365 Rv3011c 51240.8 4.99 16 322 100 1504 0.28 Cystathionine betasynthase CKI28531.1 MSMEG_5270 Rv1077 48750.9 5.03 12 281 100 3805 0.33 Phage shock protein PspA CKH69159.1 MSMEG_2695 Rv2744c 30273.2 5.55 16 231...”
- Comparative proteomic analysis of sequential isolates of Mycobacterium tuberculosis from a patient with pulmonary tuberculosis turning from drug sensitive to multidrug resistant
Singh, The Indian journal of medical research 2015 - “...the 27 upregulated proteins, eight were hypothetical protein (Rv2004c), probable glutamyl-tRNA (GLN) amidotransferase A gatA (Rv3011c), possible phosphoserine aminotransferase SerC (Rv0884c), probable lipase/esterase LipN (Rv2970c), probable phosphoglycerate kinase Pgk (Rv1437), conserved hypothetical protein with FHA domain, GarA (Rv1827), bacterioferritin (Rv1876) and conserved hypothetical protein (Rv0543) and...”
- Disruption of cell wall fatty acid biosynthesis in Mycobacterium tuberculosis using a graph theoretic approach
Baths, Theoretical biology & medical modelling 2011 - “...12 RV3280 11.5 RV2502C 11.5 RV3799C 11.5 RV0974C 11.5 RV2247 11.5 RV2888C 10 RV3375 10 RV3011C 10 RV1263 10 RV2363 10 RV1384 9 package nearnessindex; import java.util.Scanner; import java.util.regex .*; import java.io .*; /** * * @author Veeky */ public class Main { static double i,iT...”
- Mutually exclusive genotypes for pyrazinamide and 5-chloropyrazinamide resistance reveal a potential resistance-proofing strategy
Baughn, Antimicrobial agents and chemotherapy 2010 - “...protein homolog) Rv1263 (30%), Rv2363 (35%), Rv2888c (29%), Rv3011c (33%), Rv3175 (44%), and Rv3375 (35%). Although, this basal level of amidase activity was...”
- Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories
Ioerger, Journal of bacteriology 2010 - “...Rv2450c Rv2495c Rv2614A Rv2627c Rv2680 Rv2695 Rv2896c Rv2932 Rv3011c Rv3144c NC NC Rv3331 NC Rv3479 Rv3655c Rv3704c Rv3911 Rv3919c Gene VOL. 192, 2010 GENOMIC...”
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MSMEG_2365 glutamyl-tRNA(Gln) amidotransferase subunit A from Mycobacterium smegmatis str. MC2 155
WP_003893733 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Mycolicibacterium smegmatis MC2 51
53% identity, 99% coverage
gatA / Q9RTA9 glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7; EC 6.3.5.6) from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (see paper)
55% identity, 90% coverage
Q9X0Z9 glutaminyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.7) from Thermotoga maritima (see paper)
TM1272 glutamyl tRNA-Gln amidotransferase, subunit A from Thermotoga maritima MSB8
50% identity, 94% coverage
- PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence
Bharanikumar, PeerJ 2018 - “...exp(logStrength) Predicted class TM0373 ttgaca tataat Strong 4.6845788997 Strong TM1016 ttgaat tttaat Strong 0.3808572257 Strong TM1272 ttgaca tttaat Strong 1.6386551999 Strong TM1429 ttgaca tataat Strong 4.6845788997 Strong TM1667 ttgaaa tataat Strong 2.5859432664 Strong TM1780 ttcata tataat Strong 0.463878289 Strong Tmt11 ttgaat taaaat Strong 0.4665383797 Strong TM0032...”
- Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
Ovchinnikov, eLife 2014 - “...Joint Center for Structural Genomics (JCSG) 2006 , Crystal structure of Glutamyl-tRNA(Gln) amidotransferase subunit A (tm1272) from THERMOTOGA MARITIMA at 1.80 A resolution , 2GI3 ; http://dx.doi.org/10.2210/pdb2gi3/pdb , Publicly available at the RCSB Protein Data Bank. Lokanath NK , , RIKEN Structural Genomics/Proteomics Initiative (RSGI) 2007...”
- Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes
Dekhtyar, BMC bioinformatics 2008 - “...detected with the score parameters sUP = 13, s35 = 6, s10 = 5; TMt11, TM1272, TM0032 and TM1490 were detected with sUP = 12, s35 = 6, s10 = 5 and used for analysis in a cell-free system (see Fig. 3). We selected 13 candidate...”
- “...the reference P tac promoter (Fig. 4 ). The gene expression from the promoter P TM1272 was similar to that of P tac , whereas P TM0032 was reduced almost threefold. However, higher expression was detected from the other 11 promoters; the greatest expression level was...”
WD0505 glutamyl-tRNA(Gln) amidotransferase, A subunit from Wolbachia endosymbiont of Drosophila melanogaster
46% identity, 98% coverage
- Rapid evolution ofWolbachiagenomes in mosquito cell culture
Martinez, 2023 - Forward genetics in Wolbachia: Regulation of Wolbachia proliferation by the amplification and deletion of an addictive genomic island
Duarte, PLoS genetics 2021 - “...respectively. The copy number of three genes outside the Octomom region ( w Mel loci WD0505 , WD0519 , and rpoD ) were also determined. Five females carrying w MelCS_b, w MelPop2, and w MelOctoless were used in the analysis. The copy number of w MelPop2...”
- Parallel Sequencing of Wolbachia wCer2 from Donor and Novel Hosts Reveals Multiple Incompatibility Factors and Genome Stability after Host Transfers
Morrow, Genome biology and evolution 2020 - “...w Rec, and w Mel showed a contiguous sequence in w Cer2 joining homologs of WD0505 directly to WD0519, representing an indel of 23,772bp. Similarly, neither w Au nor w Rec contained the octomom region, but both included a sequence homologous to WD0506, and were contiguous...”
- Mutualism breakdown by amplification of Wolbachia genes
Chrostek, PLoS biology 2015 - “...), in the flanking repeated region ( WD0506/WD0515 ), in the immediately adjacent region ( WD0505 and WD0519 ), and in other locations of the chromosome ( wsp and rpoD ) in w MelCS_b (A) and w MelPop (B) (both in DrosDel isogenic background). The expression...”
- “...expression levels of Octomom gene WD0514 and genes outside Octomom ( wsp , rpoD , WD0505 , and WD0519 ) are not significantly different between the two Wolbachia variants. Relative expression for each gene is calculated using gmk as a reference gene and is relative to...”
- Wolbachia variants induce differential protection to viruses in Drosophila melanogaster: a phenotypic and phylogenomic analysis
Chrostek, PLoS genetics 2013 - “...Relative amounts of genomic copy number of Octomom genes (WD050614), genes adjacent to Octomom region (WD0505 and WD0519) and control gene rpoD in wMel, wMelCS_a, wMelCS_b and wMelPop were calculated using wsp as a reference gene. Values are relative to median of wMelCS_b samples. Each point...”
- “...the same relative amount in wMel, wMelCS_a, wMelCS_b. The genes immediately outside the Octomom region WD0505 and WD0519, as well as two other control genes located elsewhere in the genome, rpoD and gmk , show the same copy number in wMelPop and in the other wMel...”
- Distribution, expression, and motif variability of ankyrin domain genes in Wolbachia pipientis
Iturbe-Ormaetxe, Journal of bacteriology 2005 - “...in the wMel genome and anneal to single-copy genes (WD0505 and WD0523, respectively). Sequencing of ANK genes in the Wolbachia wAu strain. ANK genes from the...”
- “...by PCR amplification of the sequence between the single-copy WD0505 and WD0523 genes that flank this region. The distance between the PCR primers (P5 and P6)...”
GATA_ARATH / Q9LI77 Glutamyl-tRNA(Gln) amidotransferase subunit A, chloroplastic/mitochondrial; Glu-AdT subunit A; EC 6.3.5.7 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G25660 glutamyl-tRNA(Gln) amidotransferase, putative from Arabidopsis thaliana
50% identity, 87% coverage
- function: Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in chloroplasts and mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln).
catalytic activity: L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O = L-glutaminyl- tRNA(Gln) + L-glutamate + ADP + phosphate + H(+) (RHEA:17521)
subunit: Subunit of the heterotrimeric GatCAB amidotransferase (AdT) complex, composed of A, B and C subunits. - Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...Peptidyl-prolyl cis-trans isomerase CYP37 79 P82869, At3g15520 Synthesis Glutamyl-tRNA (Gln) amidotransferase subunit A 46, 47 Q9LI77, At3g25660 LIPID METABOLISM 3-oxoacyl-[acyl-carrier-protein] reductase 97 P33207, At1g24360 3-oxoacyl-[acyl-carrier-protein] synthase I 59, 85 P52410, At5g46290 Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta 47, 59 P56765, AtCg00500 Biotin carboxyl carrier protein...”
- Dissection of the IDA promoter identifies WRKY transcription factors as abscission regulators in Arabidopsis
Galindo-Trigo, Journal of experimental botany 2024 - “...S3 . The IDL1 promoter comprises 1557 bp between its TIS and the upstream gene AT3G25660 . The IDL2 promoter comprises 2084 bp upstream of its TIS. The IDL3 promoter comprises 1974 bp upstream of its TIS. The WRKY57 promoter covers 2071 bp upstream of its...”
- Beyond the Usual Suspects: Physiological Roles of the Arabidopsis Amidase Signature (AS) Superfamily Members in Plant Growth Processes and Stress Responses
Moya-Cuevas, Biomolecules 2021 - “...At4g34880 gene might function in leaf vascular tissues during sink-to-source transition [ 42 ], and At3g25660 likely interacts with the Glu-tRNA(Gln) amidotransferase subunit B (GAT-B) [ 43 ]. 2.1.1. AMI1 The Atypical Member of the Family The apparent molecular mass of AMI1 is around 45 kDa,...”
- Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...cis-trans isomerase CYP37 79 P82869, At3g15520 Synthesis Glutamyl-tRNA (Gln) amidotransferase subunit A 46, 47 Q9LI77, At3g25660 LIPID METABOLISM 3-oxoacyl-[acyl-carrier-protein] reductase 97 P33207, At1g24360 3-oxoacyl-[acyl-carrier-protein] synthase I 59, 85 P52410, At5g46290 Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta 47, 59 P56765, AtCg00500 Biotin carboxyl carrier protein of...”
- De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome
Munusamy, Scientific reports 2017 - “...analysis, and from previous studies, to be regulated by the miR156 21 22 . The AT3G25660 gene encodes an amidase family protein, and it is among those predicted to be translationally down-regulated under the impact of stress response in our Arabidopsis transgenic plants. It has a...”
- “...target regions between the miRNA and the mRNA target. As indicated in the results, gene AT3G25660 of YNdown group was predicted to bind to ath-miR5021 with complete complementarity in the central region of the binding site. Studies have discovered 31 49 that perfect complementarity in the...”
- Functional characterization of cis-elements conferring vascular vein expression of At4g34880 amidase family protein gene in Arabidopsis
Wu, PloS one 2013 - “...mtOM64 and Toc64-III proteins forms the first group. The second group consists of FAAH and At3g25660. Two remained proteins encoded by At5g07360 and At4g34880 branch directly from the origin [17] . To date, AMI1, one of the two known members so far in the AS family,...”
- Widespread dual targeting of proteins in land plants: when, where, how and why
Carrie, Plant signaling & behavior 2013 - “...thaliana Arabidopsis thaliana At3g25740 At3g56830 At3g25660 Arabidopsis thaliana Arabidopsis thaliana At3g55400 At3g23830 Arabidopsis thaliana Arabidopsis...”
- Using the Yeast Three-Hybrid System to Identify Proteins that Interact with a Phloem-Mobile mRNA
Cho, Frontiers in plant science 2012 - “...2E60 TC202398 10 #535 AT2G23610 ATMES3, MES3 | methyl esterase 3 5E41 TC221190 10 #537 AT3G25660 Amidase family protein 2E73 CV506455 50 #538 AT1G18080 ATARCA (Transducin/WD40 repeat-like superfamily protein) E118 TC197724 5 #539 AT2G31160 LSH3 | Protein of unknown function (DUF640) 1E54 CV502385 50 #542 AT2G42610...”
- “...#732 AT2G47730 Glutathione transferase belonging to the phi class of GSTs 4E69 TC218491 5 #733 AT3G25660 Amidase family protein 2E73 CV506455 5 #735 AT4G13350 NIG | NSP (nuclear shuttle protein)-interacting GTPase 4E07 TC200976 5 #736 AT1G07890 Cytosolic ascorbate peroxidase APX1 E116 TC195529 5 #737 AT4G14300 RNA-binding...”
- Reactive oxygen species and transcript analysis upon excess light treatment in wild-type Arabidopsis thaliana vs a photosensitive mutant lacking zeaxanthin and lutein
Alboresi, BMC plant biology 2011 - “...-1,14 248404_at AT5G51460 trehalose-6-phosphate phosphatase (TPPA) -1,13 248402_at AT5G52100 dihydrodipicolinate reductase family protein -1,13 256728_at AT3G25660 glutamyl-tRNA(Gln) amidotransferase -1,12 248663_at AT5G48590 expressed protein -1,12 245984_at AT5G13090 expressed protein -1,12 250663_at AT5G07110 prenylated rab acceptor (PRA1) -1,11 254011_at AT4G26370 antitermination NusB domain -1,10 261439_at AT1G28395 expressed protein...”
- More
LIMLP_07120 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Leptospira interrogans serovar Manilae
47% identity, 96% coverage
- Leptospira interrogans biofilm transcriptome highlights adaption to starvation and general stress while maintaining virulence
Davignon, NPJ biofilms and microbiomes 2024 - “...1.9), involved in ribosome biogenesis, and several genes involved in aminoacyl-tRNA biosynthesis, such as gatA (LIMLP_07120, FC 1.8), gatB (LIMLP_01160, FC 1.5), asnS (LIMLP_10110, FC 1.4), and thrS (LIMLP_12290, FC 1.6), also exhibited downregulation. This suggests a substantial decrease in translational activity during biofilm formation. However,...”
HVO_1054 aspartyl-tRNA(Asn) amidotransferase subunit A from Haloferax volcanii DS2
57% identity, 83% coverage
AF2329 Glu-tRNA amidotransferase, subunit A (gatA-2) from Archaeoglobus fulgidus DSM 4304
49% identity, 92% coverage
CPn0003 Glu tRNA Gln Amidotransferae (A subunit) from Chlamydophila pneumoniae CWL029
CP0772 glutamyl-tRNA amidotransferase subunit A from Chlamydophila pneumoniae AR39
47% identity, 92% coverage
CAB286 glutamyl-tRNA amidotransferase subunit A from Chlamydophila abortus S26/3
46% identity, 96% coverage
SSO0957 Glutamyl-tRNA amidotransferase, subunit A (gatA-2) from Sulfolobus solfataricus P2
42% identity, 97% coverage
FTL_1842 Glutamyl-tRNA(Gln) amidotransferase subunit A from Francisella tularensis subsp. holarctica
44% identity, 93% coverage
- Francisella tularensis: FupA mutation contributes to fluoroquinolone resistance by increasing vesicle secretion and biofilm formation
Siebert, Emerging microbes & infections 2019 - “...106.53 8,1905E-06 7,66110499 4,451,26 FTL_1835 Bcr/CflA family drug resistance efflux transporter 10.788 4,2138E-05 4,74375095 2,450,50 FTL_1842 Aspartyl/glutamyl-tRNA amidotransferase subunit A 25.759 0,00070266 3,29921922 3,50,37 FTL_0146 ABC transporter, ATP-binding protein 66.127 0,00103677 2,64293944 1,890,38 FTL_0012 Recombinase A 23.,629 0,00127529 3,38036766 1,860,48 FTL_1644 Glycerol kinase 1.5761 0,001313 3,18959478...”
- “...The LVS fupA/B OMVs also contained more proteins playing a role in replication (FTL_1025, FTL_1407, FTL_1842, FTL_1850, and FTL_1931), glycerolipid (FTL_1644), carbohydrate (FTL_1591 and FTL_1899), and cofactor and vitamin (FTL_1274) metabolism. Some of the differentially-expressed proteins identified may play a direct role in the antibiotic-resistance phenotype...”
Q9LCX3 Glutamyl-tRNA(Gln) amidotransferase subunit A from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
50% identity, 95% coverage
3kfuE / Q9LCX3 Crystal structure of the transamidosome (see paper)
50% identity, 95% coverage
jhp0769 GLU-TRNA AMIDOTRANSFERASE, SUBUNIT A from Helicobacter pylori J99
47% identity, 83% coverage
Q0VFI5 Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial from Xenopus tropicalis
40% identity, 91% coverage
- Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.
Hathazi, The EMBO journal 2020 - “...mouse (Q9CXJ1, Q9DAR5, Q9CZN8, P05202, D3Z7P3), zebrafish (Q0P499, Q503J2, F1QAJ4, Q7SYK7, Q8JFS4), frog (Q66JG3, F6TJB0, Q0VFI5, Q28F67, F7B417) and chicken (Q5ZJ66, Q5ZKW0, F1NLA0, P00508, A0A1D5PNV1). Schematic diagram of affected proteins showing their contribution to (i) mitochondrial protein translation (EARS2 which aminoacylates mttRNA Glu and mttRNA Gln...”
HP0830 Glu-tRNA(Gln) amidotransferase, subunit A (gatA) from Helicobacter pylori 26695
P56114 Glutamyl-tRNA(Gln) amidotransferase subunit A from Helicobacter pylori (strain ATCC 700392 / 26695)
48% identity, 83% coverage
- The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
Xu, Frontiers in microbiology 2021 - “...fecA 1.1454 HP0810 rsmD 1.102 HP0811 Predicted gene 2.0849 HP0824 ahpc 1.201 HP0829 guaB 1.6093 HP0830 gatA 2.1157 HP0834 engA 1.0829 HP0876 frpB 2.1815 HP0959 Predicted gene 1.1905 HP0960 glyQ 1.6042 HP0961 gpsA 3.3854 HP0983 Predicted gene 1.2053 HP1023 Predicted gene 1.1999 HP1029 Predicted gene 1.2139...”
- Aconitase Functions as a Pleiotropic Posttranscriptional Regulator in Helicobacter pylori
Austin, Journal of bacteriology 2015 - “...HP0232 HP0630 HP0620 HP0310 HP1275 HP0835 HP1495 HP0830 HP0110 HP1196 Unregulated membrane proteins HP1205 HP1501 HP1562 Protein description Mean fold change...”
- Acid-induced gene expression in Helicobacter pylori: study in genomic scale by microarray
Ang, Infection and immunity 2001 - “...of the NADH-ubiquinone oxidoreductase NQO4 subunit, (iv) HP0830, which encodes the GlutRNA amidotransferase A subunit; (v) HP0232, which encodes a secreted...”
- “...HP0588 HP0911 HP1304 HP1104 HP1470 HP0196 HP0214 HP0743 HP0830 HP0331 HP0237 HP0265 HP0295 HP1209 HP1050 HP1539 HP1540 HP1035 HP0680 HP0786 HP0103 HP1069 HP1543...”
- Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis
Chalker, Journal of bacteriology 2001 - “...vitro. In five cases (HP1140 [birA], HP0657 [ymxG], HP0830 [gatA], HP0658 [gatB], and HP0975 [gatC]) this analysis represents to our knowledge the first...”
- Metabolism and genetics of Helicobacter pylori: the genome era
Marais, Microbiology and molecular biology reviews : MMBR 1999 - “...al. (3) have proposed an alternative mechanism involving HP0830, HP0658, and HP0975, homologous to the gatABC genes of B. subtilis, whose products amidate...”
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25995 HP_1457 88 P96786 fliD 89 O26084 HP_1564 90 O25993 HP_1454 91 O25158 HP_0397 92 P56114 gatA 93 P56109 fba 94 O25825 HP_1227 95 O25856 NQO3 96 O34523 Omp29 97 O25927 lpxA 98 O25134 HP_0370 99 O25399 HP_0690 100 P56029 rplA 101 O25738 HP_1110 102 O25414...”
- “...P56458 serS 168 O25372 gatB 169 O24950 HP_0138 170 O25373 HP_0659 171 O25998 HP_1462 172 P56114 gatA 173 O25546 HP_0879 174 O25668 CbpA 175 P56067 cysM 176 O25469 HP_0780 177 O25249 pgbA 178 O25069 DppA 179 O25873 HP_1286 180 O25230 HP_0486 181 O24909 HP_0080 182 P56106...”
Hbut_0594 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA from Hyperthermus butylicus DSM 5456
48% identity, 92% coverage
- The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota
Anderson, BMC genomics 2009 - “...of the three to have an Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase, but the A subunit of this enzyme (Hbut_0594) has a frameshift. Since this appears to be an essential enzyme for H. butylicus , the gene may still be functional. Discussion The crenarchaeotes H. butylicus , S. marinus ,...”
- The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C
Brügger, Archaea (Vancouver, B.C.) 2007 - “...produced from phenylalanine via 2-phenylacetamid (Hbut_0228 and Hbut_0594), but since no mechanism is known for converting the fermentation product...”
GATA_HUMAN / Q9H0R6 Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial; Glu-AdT subunit A; Glutaminyl-tRNA synthase-like protein 1; EC 6.3.5.7 from Homo sapiens (Human) (see 3 papers)
Q9H0R6 glutaminyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.7) from Homo sapiens (see paper)
NP_060762 glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial from Homo sapiens
38% identity, 89% coverage
- function: Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln).
catalytic activity: L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O = L-glutaminyl- tRNA(Gln) + L-glutamate + ADP + phosphate + H(+) (RHEA:17521)
subunit: Subunit of the heterotrimeric GatCAB amidotransferase (AdT) complex, composed of A (QRSL1), B (GATB) and C (GATC) subunits - Genetic defects in mtDNA-encoded protein translation cause pediatric, mitochondrial cardiomyopathy with early-onset brain disease.
Kamps, European journal of human genetics : EJHG 2018 - GeneRIF: Homozygous intronic variant (c.850-3A > G) in the QRSL1 was identified in a child with cardiomyopathy with early-onset brain disease.
- Identification of N-acylethanolamines in Dictyostelium discoideum and confirmation of their hydrolysis by fatty acid amide hydrolase
Hayes, Journal of lipid research 2013 - “...as glutamyl-tRNA tained for Homo sapiens (NP_060762), Mycobacterium tuberculosis (NP_335746), Archaeoglobus fulgidus DSM 4304 (NP_070778), and Plasmodium...”
- Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Hendrickson, PloS one 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Biogenesis of glutaminyl-mt tRNAGln in human mitochondria.
Nagao, Proceedings of the National Academy of Sciences of the United States of America 2009 - GeneRIF: Studies showed in vitro Gln-tRNA(Gln) formation catalyzed by the recombinant mtGluRS and hGatCAB.
- Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts.
Vieira, Genetics in medicine : official journal of the American College of Medical Genetics 2008 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.
Hathazi, The EMBO journal 2020 - “...across species using Jalview software. Analysis was performed using protein sequences from human (Q5JPH6, O75648, Q9H0R6, P00505, O94925), mouse (Q9CXJ1, Q9DAR5, Q9CZN8, P05202, D3Z7P3), zebrafish (Q0P499, Q503J2, F1QAJ4, Q7SYK7, Q8JFS4), frog (Q66JG3, F6TJB0, Q0VFI5, Q28F67, F7B417) and chicken (Q5ZJ66, Q5ZKW0, F1NLA0, P00508, A0A1D5PNV1). Schematic diagram of...”
- Pathogenic variants in glutamyl-tRNAGln amidotransferase subunits cause a lethal mitochondrial cardiomyopathy disorder
Friederich, Nature communications 2018 - “...Structural modeling of the human GatCAB complex Amino acid sequences of the GatC (O43716), GatA (Q9H0R6), and GatB (O75879) subunits were retrieved from UniProt 55 and parsed through SWISS-MODEL 56 to search for modeling templates. Templates were chosen considering coverage and identity: GatC was modelled to...”
Q9CZN8 glutaminyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.7) from Mus musculus (see paper)
38% identity, 90% coverage
- Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.
Hathazi, The EMBO journal 2020 - “...was performed using protein sequences from human (Q5JPH6, O75648, Q9H0R6, P00505, O94925), mouse (Q9CXJ1, Q9DAR5, Q9CZN8, P05202, D3Z7P3), zebrafish (Q0P499, Q503J2, F1QAJ4, Q7SYK7, Q8JFS4), frog (Q66JG3, F6TJB0, Q0VFI5, Q28F67, F7B417) and chicken (Q5ZJ66, Q5ZKW0, F1NLA0, P00508, A0A1D5PNV1). Schematic diagram of affected proteins showing their contribution to...”
Q5FWT5 Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial from Rattus norvegicus
38% identity, 90% coverage
- The mitochondrial proteomic changes of rat hippocampus induced by 28-day simulated microgravity.
Ji, PloS one 2022 - “...Hibadh 3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.66 0.001062 MESD_RAT Q5U2R7 Mesd LRP chaperone MESD 1.65 0.010713 GATA_RAT Q5FWT5 Qrsl1 Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial 1.65 0.014454 FUMH_RAT P14408 Fh Fumarate hydratase, mitochondrial 1.65 0.000491 A0A0G2K9G3_RAT A0A0G2K9G3 Mrps24 Mitochondrial ribosomal protein S24 1.65 0.00209 D4ADD7_RAT D4ADD7 Glrx5 Glutaredoxin 5...”
F1QAJ4 Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial from Danio rerio
36% identity, 90% coverage
- Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.
Hathazi, The EMBO journal 2020 - “...human (Q5JPH6, O75648, Q9H0R6, P00505, O94925), mouse (Q9CXJ1, Q9DAR5, Q9CZN8, P05202, D3Z7P3), zebrafish (Q0P499, Q503J2, F1QAJ4, Q7SYK7, Q8JFS4), frog (Q66JG3, F6TJB0, Q0VFI5, Q28F67, F7B417) and chicken (Q5ZJ66, Q5ZKW0, F1NLA0, P00508, A0A1D5PNV1). Schematic diagram of affected proteins showing their contribution to (i) mitochondrial protein translation (EARS2 which...”
NP_650775 Glutamyl-tRNA amidotransferase, subunit A from Drosophila melanogaster
41% identity, 86% coverage
O69768 Amidase from Pseudomonas putida
40% identity, 96% coverage
GATA_YEAST / Q03557 Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial; Glu-AdT subunit A; HMG2-induced ER-remodeling protein 2; Loss of respiratory capacity protein 6; EC 6.3.5.7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
YMR293C Lrc6p from Saccharomyces cerevisiae
NP_014021 glutamyl-tRNA(Gln) amidotransferase subunit HER2 from Saccharomyces cerevisiae S288C
35% identity, 91% coverage
- function: Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). Required for HMG2-induced ER-remodeling.
catalytic activity: L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O = L-glutaminyl- tRNA(Gln) + L-glutamate + ADP + phosphate + H(+) (RHEA:17521)
subunit: Subunit of the heterotrimeric GatFAB amidotransferase (AdT) complex, composed of A (HER2), B (PET112) and F (YGR102C) subunits - Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae
Stenger, Microbial cell (Graz, Austria) 2020 - “...PET112 YBL080C GEP3 YOR205C MRPL33 YMR286W PET122 YER153C GEP5 YLR091W MRPL36 YBR122C PET123 YOR158W HER2 YMR293C MRPL37 YBR268W PET309 YLR067C IFM1 YOL023W MRPL38 YKL170W PET494 YNR045W IMG1 YCR046C MRPL4 YLR439W PET54 YGR222W IMG2 YCR071C MRPL40 YPL173W RMD9 YGL107C MEF1 YLR069C MRPL49 YJL096W RML2 YEL050C MEF2 YJL102W...”
- “...RNA maturation AIM10 YER087W MRPL13 YKR006C MSF1 YPR047W GEP3 YOR205C MRPL22 YNL177C MTG1 YMR097C HER2 YMR293C MRPL32 YCR003W PET111 YMR257C IFM1 YOL023W MRPL38 YKL170W PET112 YBL080C IMG2 YCR071C MRPL6 YHR147C QRI5 YLR204W MHR1 YDR296W MRPL9 YGR220C RSM7 YJR113C MRF1 YGL143C MRPS5 YBR251W MRM1 YOR201C MSE1 YOL033W...”
- Trans-kingdom rescue of Gln-tRNAGln synthesis in yeast cytoplasm and mitochondria
Liao, Nucleic acids research 2012 - “...cytoplasmic GlnRS was encoded by the test plasmid. Complementation assays for mitochondrial GluAdT activity The Ymr293c (gene encoding GatA) knockout strain was purchased from Open Biosystems (Lafayette, CO, USA) and maintained by a plasmid carrying the wild-type GatA gene and a URA3 marker. Complementation assays for...”
- Genome-wide metabolic (re-) annotation of Kluyveromyces lactis
Dias, BMC genomics 2012 - “...versus KEGG annotation Gene KEGG New annotation S. cerevisiae homologue Protein KLLA0A09845g 6.3.5.6, 6.3.5.7 6.3.5.7 YMR293C glutamyl-tRNA(Gln) amidotransferase KLLA0E20659g 6.3.5.6, 6.3.5.7 6.3.5.7 YBL080C glutamyl-tRNA(Gln) amidotransferase KLLA0B07513g 2.7.1.105, 3.1.3.46 3.1.3.46 YJL155C fructose-2,6-bisphosphatase KLLA0E07173g 4.2.1.51, 5.4.99.5 4.2.1.51 YNL316C prephenate dehydratase KLLA0E10143g 3.1.3.12, 2.4.1.15 3.1.3.12 YDR074W trehalose-phosphatase KLLA0F20548g 2.6.1.19,...”
- Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism
Rintala, Omics : a journal of integrative biology 2011 - “...YMR166C) and genes related to respiration (COQ10, DIA4, MAM33, YMR293C, COX23, ATP12, ATP11, COX17). Genes in this cluster were also enriched in the PUF3 30 UTR...”
- Yeast mitochondrial Gln-tRNA(Gln) is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS
Frechin, Genes & development 2009 - “...the Pet112-TAP fusion protein. These two interactants are Ymr293c and Ygr102c. Ymr293c is annotated as being an amidase that displays an amidohydrolase...”
- “...previously (Bailly et al. 2007). Genome Database). In addition, YMR293C has recently been renamed HER2 (Hmg2p ER remodeling) because it has been reported to be...”
- Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae
Merz, Genome biology 2009 - “...highly penetrant pet genes ( YDR065w , YGR150c , YJL046w , YLL033w , YLR091w , YMR293c , YOR305w , and YPR116w ) encode previously uncharacterized proteins, and earlier studies have revealed a respiratory-deficient phenotype for two additional ORFs of unknown function that were not covered by...”
- “...(GEP5) YLR091w [ 6 , 34 , 35 ] - - Absent Absent RRG6 (HER2) YMR293c [ 6 , 34 , 35 ] - - Altered Absent RRG7 YOR305w [ 35 ] + + ND ND RRG8 YPR116w [ 35 ] - - Altered Absent RRG9...”
- Biogenesis of glutaminyl-mt tRNAGln in human mitochondria
Nagao, Proceedings of the National Academy of Sciences of the United States of America 2009 - “...in mitochondria (29). A null mutant of YMR293c exhibited abnormal mitochondrial morphology (6) and respiratory defects (28). Although an apparent homolog...”
- The genetic interactome of prohibitins: coordinated control of cardiolipin and phosphatidylethanolamine by conserved regulators in mitochondria
Osman, The Journal of cell biology 2009 - “...IMS SL GEP3 YOR205c M GD GEP4 YHR100c M SL GEP5 YLR091w M GD GEP6 YMR293c M SL GEP7 YGL057c M GD GEP8 YER093c-A ND SL GEP9 YNL170w ND SL Diverse PSD1 a YNL169c IM SL CRD1 b YDL142c IM SL HMI1 YOL095c IM/MA GD MRE11...”
- More
- Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases.
Araiso, Nucleic acids research 2014 - GeneRIF: The crystal structure of yeast mitochondrial GatFAB complex.
- Mutations in the Drosophila mitochondrial tRNA amidotransferase, bene/gatA, cause growth defects in mitotic and endoreplicating tissues
Morris, Genetics 2008 - “...human-- CAB66614; yeast (S. cerevisiae)-- Q03557; bacteria (the cyanobacteria, Prochlorococcus marinus)--YP_291459. Arrows signify lesions in gatA...”
4n0iA / Q03557 Crystal structure of s. Cerevisiae mitochondrial gatfab in complex with glutamine (see paper)
37% identity, 83% coverage
- Ligand: glutamine (4n0iA)
MMP1510 Asp-tRNAAsn/Glu-tRNAGln amidotransferase subunit A from Methanococcus maripaludis S2
35% identity, 92% coverage
I7FF89 Amidase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
A0QRE7 Amidase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_1090 amidase from Mycobacterium smegmatis str. MC2 155
36% identity, 97% coverage
- Identification of a mycobacterial hydrazidase, an isoniazid-hydrolyzing enzyme.
Sakiyama, Scientific reports 2023 - “...using peptide mass fingerprinting. The MASCOT search identified an amidase named PzaA (UniProtKB accession number: I7FF89) as the most probable candidate. The recovery rate was 64% (Supplementary Data S1 ). This enzyme is known to hydrolyze pyrazinamide and nicotinamide, but its physiological role remains unknown. To...”
- Cell Wall Proteomics Reveal Phenotypic Adaption of Drug-Resistant Mycobacterium smegmatis to Subinhibitory Rifampicin Exposure.
Giddey, Frontiers in medicine 2021 - “...0.013 1.432 CD A0QNH6 SaeC Putative ESX-1 scaffolding and assembly protein SaeC 0.042 1.293 CD A0QRE7 MSMEG_1090 Amidase 0.006 1.291 CD A0R3Y8 MSMEG_5642 Acetyl-coenzyme a carboxylase carboxyl transferase 0.039 1.237 CD A0R3I6 MSMEG_5486 Peptidase S1 and S6, chymotrypsin/Hap 0.002 1.111 CD A0R3U0 MSMEG_5593 Pyruvate dehydrogenase 0.034...”
- Cell Wall Proteomics Reveal Phenotypic Adaption of Drug-Resistant Mycobacterium smegmatis to Subinhibitory Rifampicin Exposure
Giddey, Frontiers in medicine 2021 - “...1.432 CD A0QNH6 SaeC Putative ESX-1 scaffolding and assembly protein SaeC 0.042 1.293 CD A0QRE7 MSMEG_1090 Amidase 0.006 1.291 CD A0R3Y8 MSMEG_5642 Acetyl-coenzyme a carboxylase carboxyl transferase 0.039 1.237 CD A0R3I6 MSMEG_5486 Peptidase S1 and S6, chymotrypsin/Hap 0.002 1.111 CD A0R3U0 MSMEG_5593 Pyruvate dehydrogenase 0.034 1.100...”
- Nitrogen starvation-induced transcriptome alterations and influence of transcription regulator mutants in Mycobacterium smegmatis
Jeßberger, BMC research notes 2013 - “...msmeg_6264 5.06 Putative oxidoreductase msmeg_2523 5.11 Efflux ABC transporter, permease protein, putative msmeg_4381 5.14 Amidase msmeg_1090 5.24 Amidase msmeg_1508 5.54 Amino acid permease-associated region msmeg_5729 5.75 Hydantoin racemase msmeg_6733 6.32 Hydrolase, carbon-nitrogen family msmeg_2748 6.36 Soluble pyridine nucleotide transhydrogenase ( sthA ) msmeg_1085 6.41 Dipeptide transport...”
- “...unspecific or no binding. Binding was not detected for the nirB, msmeg_1052 , msmeg_1084 , msmeg_1090 , msmeg_1293 , msmeg_2748 , msmeg_2981 , msmeg_4638 , narK , msmeg_5734 , glnR , msmeg_6258 , msmeg_6734 and msmeg_6816 upstream region (Figure 4 B). In these cases, longer DNA...”
- Mutually exclusive genotypes for pyrazinamide and 5-chloropyrazinamide resistance reveal a potential resistance-proofing strategy
Baughn, Antimicrobial agents and chemotherapy 2010 - “...mc2155 MSMEG_1088::magellan4 mc2155 MSMEG_1088 mc27031 MSMEG_1090 mc2155 MSMEG_1090 mc22612 MSMEG_1090 Spontaneous 5-Cl PZAr mutant mc2155...”
- “...(mc27031 and mc27032, respectively) and after deletion of MSMEG_1090 (pzaA) from strains mc27031 (mc27034) and 155 (mc27035). derivatized using an Alltech kit...”
CNBD1400 hypothetical protein from Cryptococcus neoformans var. neoformans B-3501A
39% identity, 82% coverage
- Novel and unique domains in aminoacyl-tRNA synthetases from human fungal pathogens Aspergillus niger, Candida albicans and Cryptococcus neoformans
Datt, BMC genomics 2014 - “...Asn synthase CNBK3010 Mito 572 1.7e-196 34 Asn synthase CNBL0870 Mito 592 1.6e-65 34 GatA CNBD1400 Mito 493 1.7e-119 33 GatB CNBG4210 Mito 521 1.7e-176 37 NA in e-value indicates fungal sequences that could be identified by HMM search and were retrieved from NCBI using keyword...”
- “...amidotransferases activity two Asn synthases (CNBK3010 and CNBL0870) and other two Gln synthases (subunit A (CNBD1400) and subunit B (CNBG4210)). We were not able to identify any homolog for GatF subunit. Interestingly, all these four amidotranferases were predicted to localize within the mitochondria (Table 3 )....”
atzE / Q936X3 1-carboxybiuret hydrolase catalytic subunit (EC 3.5.1.3; EC 3.5.1.131) from Pseudomonas sp. (strain ADP) (see 2 papers)
ATZE_PSESD / Q936X3 1-carboxybiuret hydrolase subunit AtzE; EC 3.5.1.131 from Pseudomonas sp. (strain ADP) (see 2 papers)
Q936X3 1-carboxybiuret hydrolase (EC 3.5.1.131) from Pseudomonas sp. ADP (see paper)
6c6gA / Q936X3 An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. Inhibitor bound complex. (see paper)
39% identity, 94% coverage
- function: Hydrolyzes 1-carboxybiuret to urea-1,3-dicarboxylate and NH(3).
catalytic activity: 1-carboxybiuret + H2O = urea-1,3-dicarboxylate + NH4(+) (RHEA:58900)
subunit: Heterotetramer consisting of 2 AtzE and 2 AtzG subunits. - Ligand: calcium ion (6c6gA)
MPN237 Glu-tRNA amidotransferase, subunit A (gatA) from Mycoplasma pneumoniae M129
33% identity, 86% coverage
PFLU3208 putative glutamyl-tRNA amidotransferase subunit A from Pseudomonas fluorescens SBW25
37% identity, 81% coverage
AMDA_RHIRD / Q9AHE8 Urethanase; Enantioselective amidase; Ethyl carbamate-degrading amidase; EC 3.5.1.75 from Rhizobium radiobacter (Agrobacterium tumefaciens) (Agrobacterium radiobacter) (see 3 papers)
35% identity, 78% coverage
- function: Hydrolase that can catalyze the degradation of ethyl carbamate (also called urethane), a probable human carcinogen widely found in alcoholic beverages (PubMed:34148792, PubMed:35653287). Can also use methyl carbamate, butyl carbamate, acetamide and urea (PubMed:34148792, PubMed:35653287). Also catalyzes the enantioselective hydrolysis of 2-phenylpropionamide, alpha-chlorophenylacetamide, 2- methyl-3-phenylpropionamide and alpha-methoxyphenylacetamide to the corresponding acids (PubMed:11429459). Is inactive on benzamide and L- glutamine (PubMed:34148792).
catalytic activity: urethane + H2O + H(+) = ethanol + NH4(+) + CO2 (RHEA:21372)
subunit: Homooctamer.
Psyr_2208 Amidase from Pseudomonas syringae pv. syringae B728a
36% identity, 81% coverage
NEQ360 NEQ360 from Nanoarchaeum equitans Kin4-M
36% identity, 83% coverage
P22984 amidase (EC 3.5.1.4) from Rhodococcus erythropolis (see 2 papers)
Q7DKE4 amidase (EC 3.5.1.4) from Rhodococcus sp. N-771 (see paper)
amdA / AAA62721.1 enantiomer-selective amidase from Brevibacterium sp (see paper)
CAA38009.1 amidase from Rhodococcus sp (see paper)
39% identity, 80% coverage
3a1iA / Q7DKE4 Crystal structure of rhodococcus sp. N-771 amidase complexed with benzamide (see paper)
38% identity, 82% coverage
- Ligand: benzamide (3a1iA)
MG_099 glutamyl-tRNA amidotransferase subunit A from Mycoplasma genitalium G37
31% identity, 85% coverage
- Transcriptional response of Mycoplasma genitalium to osmotic stress
Zhang, Microbiology (Reading, England) 2011 - “...MG_097 Uracil-DNA glycosylase, putative 3.68 0.00002 0.00136 MG_098 Glutamyl-tRNA/aspartyl-tRNA amidotransferase, C subunit 3.60 0.00014 0.00136 MG_099 Glutamyl-tRNA/aspartyl-tRNA amidotransferase, A subunit 2.53 0.00589 0.00246 MG_149* Lipoprotein, putative 9.98 0.00001 0.00136 MG_478* Conserved hypothetical protein, previously MG_149.1 5.30 0.00001 0.00136 MG_240 Conserved hypothetical protein 2.87 0.00219 0.00156 MG_248...”
B1GY01 nitrilase (EC 3.5.5.1) from Rhodococcus erythropolis (see paper)
38% identity, 79% coverage
B4XEY3 Amidase (Fragment) from Rhodococcus erythropolis
38% identity, 79% coverage
- Metabolic perceptrons for neural computing in biological systems
Pandi, Nature communications 2019 - “...identifier: UniProtKB - Q52036 Benzamide transforming enzyme (Amidase (EC: 3.5.1.4), Rhodococcus erythropolis) identifier: UniProtKB - B4XEY3 Sequence and source of all the genes and parts are available in Supplementary Table 5 and the plasmids used in this study (Addgene deposit) are listed in Supplementary Table 6...”
ECA3499 probable amidase from Erwinia carotovora subsp. atroseptica SCRI1043
35% identity, 96% coverage
- Enterobacterial small mobile sequences carry open reading frames and are found intragenically--evolutionary implications for formation of new peptides
Delihas, Gene regulation and systems biology 2007 - “...present in these loci. Gene loci shown represent large proteins that have conserved domains ( ECA3499 , amidase and ECA0168 , L-threonine 3-dehydrogenase), unique open reading frames displaying sequence similarities to conserved motifs ( YPO3245 hypothetical protein with PapB motif and PLU3667 hypothetical protein, HlyD motif),...”
- “...the consensus repeat RU-1 sequence and the SeRU-1 in S. enterica were used. E. carotovora, ECA3499 (amidase) ECA3499 encodes a predicted 496 amino acid amidase in Erwinia carotovora subsp. atroseptica SCRI1043 ( Bell et al. 2004 ). The ECA3499 sequence displays a conserved amidase domain that...”
MKK01_RS13030 amidase from Klebsiella variicola subsp. variicola
36% identity, 82% coverage
Rv3375 PROBABLE AMIDASE AMID (ACYLAMIDASE) (ACYLASE) from Mycobacterium tuberculosis H37Rv
BCG_3446 putative amidase amiD from Mycobacterium bovis BCG str. Pasteur 1173P2
37% identity, 97% coverage
- Enhancement of mycobacterial pathogenesis by host interferon-γ
Hop, Cellular and molecular life sciences : CMLS 2024 - “...examined whether IFN could directly modulate the expression of their homologs, PpsB (Rv2932) and AmiD (Rv3375) in M. tuberculosis. We cultured M. tuberculosis in the presence of 10g/ml BSA, IFN or TNF, and analyzed the expression of PpsB and AmiD at different time points by immunoblotting....”
- Proteomics of Culture Filtrate of Prevalent Mycobacterium tuberculosis Strains: 2D-PAGE Map and MALDI-TOF/MS Analysis
Kumar, SLAS discovery : advancing life sciences R & D 2017 (PubMed)- “...desorption ionization-time-of-flight mass spectrometry. As a result, we could identify 12 CF proteins (Rv0066c, Rv1310, Rv3375, Rv1415, Rv0567, Rv1886c, Rv3803c, Rv3804c, Rv2031c, Rv1038c, Rv2809, and Rv1911c), which were consistently increased in all prevalent M. tuberculosis strains, and interestingly, two CF proteins (Rv2809, Rv1911c) were identified with...”
- A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
Bhagavat, Scientific reports 2017 - “...of F1 ATP synthase-like Rv1293 Diaminopimelate decarboxylase LysA (DAP decarboxylase) 5 Amidase signature (AS) enzymes Rv3375 Probable amidase AmiD (acylamidase) (acylase) 6 ClpP/crotonase Rv2486 Probable enoyl-CoA hydratase EchA14 (enoyl hydrase) 7 Rhodanese/Cell cycle control phosphatase Rv2291 Probable thiosulfate sulfurtransferase SseB 8 alpha/beta-Hydrolases Rv1683 Possible bifunctional enzyme;...”
- Combining cheminformatics methods and pathway analysis to identify molecules with whole-cell activity against Mycobacterium tuberculosis
Sarker, Pharmaceutical research 2012 - “...(Rv1568), bioF1 (Rv1569), bioB (Rv1589), argJ (Rv1653), pks12 (Rv2048c), plsC (Rv2483c), Rv2857c, ddlA (Rv2981c), amiD (Rv3375), fabG (Rv3502c), fadA6 (Rv3556c), and hycD (Rv0084) belong to more than one TBCyc pathway. From the reactions catalyzed by the corresponding essential enzymes, substrate metabolites were identified. Their 2D structures,...”
- Disruption of cell wall fatty acid biosynthesis in Mycobacterium tuberculosis using a graph theoretic approach
Baths, Theoretical biology & medical modelling 2011 - “...14.5 RV0263C 12 RV3280 11.5 RV2502C 11.5 RV3799C 11.5 RV0974C 11.5 RV2247 11.5 RV2888C 10 RV3375 10 RV3011C 10 RV1263 10 RV2363 10 RV1384 9 package nearnessindex; import java.util.Scanner; import java.util.regex .*; import java.io .*; /** * * @author Veeky */ public class Main { static...”
- Mutually exclusive genotypes for pyrazinamide and 5-chloropyrazinamide resistance reveal a potential resistance-proofing strategy
Baughn, Antimicrobial agents and chemotherapy 2010 - “...(35%), Rv2888c (29%), Rv3011c (33%), Rv3175 (44%), and Rv3375 (35%). Although, this basal level of amidase activity was sufficient for utilization of...”
- Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis
Veyrier, BMC evolutionary biology 2009 - “...of a virulence locus, not yet functionally characterized, acquired via horizontal genes transfer . The Rv3375 locus is represented from Rv3374 to Rv3381c, genes colored in black are those detect as HGT (or HGT vehicle). A graphical representation of the GC content, across a 100 Kb...”
- “...acquisition in two of three lineages. The last example presented in Figure 5 is the Rv3375 locus, which comprises the insertion of two clusters of foreign genes (two genes acquired in list C and three genes acquired in List D). Again, there are transposase elements close...”
- Gene deletions in Mycobacterium bovis BCG stimulate increased CD8+ T cell responses
Panas, Infection and immunity 2014 - “...complementation of the operon containing the BCG_3445 and BCG_3446 genes. (C) Primary SIINFEKLspecific CD8 T cell responses at day 7 induced by the ICO...”
- “...**, P 0.01. operon containing echA18 (BCG_3445) and amiD (BCG_3446), which we complemented by using a cloned fragment that included both genes as well as their...”
MSMEG_1088 glutamyl-tRNA(Gln)/aspartyl-tRNA(Asn) amidotransferase, A subunit from Mycobacterium smegmatis str. MC2 155
38% identity, 95% coverage
I4W82_22600 amidase from Klebsiella michiganensis
35% identity, 82% coverage
ACIAD1618 amidase from Acinetobacter sp. ADP1
34% identity, 83% coverage
- iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
Jiang, Frontiers in microbiology 2019 - “...ACIAD1286 0.48 0.63 0.76 0.63 Succinylglutamate desuccinylase astE ACIAD1289 0.17 0.82 0.69 0.66 Amidase amdA ACIAD1618 0.68 0.06 0.58 0.27 Acetyl-CoA acetyltransferase dcaF ACIAD1689 0.43 0.69 0.54 0.53 Polyphosphate kinase ppk ACIAD1782 0.77 0.51 0.36 0.48 Tellurium resistance protein terZ ACIAD1952 0.68 0.65 0.81 0.7 Tellurium...”
- “...lysS ACIAD1069 0.51 0.72 0.61 0.56 Cyanophycin synthetase ACIAD1279 0.19 0.12 0.23 0.23 Amidase amdA ACIAD1618 0.68 0.06 0.58 0.27 CTP synthetase pyrG ACIAD2003 0.82 0.74 0.62 0.7 Bifunctional biotin carboxylase/biotin carboxyl carrier protein bccA ACIAD2517 0.52 0.48 0.67 0.59 Pantoatebeta-alanine ligase panC ACIAD3060 0.79 0.82...”
cahA / BAC15598.1 carbaryl hydrolase from Arthrobacter sp. RC100 (see paper)
37% identity, 90% coverage
PputUW4_03350 amidase from Pseudomonas sp. UW4
36% identity, 82% coverage
- The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4
Duan, PloS one 2013 - “...tryptophan is converted to IAM by tryptophan 2-monooxygenase (PputUW4_04962) and then to IAA by amidase (PputUW4_03350). In the IAN pathway, tryptophan is converted to indole-3-acetaldoxime and then to IAN by indoleacetaldoxime dehydratase (PputUW4_03348). Next, IAA can be produced directly through IAN by nitrilase (PputUW4_02461). Alternatively, IAN...”
- “...by nitrile hydratase (PputUW4_03351 and PputUW4_03352), and then IAM is converted to IAA by amidase (PputUW4_03350). Future work will involve an experimental confirmation of the putative functions of the above-mentioned genes in IAA biosynthesis. A search of the sequenced Pseudomonas genomes for UW4-like IAA pathway associated...”
amdA / P27765 nicotinamidase (EC 3.5.1.19) from Pseudomonas chlororaphis (see paper)
P27765 Amidase from Pseudomonas chlororaphis
36% identity, 81% coverage
JNO42_09225 amidase from Pseudomonas putida
34% identity, 80% coverage
WP_046196360 indoleacetamide hydrolase from Burkholderia contaminans
34% identity, 97% coverage
TTHA1797 probable amidase from Thermus thermophilus HB8
37% identity, 88% coverage
AF_1954 amidase from Archaeoglobus fulgidus DSM 4304
33% identity, 93% coverage
SHIWSC3_PJ0040 amidase from Shinella sp. WSC3-e
35% identity, 96% coverage
- A Novel Sulfatase for Acesulfame Degradation in Wastewater Treatment Plants as Evidenced from <i>Shinella</i> Strains
Liu, Environmental science & technology 2024 - “...were used to search for sequences related to the acesulfame sulfatase (SHIWSC3_PJ0001) and ANSA amidase (SHIWSC3_PJ0040) from Shinella sp. WSC3-e in nonredundant sequence database and whole genome shotgun contigs databases, respectively ( Text S3 ). Furthermore, raw sequence files of shotgun metagenome and metatranscriptome projects in...”
- “...strain Bosea sp. 3-1B ( Figure 1 ). Besides the gene for the ANSA amidase (SHIWSC3_PJ0040), two other coding sequences (SHIWSC3_PJ0052 and _PJ0041) are present in the Shinella ANSA amidase gene cluster, encoding a TauE/SafE export protein and a LysR-like transcriptional regulator, respectively. In addition to...”
BMAA1320 amidase from Burkholderia mallei ATCC 23344
35% identity, 97% coverage
FAAH_MEDTR / G7ISB0 Fatty acid amide hydrolase; N-acylethanolamine amidohydrolase; EC 3.5.1.- from Medicago truncatula (Barrel medic) (Medicago tribuloides) (see paper)
34% identity, 72% coverage
- function: Catalyzes the hydrolysis of bioactive endogenous fatty acid amides to their corresponding acids (PubMed:16624618). The hydrolysis of endogenous amidated lipids terminates their participation as lipid mediators in various signaling systems (Probable). Converts a wide range of N-acylethanolamines (NAEs) to their corresponding free fatty acids and ethanolamine (PubMed:16624618).
catalytic activity: N-(9Z,12Z-octadecadienoyl)-ethanolamine + H2O = ethanolamine + (9Z,12Z)-octadecadienoate (RHEA:35567)
subunit: Forms homodimers.
P95896 amidase (EC 3.5.1.4); nitrilase (EC 3.5.5.1) from Saccharolobus solfataricus (see 3 papers)
WP_009990155 amidase from Saccharolobus solfataricus P2
SSO2122 Glutamyl-tRNA amidotransferase, subunit A (gatA-3) from Sulfolobus solfataricus P2
30% identity, 82% coverage
- Identification of the amino acid residues affecting the catalytic pocket of the Sulfolobus solfataricus signature amidase.
Elisa, Protein and peptide letters 2010 (PubMed)- GeneRIF: Studies using Functional Residue Automatic Prediction indicate Arg197, Lys209 and Asp228 are important for the catalytic activity (in addition to well-known catalytic residues).
- Characterization of mutants of Sulfolobus solfataricus signature amidase able to hydrolyse R-ketoprofen amide.
Giordano, Protein and peptide letters 2008 (PubMed)- GeneRIF: Results show that amidase mutations do not specifically affect residues near the active site, or directly interacting with the substrate.
- Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea
Zweerink, Nature communications 2017 - “...serine aminopeptidase (SSO2518, MW 40.5kDa), a proline iminopeptidase (Pip, SSO3115, MW 36.0kDa), and 2 amidases (SSO2122, MW 55.7kDa and GatA-1, SSO0765, MW 44.1kDa). In total, we robustly identified 10 serine hydrolases out of the 18 predicted hydrolases (56%). This number is comparable to the identifications from...”
- Discovery and characterization of a second extremely thermostable (+)-γ-lactamase from Sulfolobus solfataricus P2
Zhu, Journal of bioscience and bioengineering 2016 (PubMed)- “...residues, in contrast to a previously reported (+)- -lactamase (Sso2122) with 504 amino acid residues from the same strain. Herein, we demonstrate that a...”
- “...Sso2810 was biochemically characterized and compared to Sso2122, with phylogenetic analysis indicating different evolutionary histories for the two encoding...”
PVX_089895 glutamyl-tRNA(Gln) amidotransferase subunit A, putative from Plasmodium vivax
30% identity, 81% coverage
mhp029 glutamyl-tRNA amidotransferase subunit A from Mycoplasma hyopneumoniae 232
29% identity, 85% coverage
BMEII0289 glutamyl-tRNA(GLN) amidotransferase subunit A from Brucella melitensis 16M
33% identity, 96% coverage
BCAM0265 putative amidase from Burkholderia cenocepacia J2315
36% identity, 95% coverage
BMEA_RS14895 amidase from Brucella melitensis ATCC 23457
33% identity, 96% coverage
MSMEG_3400 glutamyl-tRNA(Gln) amidotransferase subunit A from Mycobacterium smegmatis str. MC2 155
34% identity, 62% coverage
- Nitrogen starvation-induced transcriptome alterations and influence of transcription regulator mutants in Mycobacterium smegmatis
Jeßberger, BMC research notes 2013 - “...ATP-binding protein msmeg_6260 16.11 Glutamine synthetase, type III ( glnT ) msmeg_4206 16.44 Molybdopterin oxidoreductase msmeg_3400 17.66 Glutamyl-tRNA(Gln) amidotransferase subunit A msmeg_0572 17.72 Conserved hypothetical protein msmeg_2427 18.22 Protein P-II uridylyltransferase ( glnD ) msmeg_4637 18.43 Conserved hypothetical protein msmeg_3401 18.68 LamB-YcsF family protein msmeg_1988 18.75...”
- “...msmeg_0779 , msmeg_1293 , msmeg_2184 , the amtB-glnK-glnD operon, msmeg_2522 , msmeg_2526 , urtA , msmeg_3400 , glnA , glnA2 , amtA , msmeg_5730 , amt1 , msmeg_6261 and msmeg_6816 (Figure 3 B). Figure 3 Verification of DNA affinity microarray results by quantitative RT-PCR. Total RNA...”
- GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
Vindal, BMC genomics 2007 - “...were selected using GntR Pfam profile [ 29 ]. Among all predicted GntRs one protein (MSMEG_3400) was discarded for this study because of its unusual size (741 amino acid) and its annotation as glutamyl-tRNA(Gln) amidotransferase subunit A. Rest of the GntR regulators were retrieved from the...”
DDB_G0275967 amidase family protein from Dictyostelium discoideum AX4
31% identity, 69% coverage
- Identification and recombinant expression of anandamide hydrolyzing enzyme from Dictyostelium discoideum
Neelamegan, BMC microbiology 2012 - “...bioinformatics approach searching for a human FAAH homolog in the Dictyostelium genome. Dictyostelium DNA sequence DDB_G0275967 ( http://dictybase.org/gene ) [GenBank: XM_638290] containing coding sequences for characteristic amidase signature motifs [ 19 ] was identified and found to be located on chromosome 2 in the annotated Dictyostelium...”
- “...(AS) motifs were identified in the annotated genome data base ( http://dictybase.org ) and ortholog DDB_G0275967 ( http://dictybase.org/gene ) [GenBank: XM_638290] was selected for further functional characterization. Domain architecture analyses and amino acid sequence homology comparisons among FAAH from different species were done using sequence analysis...”
WP_018091606 amidase family protein from Streptomyces sp. FxanaC1
37% identity, 98% coverage
FRAAL3665 putative amidase from Frankia alni ACN14a
34% identity, 95% coverage
AMID_RHORH / P84650 Enantioselective amidase; EC 3.5.1.4 from Rhodococcus rhodochrous
36% identity, 80% coverage
- catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
subunit: Homooctamer.
FAAH_ORYSJ / Q0JFH7 Fatty acid amide hydrolase; N-acylethanolamine amidohydrolase; EC 3.5.1.- from Oryza sativa subsp. japonica (Rice) (see paper)
32% identity, 70% coverage
- function: Catalyzes the hydrolysis of bioactive endogenous fatty acid amides to their corresponding acids (PubMed:16624618). The hydrolysis of endogenous amidated lipids terminates their participation as lipid mediators in various signaling systems (Probable). Converts a wide range of N-acylethanolamines (NAEs) to their corresponding free fatty acids and ethanolamine (PubMed:16624618).
catalytic activity: N-(9Z,12Z-octadecadienoyl)-ethanolamine + H2O = ethanolamine + (9Z,12Z)-octadecadienoate (RHEA:35567)
catalytic activity: N-hexadecanoylethanolamine + H2O = ethanolamine + hexadecanoate (RHEA:45064)
catalytic activity: N-dodecanoylethanolamine + H2O = dodecanoate + ethanolamine (RHEA:45456)
subunit: Forms homodimers.
F6B93_19200 amidase from Mycobacterium spongiae
35% identity, 93% coverage
PA4342 probable amidase from Pseudomonas aeruginosa PAO1
33% identity, 96% coverage
Bdiaspc4_22345 amidase from Bradyrhizobium diazoefficiens
bll4303 bll4303 from Bradyrhizobium japonicum USDA 110
34% identity, 95% coverage
6diiH / Q7XJJ7 Structure of arabidopsis fatty acid amide hydrolase in complex with methyl linolenyl fluorophosphonate (see paper)
32% identity, 71% coverage
- Ligand: methyl-9z,12z,15z-octadecatrienylphosphonofluoridate (6diiH)
FAAH_ARATH / Q7XJJ7 Fatty acid amide hydrolase; AtFAAH; N-acylethanolamine amidohydrolase; EC 3.5.1.99 from Arabidopsis thaliana (Mouse-ear cress) (see 10 papers)
Q7XJJ7 fatty acid amide hydrolase (EC 3.5.1.99) from Arabidopsis thaliana (see paper)
NP_201249 fatty acid amide hydrolase from Arabidopsis thaliana
AT5G64440 AtFAAH (Arabidopsis thaliana fatty acid amide hydrolase); N-(long-chain-acyl)ethanolamine deacylase/ amidase from Arabidopsis thaliana
32% identity, 72% coverage
- function: Catalyzes the hydrolysis of bioactive endogenous fatty acid amides to their corresponding acids (PubMed:12824167). The hydrolysis of endogenous amidated lipids terminates their participation as lipid mediators in various signaling systems (Probable). Converts a wide range of N-acylethanolamines (NAEs) to their corresponding free fatty acids and ethanolamine (PubMed:12824167, PubMed:16624618, PubMed:16738862, PubMed:16880402). Can use oleamide as substrate, but not indole-3-acetamide, 1-naphtalene-acetamide, nicotinic acid amide or L-asparagine (PubMed:16738862). Can use 2-arachidonylglycerol as substrate (PubMed:19801664). Participates in the regulation of plant growth (PubMed:16880402). Hydrolyzes N-dodecanoylethanolamine, which is has a growth inhibitory effect on seedling growth (PubMed:28112243). Involved in plant defense signaling (PubMed:18643971). Involved in abscisic acid (ABA) signaling through mechanisms that are independent of the catalytic activity (PubMed:19801664). Involved in the regulation of flowering time (PubMed:22645580). Catalyzes the hydrolysis of N-acyl L-homoserine lactones (AHLs), which are a class of signaling molecules produced by bacteria for quorum sensing (PubMed:24918118). Accumulation of L-homoserine appears to encourage plant growth at low concentrations by stimulating transpiration, but higher concentrations inhibit growth by stimulating ethylene production (PubMed:24918118).
catalytic activity: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + H2O = ethanolamine + (5Z,8Z,11Z,14Z)-eicosatetraenoate (RHEA:26136)
catalytic activity: N-(9Z,12Z-octadecadienoyl)-ethanolamine + H2O = ethanolamine + (9Z,12Z)-octadecadienoate (RHEA:35567)
catalytic activity: N-hexadecanoylethanolamine + H2O = ethanolamine + hexadecanoate (RHEA:45064)
catalytic activity: N-tetradecanoylethanolamine + H2O = tetradecanoate + ethanolamine (RHEA:45452)
catalytic activity: N-dodecanoylethanolamine + H2O = dodecanoate + ethanolamine (RHEA:45456)
subunit: Forms homodimers.
disruption phenotype: No visible phenotype under normal growth conditions (PubMed:16880402). Enhanced sensitivity to inhibition of seedling growth induced by exogenous N-acylethanolamine. - Structural analysis of a plant fatty acid amide hydrolase provides insights into the evolutionary diversity of bioactive acylethanolamides.
Aziz, The Journal of biological chemistry 2019 - GeneRIF: comparison of the apo and ligand-bound AtFAAH structures identified three discrete sets of conformational changes that accompany ligand binding, suggesting a unique "squeeze and lock" substrate-binding mechanism
- A chemical genetic screen uncovers a small molecule enhancer of the N-acylethanolamine degrading enzyme, fatty acid amide hydrolase, in Arabidopsis.
Khan, Scientific reports 2017 - GeneRIF: our study demonstrates the feasibility of using an unbiased chemical genetic approach to identify new pharmacological tools for manipulating FAAH- and NAE-mediated physiological processes in plants.
- Identification of N-acylethanolamines in Dictyostelium discoideum and confirmation of their hydrolysis by fatty acid amide hydrolase
Hayes, Journal of lipid research 2013 - “...FAAH sequence was obtained for Arabidopsis thaliana (NP_201249). Other amidase signature sequence proteins, most Gln amidotransferases, were obannotated as...”
- Mutations in Arabidopsis fatty acid amide hydrolase reveal that catalytic activity influences growth but not sensitivity to abscisic acid or pathogens.
Kim, The Journal of biological chemistry 2009 - GeneRIF: AtFAAH influences plant growth and interacts with ABA signaling and plant defense through distinctly different mechanisms
- Overexpression of a fatty acid amide hydrolase compromises innate immunity in Arabidopsis.
Kang, The Plant journal : for cell and molecular biology 2008 (PubMed)- GeneRIF: Overexpression of AtFAAH inhibits innate immunity against Pseudomonas syringae in Arabidopsis, and plants had lower amounts of jasmonic acid, abscisic acid, and salicylic acid.
- Manipulation of Arabidopsis fatty acid amide hydrolase expression modifies plant growth and sensitivity to N-acylethanolamines.
Wang, Proceedings of the National Academy of Sciences of the United States of America 2006 - GeneRIF: AtFAAH is one, but not the only, modulator of endogenous N-Acylethanolamines (NAE) levels in plants, and that NAE depletion likely participates in the regulation of plant growth [fatty acid amide hydrolase] [AtFAAH]
- Transcriptomic analyses in the gametophytes of the apomictic fern Dryopteris affinis
Ojosnegros, Planta 2024 - “...36 3 23280-519 Q9SGN6 NSL1 NECROTIC SPOTTED LESIONS 1 68 612 610 173 1 283857-78 Q7XJJ7 FAAH FATTY ACID AMIDE HYDROLASE 66 607 210 149 2 114632-232 Q9FM96 PSL4 PRIORITY IN SWEET LIFE 4 73 647 110 64 1 253585-97 Q94AQ6 SRT2 SIRTUIN 2 42 373...”
- Structural analysis of a plant fatty acid amide hydrolase provides insights into the evolutionary diversity of bioactive acylethanolamides
Aziz, The Journal of biological chemistry 2019 (secret) - Synthesis of phenoxyacyl-ethanolamides and their effects on fatty acid amide hydrolase activity
Faure, The Journal of biological chemistry 2014 - “...and the plasmid AtFAAH-pTrcHis2 (At5g64440, UniProt number Q7XJJ7) was constructed as described previously (7). The expression constructs were introduced into...”
- “...different purified recombinant proteins: At-FAAH (UniProt number Q7XJJ7) and rat FAAH (NCB accession number NP_077046) (34). Expression and purification of...”
- Enhanced seedling growth by 3-n-pentadecylphenolethanolamide is mediated by fatty acid amide hydrolases in upland cotton (Gossypium hirsutum L.)
Arias-Gaguancela, Plant direct 2022 - “...2.1 Binary vector and cotton transformation for AtFAAH transgenic production The coding sequence of AtFAAH (AT5G64440) was cloned into the binary vector pCambia1390 under the control of CaMV 35S promoter (Wang et al., 2006 ). AtFAAH in the pCambia1390 vector was electroporated in A. tumefaciens strain...”
- “...FAAH genes from cotton Sequences of the Arabidopsis fatty acid amide hydrolase (AtFAAH) gene locus (AT5G64440) were retrieved from TAIR website ( https://www.arabidopsis.org/ ). AtFAAH was used as template to search for cotton homologs in NCBI ( https://www.ncbi.nlm.nih.gov/ ), CottonGen ( http://www.cottongen.org ) and ccNET (...”
- Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism
Arias, Plant biotechnology journal 2022 - “...Glyma.05G195500 4.4 4.5 4.1 4.7 4.5 4.8 4.7 4.3 2.5 4.0 2.5 4.0 1089 0.98 AT5G64440 Fatty acid amide hydrolase Glyma.03G168700 1.4 1.2 1.4 1.7 1.3 1.4 1.8 1.1 1.7 1.9 1896 0.98 AT5G43940 Alcohol dehydrogenase 2 Glyma.17G231400 1.3 1.1 1.8 2.0 1.7 1.7 1.8 1.1...”
- “...Glyma.08G003100 3.8 3.9 3.5 4.3 3.9 4.3 4.6 4.6 1.6 3.6 3.0 4.7 936 0.94 AT5G64440 Fatty acid amide hydrolase Glyma.11G233700 1.1 1.3 1.0 1.2 1.3 1.2 1.5 800 0.93 AT3G56130 Biotin/lipoyl attachment domaincontaining protein Glyma.10G215400 1.1 1.8 1.7 2.0 1.9 1.8 1.2 1.6 1.6 121...”
- Population genomics demystifies the defoliation phenotype in the plant pathogen Verticillium dahliae
Zhang, The New phytologist 2019 - “...proteins in the genome (Chen etal ., 2018 ). In Arabidopsis, the enzymes encoded by At5g64440 ( AtFAAH ) and At1g08980 ( AMI1 ) have been shown to exhibit NAE hydrolytic activity (Shrestha etal ., 2003 ). Interestingly, direct inoculation of cotton plants with the D...”
- An Arabidopsis Clathrin Assembly Protein with a Predicted Role in Plant Defense Can Function as an Adenylate Cyclase
Chatukuta, Biomolecules 2018 - “...profiling of leaves from wild type and AtFAAH (E-MEXP-1094). Leaf samples from 4-week-old OE7a-1 (AtFAAH (AT5G64440) overexpression line) plants, inoculated with the non-host pathogen Pseudomonas syringae pv syringae for 12 h. Genotype: Transgenic Col-0 (n = 3). P. syringae pv tomato study 2, (OE7a-1)/untreated disc samples...”
- A chemical genetic screen uncovers a small molecule enhancer of the N-acylethanolamine degrading enzyme, fatty acid amide hydrolase, in Arabidopsis
Khan, Scientific reports 2017 - “...15 16 . Functional analyses of one Arabidopsis FAAH (AtFAAH ) encoded by the gene At5g64440 led to modified responses of seedlings to exogenous NAE. For instance, seedlings of transfer (T)-DNA knockouts to AtFAAH (Atfaah ) were more severely inhibited by N -lauroylethanolamine (NAE 12:0) compared...”
- “...media with 40M NAE 12:0 for an additional 3 days. Plasmid construction The plasmid AtFAAH-pTrcHis2 (At5g64440 ) used for expression of AtFAAH protein for in vitro assays was described in Shrestha et al . 15 . The Rat-FAAH-pTrcHis2 (NP_077046) construct was a gift of Dr. Benjamin...”
- Shoot chloride exclusion and salt tolerance in grapevine is associated with differential ion transporter expression in roots
Henderson, BMC plant biology 2014 - “...O-methyltransferase 1 oomt1 NG2_6989_23958 VIT_06s0004g05440 GSVIVT01024878001 AT2G29260 1.23 3.46E-17 33.27 Tropinone reductase NG2_5127_34182 VIT_03s0097g00620 GSVIVT01038529001 AT5G64440 1.71 4.59E-17 32.98 N-acylethanolamine amidohydrolase NG2_7581_45053 VIT_06s0080g00800 GSVIVT01036089001 AT5G22360 2.01 7.43E-17 32.47 Vesicle-associated membrane protein 714 NG2_12628_32903 VIT_10s0071g00440 GSVIVT01034406001 AT4G11900 3.24 7.90E-17 32.40 Serine/threonine-protein kinase receptor ARK3 NG2_48742_21119 VIT_08s0007g09030 GSVIVT01033230001...”
- Synthesis of phenoxyacyl-ethanolamides and their effects on fatty acid amide hydrolase activity
Faure, The Journal of biological chemistry 2014 - “...Cravatt's laboratory (34), and the plasmid AtFAAH-pTrcHis2 (At5g64440, UniProt number Q7XJJ7) was constructed as described previously (7). The expression...”
- More
AFUA_5G09140 amidase, putative from Aspergillus fumigatus Af293
33% identity, 77% coverage
- RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus
O'Keeffe, BMC genomics 2014 - “...acid and peptide transporters in gliT exposed to exogenous gliotoxin, while expression of one amidase, AFUA_5G09140, was increased log 2 3.37-fold (Table 4 ). Expression of both nitrate transporters, crnA and nrtB , which are predicted gene pairs [ 42 ], was significantly down-regulated (log 2...”
- “...0.979 5.119 0.0005 AFUA_5G01200 cp6 0.621 0.834 4.932 0.0005 AFUA_8G00410 metAP 0.113 0.987 5.196 0.0005 AFUA_5G09140 - 0.443 0.910 3.372 0.002 AFUA_5G02990 - 0.805 0.512 4.047 0.0005 AFUA_1G09120 - 0.272 0.962 2.985 0.002 AFUA_8G00800 - 0.641 0.899 6.795 0.0005 AFUA_1G12240 - 0.347 0.964 5.161 0.0005 AFUA_8G02550...”
1m21A / Q8RJN5 Crystal structure analysis of the peptide amidase pam in complex with the competitive inhibitor chymostatin (see paper)
35% identity, 94% coverage
DKG71_30355 amidase from Streptomyces sp. NEAU-S7GS2
33% identity, 97% coverage
MANHY_PSEPU / Q84DC4 Mandelamide hydrolase; EC 3.5.1.86 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 3 papers)
32% identity, 95% coverage
- function: Hydrolyzes both the R- and the S-enantiomers of mandelamide, and phenylacetamide. Has lower activity on 3-phenylpropionaide and lactamide. Does not hydrolyze benzamide. Hydrolyzes esters and amides with little steric bulk. Preferentially hydrolyzes aromatic substrates.
catalytic activity: (R)-mandelamide + H2O = (R)-mandelate + NH4(+) (RHEA:22876)
subunit: Monomer.
WP_021076225 indoleacetamide hydrolase from Bradyrhizobium sp.
33% identity, 97% coverage
pam / GI|19744118 peptide amidase from Stenotrophomonas maltophilia (see paper)
pam / CAC93616.1 peptide amidase from Stenotrophomonas maltophilia (see paper)
Q8RJN5 Amidase from Stenotrophomonas maltophilia
35% identity, 86% coverage
bll2914 bll2914 from Bradyrhizobium japonicum USDA 110
34% identity, 84% coverage
F6N111 aryl-acylamidase (EC 3.5.1.13) from Paracoccus sp. M1-1 (see paper)
G9FKH7 amidase (EC 3.5.1.4) from Paracoccus sp. (see paper)
28% identity, 100% coverage
VDAG_09707 amidase from Verticillium dahliae VdLs.17
32% identity, 76% coverage
Q8I1S6 glutaminyl-tRNA synthase (glutamine-hydrolysing) (subunit 2/2) (EC 6.3.5.7) from Plasmodium falciparum (see paper)
PF3D7_0416100 glutamyl-tRNA(Gln) amidotransferase subunit A from Plasmodium falciparum 3D7
45% identity, 22% coverage
- Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium Moorea producens
Sweeney-Jones, Marine drugs 2020 - “...protein, ARP1 0.50 0.77 Q8I1V9 Actin-like protein, putative 0.50 0.77 Q8IKV8 Sortilin, putative 0.48 0.45 Q8I1S6 Glutamyl-tRNA(Gln) amidotransferase subunit A, putative 0.46 0.26...”
- South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains
Singh, F1000Research 2016 - “...3.8 PF3D7_1358300 rhomboid protease ROM7 (ROM7) 5.5 1.5 3.7 PF3D7_1343700 kelch protein 4.2 1.1 3.7 PF3D7_0416100 glutamyl-tRNA(Gln) amidotransferase subunit A 8.0 2.2 3.6 PF3D7_0423400 asparagine-rich protein (AARP) 9.0 2.5 3.5 PF3D7_1210900 GPI mannosyltransferase I+(PIG-M) 5.0 1.4 3.5 PF3D7_1015800 ribonucleotide reductase small subunit 5.0 1.5 3.3 PF3D7_1217600...”
- Recent advances in the biology and drug targeting of malaria parasite aminoacyl-tRNA synthetases
Khan, Malaria journal 2016 - “...PF3D7_1126000 a PF3D7_1126000 a Other enzymes D tyrosyl-tRNA deacylase PF3D7_1108200 a P43 PF3D7_1442300 Glutamyl-tRNA amidotransferase PF3D7_0416100 (A) PF3D7_0628800 (B) a Indicate genes containing editing activity Fig.2 Cellular distribution of 36 malaria parasite aminoacyl-tRNA synthetases (aaRSs). All 36 aaRSs are encoded by the nuclear genome. 16 aaRSs...”
- Plasmodium Apicoplast Gln-tRNAGln Biosynthesis Utilizes a Unique GatAB Amidotransferase Essential for Erythrocytic Stage Parasites
Mailu, The Journal of biological chemistry 2015 - “...bacterial glutamyl-tRNA amidotransferase (Glu-AdT) as follows: GatA (PF3D7_0416100, 96 kDa, 826 amino acids) and GatB (PF3D7_0628800, 102 kDa, 882 amino acids)...”
- “...sequence (Pf3D7_1357200, amino acids 78 -574) (23), PfGatA (Pf3D7_0416100, amino acids 101- 827), and PfGatB (Pf3D7_0628800, amino acids 96 - 884). PfGluRS was...”
- A nondiscriminating glutamyl-tRNA synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway
Mailu, The Journal of biological chemistry 2013 - “...GatB subunit tRNAGlu tRNAGln PF3D7_1357200 PF3D7_0416100 PF3D7_0628800 Apicoplasta Apicoplasta PBANKA_113350 PBANKA_071810 PBANKA_112750 Apicoplastb Apicoplastb...”
FRAAL0363 putative amidase from Frankia alni ACN14a
35% identity, 90% coverage
FQ085_10470 amidase family protein from Planococcus sp. ANT_H30
30% identity, 98% coverage
tms2 / P0A2X0 indoleacetamide hydrolase (EC 3.5.1.4) from Rhizobium radiobacter (see paper)
31% identity, 94% coverage
RHE_RS25710 amidase from Rhizobium etli CFN 42
34% identity, 84% coverage
ST0478 396aa long hypothetical enantiomer-selective amidase from Sulfolobus tokodaii str. 7
30% identity, 90% coverage
SLIV_06435 amidase family protein from Streptomyces lividans TK24
34% identity, 87% coverage
- Enhanced protein secretion in reduced genome strains of Streptomyces lividans
Hamed, Microbial cell factories 2024 - “...S4). Proteins with hydrolytic functions were oversecreted in all RG strains examined [e.g. Amidase ( SLIV_06435 ), putative phosphodiesterase (IPR017946) ( SLIV_27875 ) and probable subtilinase-type protease inhibitor ( SLIV_34120 )] (RG1.4, 1.5, 1.9; Fig. 3 C and D and S4). Hydrolases, peptidases and proteases were...”
- Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
Rebets, Frontiers in microbiology 2018 - “...Factor, peptidoglycan cleavage, SLIV_33070), peptidoglycan amidase (SLIV_11070), NlpC/P60 subgroup amidase (SLIV_17370), endopeptidase (SLIV_04650), putative amidase (SLIV_06435), MreC (SLIV_24625) are exclusively found in the S. lividans TK24 secreted proteome ( Gordon et al., 2008 ; Haiser et al., 2009 ; Ladwig et al., 2015 ; Sexton et...”
BPSS2307 putative amidase from Burkholderia pseudomallei K96243
37% identity, 85% coverage
A0A509AHQ9 glutaminyl-tRNA synthase (glutamine-hydrolysing) (subunit 2/2) (EC 6.3.5.7) from Plasmodium berghei (see paper)
35% identity, 39% coverage
PP0613 amidase family protein from Pseudomonas putida KT2440
31% identity, 93% coverage
ArtHe_01245 amidase from Arthrobacter sp. Helios
34% identity, 87% coverage
hydA / A0A0A1H115 4-hydroxybenzoate 1-phenylethylidene hydrazidase from Microbacterium hydrocarbonoxydans (see paper)
31% identity, 97% coverage
YP_001967410 Iah from Agrobacterium tumefaciens
31% identity, 94% coverage
LOC107319872 fatty acid amide hydrolase-like from Coturnix japonica
33% identity, 69% coverage
WP_010677135 amidase family protein from Bacillus timonensis
33% identity, 96% coverage
5h6sC Crystal structure of hydrazidase s179a mutant complexed with a substrate (see paper)
31% identity, 97% coverage
- Ligand: 4-oxidanylbenzohydrazide (5h6sC)
P25016 Indoleacetamide hydrolase from Agrobacterium vitis
31% identity, 83% coverage
AAM_RHOER / K9NBS6 Acylamidase; EC 3.5.1.13; EC 3.5.1.14; EC 3.5.1.4 from Rhodococcus erythropolis (Arthrobacter picolinophilus) (see paper)
31% identity, 97% coverage
- function: Amidase with broad substrate specificity, catalyzing the hydrolysis of a wide range of N-substituted amides, and, to a lesser extent, the hydrolysis of non-substituted amides. Acid para- nitroanilides (4'-nitroacetanilide, Gly-pNA, Ala-pNA, Leu-pNA) are the best substrates for this enzyme. N-substituted acrylamides (isopropyl acrylamide, N,N-dimethyl-aminopropyl acrylamide, and methylene-bis- acrylamide), N-acetyl derivatives of glycine, alanine and leucine, and aliphatic amides (acetamide, acrylamide, isobutyramide, n-butyramide, and valeramide) can also be used as substrates but with less efficiency.
catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
catalytic activity: an anilide + H2O = aniline + a carboxylate + H(+) (RHEA:20297)
catalytic activity: an N-acyl-L-amino acid + H2O = an L-alpha-amino acid + a carboxylate (RHEA:15565)
catalytic activity: an N-acetyl-L-cysteine-S-conjugate + H2O = an S-substituted L- cysteine + acetate (RHEA:36855)
PA0202 probable amidase from Pseudomonas aeruginosa PAO1
31% identity, 99% coverage
- A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1
De, mSystems 2023 - “...during the cystic fibrosis lung infection. We identified elevated expression levels of a gene ( PA0202 ) involved in amino acid metabolism and two genes ( mdcC , acoB ) that function in carbon and energy metabolism ( 123 ) in module 14. As cystic fibrosis...”
- New Insights about Antibiotic Production by Pseudomonas aeruginosa: A Gene Expression Analysis
Gionco, Frontiers in chemistry 2017 - “...GUIDED ANALYSIS BLAST INTERPRO UNIPROT PFAN Gene Access Description Access Description Access Description Access Description PA0202 OPE24314.1 Amidase OPE24314.1 Amidase A0A1F0J5G9 Amidase PDOC00494 Amidase PA0203 AAT51424 MULTISPECIES: ABC transporter [Pseudomonas] WP_034003826.1 None predicted A0A069QCF8 ABC transporter PF13416 Extracellular solute binding proteins. PA0204 WP_034003826 ABC transporter permease...”
- ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
Tan, mSystems 2016 - “...or only found in a subset of the P.aeruginosa strains with published genomes, such as PA0202 to PA206, which encode putative transporter genes. 10.1128/mSystems.00025-15.9 TableS1 Top 10 associated GO terms and KEGG pathways for each node mentioned in our report. Download TableS1, DOCX file, 0.1 MB...”
- Comparative systems biology analysis to study the mode of action of the isothiocyanate compound Iberin on Pseudomonas aeruginosa
Tan, Antimicrobial agents and chemotherapy 2014 - “...upon iberin treatmenta Gene PA0140 PA0182 PA0185 PA0201 PA0202 PA0283 PA0284 PA0565 PA0849 PA0865 PA0878 PA1240 PA1260 PA1285 PA1310 PA1332 PA1334 PA1493 PA1999...”
- Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosa
McPhee, Journal of bacteriology 2006 - “...and positively PhoP regulated PA4366 2 Positively Mg PA0201 PA0202 PA0282 PA0546 PA0913 PA1559 Fold change H988 with low Mg2 concn vs H103 with high Mg2 concn...”
- A cystic fibrosis epidemic strain of Pseudomonas aeruginosa displays enhanced virulence and antimicrobial resistance
Salunkhe, Journal of bacteriology 2005 - “...absent genes/gene clusters were a transport-related cluster (PA0202 to PA0206), two bacteriophage-related clusters (PAO632 to PA0648 and PA0715 to PA0759) and...”
blr7896 blr7896 from Bradyrhizobium japonicum USDA 110
32% identity, 97% coverage
RHE_RS01105 amidase from Rhizobium etli CFN 42
30% identity, 98% coverage
PputW619_2551 amidase from Pseudomonas putida W619
31% identity, 94% coverage
D3NY90 Amidase from Azospirillum sp. (strain B510)
31% identity, 93% coverage
RHA1_RS22310 amidase from Rhodococcus jostii RHA1
33% identity, 93% coverage
- Degradation of Bile Acids by Soil and Water Bacteria
Feller, Microorganisms 2021 - “...Chol11 Cleavage of conjugated bile acids Bile salt amidase C211_RS11020 CTCNB1_RS06560 (ORF26) CTCNB1_TS06555 (ORF25) unknown (RHA1_RS22310) Nov2c227 (Bsa) C5 side-chain degradation CoA-ligase C211_RS11125 (StdA1 *) CTCNB1_RS06840 RHA1_RS28415 (CasG) Nov2c230 (SclA) ACADs C211_RS11115 (Scd1A) CTCNB1_RS06830 RHA1_RS28395 (CasC) Nov2c221 (Scd4A) C211_RS11120 (Scd1B) CTCNB1_RS06835 --- Nov2c222 (Scd4B) Enoyl-CoA hydratase...”
An02g00190 uncharacterized protein from Aspergillus niger
30% identity, 80% coverage
UV8b_01984 uncharacterized protein from Ustilaginoidea virens
30% identity, 86% coverage
- Transcriptomic and Metabolomic Analyses Provide Insights into the Pathogenic Mechanism of the Rice False Smut Pathogen Ustilaginoidea virens
Fu, International journal of molecular sciences 2023 - “...s-adenosylmethionine had a correlation higher than 0.99 with the following genes: UV8b_00446 , UV8b_06678 , UV8b_01984 , UV8b_02871 , UV8b_04468 , and UV8b_07070 . Pyruvate was negatively regulated by general amidase, s-adenosylmethionine decarboxylase proenzyme, pyrroline-5-carboxylate reductase, aspartate aminotransferase, delta 1-pyrroline-5-carboxylate dehydrogenase, and gamma-glutamyl phosphate reductase. Seven...”
M5E2I7 Amidase from Thalassolituus oleivorans MIL-1
29% identity, 95% coverage
SACE_3403 amidase from Saccharopolyspora erythraea NRRL 2338
41% identity, 53% coverage
- Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain
Peano, Microbial cell factories 2012 - “...593 metS Missense (P569S) Methionyl-tRNA synthetase SACE_2075 188 efp Frameshift (+C 504) Elongation factor P SACE_3403 474 gatA Missense (A243E) Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit SACE_5926 1027 infB Missense (A278V) Translation initiation factor 2 SACE_5919 536 Frameshift (-G 821) Pseudouridine synthase Protein turnover and chaperones SACE_1339 860...”
- “...( metS ) coding form methionyl-tRNA synthetase, SACE_0443 ( cysS paralog) encoding a cysteinyl-tRNA synthatase, SACE_3403 ( gatA ) coding for A subunit of Asp-tRNA Asn/Glu-tRNA Gln amidotransferase, and a frameshift mutation inactivating a paralogous gene (SACE_5919) coding for pseudouridine synthase. These findings emphasize the importance...”
SSO0765 Glutamyl-tRNA amidotransferase, subunit A (gatA-1) from Sulfolobus solfataricus P2
31% identity, 84% coverage
CNBH_COMTE / Q38M35 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 from Comamonas testosteroni (Pseudomonas testosteroni) (see paper)
30% identity, 97% coverage
JJQ59_09300 amidase from Cupriavidus necator
30% identity, 97% coverage
Pchl3084_1486 amidase family protein from Pseudomonas chlororaphis subsp. aureofaciens 30-84
32% identity, 84% coverage
LOC101214819 probable amidase At4g34880 from Cucumis sativus
38% identity, 56% coverage
jpw_13420 amidase from Pseudomonas asiatica
31% identity, 94% coverage
- Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium
Wang, Genes 2022 - “...the IAM pathway, tryptophan 2-mono-oxygenase (jpw_01905) is responsible for converting tryptophan to IAM, and amidase (jpw_13420 and jpw_14270) catalyzes the formation of IAA from IAM. In the TAM pathway, tryptophan is converted to TAM by the tryptophan decarboxylase (jpw_10550), and TAM is converted to indole-3-acetaldehyde (IAAld)...”
- “...transcriptional regulator jpw_25340 phoR phosphate regulon sensor histidine kinase PhoR IAA biosynthesis jpw_01905 tryptophan 2-mono-oxygenase jpw_13420 jpw_14270 amiE amidase jpw_10550 tryptophan decarboxylase jpw_23615 monoamine oxidase jpw_25045 aldehyde dehydrogenase jpw_04700 jpw_13635 jpw_14640 putative auxin efflux carriers ACC deaminase activity jpw_07635 1-aminocyclopropane-1-carboxylate deaminase Siderophore production jpw_17700 pvdL non-ribosomal...”
U5YQN5 Aspartyl-tRNA amidotransferase subunit A/glutamyl-tRNA(Gln) amidotransferase subunit a from Streptomyces sp. XY332
33% identity, 97% coverage
PA0704 amidase from Pseudomonas aeruginosa PAO1
33% identity, 97% coverage
AT5G07360 amidase family protein from Arabidopsis thaliana
26% identity, 69% coverage
BC2054 Glutamyl-tRNA(Gln) amidotransferase subunit A from Bacillus cereus ATCC 14579
29% identity, 96% coverage
XCC0292 Glu-tRNAGln amidotransferase A subunit from Xanthomonas campestris pv. campestris str. ATCC 33913
34% identity, 94% coverage
FGSG_04022 hypothetical protein from Fusarium graminearum PH-1
36% identity, 48% coverage
AFUA_1G14880 N-acylethanolamine amidohydrolase, putative from Aspergillus fumigatus Af293
30% identity, 72% coverage
A6F504 Amidase from Marinobacter algicola DG893
29% identity, 95% coverage
blr3288 blr3288 from Bradyrhizobium japonicum USDA 110
34% identity, 97% coverage
ABD05_RS34310 amidase family protein from Burkholderia pyrrocinia
33% identity, 97% coverage
lpg2355 amidase (enantiomer selective) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
29% identity, 95% coverage
LOC18033993 probable amidase At4g34880 from Citrus x clementina
37% identity, 58% coverage
glr0961 probable urea amidolyase from Gloeobacter violaceus PCC 7421
36% identity, 66% coverage
A0W34_24065 amidase from Rhodococcus sp. BH4
29% identity, 95% coverage
SAV_6697 amidase from Streptomyces avermitilis MA-4680
34% identity, 77% coverage
- Functional analysis of TetR-family regulator AmtRsav in Streptomyces avermitilis
Chen, Microbiology (Reading, England) 2013 (PubMed)- “...mobility shift assays (EMSAs), that gene cluster sav_6697- 6700 encoding a putative amidase, a urea carboxylase and two hypothetical proteins, respectively,...”
- “...very short intergenic region (16 bp) between sav_6698 and sav_6697 (Fig. 1a), suggesting that these four genes might form a putative operon, which was confirmed...”
LOC101257218 probable amidase At4g34880 from Solanum lycopersicum
30% identity, 95% coverage
iaaH / P06618 indoleacetamide hydrolase (EC 3.5.1.4) from Pseudomonas savastanoi (see 3 papers)
P06618 Indoleacetamide hydrolase from Pseudomonas savastanoi
31% identity, 87% coverage
FAAH2 / Q6GMR7 fatty-acid amide hydrolase 2 (EC 3.5.1.99; EC 3.5.1.60) from Homo sapiens (see 2 papers)
FAAH2_HUMAN / Q6GMR7 Fatty-acid amide hydrolase 2; Amidase domain-containing protein; Anandamide amidohydrolase 2; Oleamide hydrolase 2; EC 3.5.1.99 from Homo sapiens (Human) (see 2 papers)
B2C6G4 fatty acid amide hydrolase (EC 3.5.1.99) from Homo sapiens (see paper)
Q6GMR7 amidase (EC 3.5.1.4); fatty acid amide hydrolase (EC 3.5.1.99) from Homo sapiens (see 2 papers)
NP_777572 fatty-acid amide hydrolase 2 isoform 1 from Homo sapiens
26% identity, 88% coverage
- function: Catalyzes the hydrolysis of endogenous amidated lipids like the sleep-inducing lipid oleamide ((9Z)-octadecenamide), the endocannabinoid anandamide (N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)- ethanolamine), as well as other fatty amides, to their corresponding fatty acids, thereby regulating the signaling functions of these molecules (PubMed:17015445, PubMed:19926788). Hydrolyzes monounsaturated substrate anandamide preferentially as compared to polyunsaturated substrates.
catalytic activity: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + H2O = ethanolamine + (5Z,8Z,11Z,14Z)-eicosatetraenoate (RHEA:26136)
catalytic activity: (9Z)-octadecenamide + H2O = (9Z)-octadecenoate + NH4(+) (RHEA:26506)
catalytic activity: N-(9Z-octadecenoyl) ethanolamine + H2O = ethanolamine + (9Z)- octadecenoate (RHEA:45060)
catalytic activity: N-hexadecanoylethanolamine + H2O = ethanolamine + hexadecanoate (RHEA:45064)
subunit: Homodimer. - THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Enzymes.
Alexander, British journal of pharmacology 2017 - “...amide hydrolase2 NAcylethanolamine acid amidase HGNC, UniProt NAPEPLD , Q6IQ20 FAAH , O00519 FAAH2 , Q6GMR7 NAAA , Q02083 EC number 3.5.1.99 : anandamide + H 2 O <=> arachidonic acid + ethanolamine oleamide + H 2 O <=> oleic acid + NH 3 The enzyme...”
- The Concise Guide to PHARMACOLOGY 2015/16: Enzymes.
Alexander, British journal of pharmacology 2015 - “...abreviation MGL FAAH FAAH2 NAAA HGNC, UniProt MGLL , Q99685 FAAH , O00519 FAAH2 , Q6GMR7 NAAA , Q02083 EC number 3.1.1.23 3.5.1. 3.5.1. 3.5.1. Rank order of affinity 2oleoyl glycerol = 2arachidonoylglycerol anandamide [ 171 ] anandamide > oleamide > Noleoylethanolamide > Npalmitoylethanolamine [ 518...”
- The Concise Guide to PHARMACOLOGY 2013/14: enzymes.
Alexander, British journal of pharmacology 2013 - “...acid amidase Common abbreviation MGL FAAH FAAH2 NAAA HGNC, UniProt MGLL, Q99685 FAAH, O00519 FAAH2, Q6GMR7 NAAA, Q02083 EC number 3.1.1.23 3.5.1.- 3.5.1.- 3.5.1.- Rank order of affinity 2-oleoyl glycerol = 2-arachidonoylglycerol >> anandamide 199 anandamide > oleamide > N-oleoylethanolamide > N-palmitoylethanolamine 211 oleamide > N-oleoylethanolamide...”
- Proteome data set of human gingival crevicular fluid from healthy periodontium sites by multidimensional protein separation and mass spectrometry.
Carneiro, Journal of periodontal research 2012 - “...Alpha-enolase b c d e 8 7 S Q9NSC7 Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 b 2 1 Q6GMR7 Amidase domain containing protein c 3 1 P08311 Cathepsin G b 3 3 S P00450 Ceruloplasmin a b c 7 5 S P04075 Fructose-bisphosphate aldolase A d e 4 3...”
- Identification of N-acylethanolamines in Dictyostelium discoideum and confirmation of their hydrolysis by fatty acid amide hydrolase
Hayes, Journal of lipid research 2013 - “...homologs) were obtained for Homo sapiens (NP_777572), Takifugu rubripes (SINFRUP00000168827), and Drosophila melanogaster (NP_725139). Another FAAH sequence was...”
CTCNB1_RS06560 amidase from Comamonas thiooxydans
30% identity, 87% coverage
- Degradation of Bile Acids by Soil and Water Bacteria
Feller, Microorganisms 2021 - “...jostii RHA1 Sphingobium sp. Strain Chol11 Cleavage of conjugated bile acids Bile salt amidase C211_RS11020 CTCNB1_RS06560 (ORF26) CTCNB1_TS06555 (ORF25) unknown (RHA1_RS22310) Nov2c227 (Bsa) C5 side-chain degradation CoA-ligase C211_RS11125 (StdA1 *) CTCNB1_RS06840 RHA1_RS28415 (CasG) Nov2c230 (SclA) ACADs C211_RS11115 (Scd1A) CTCNB1_RS06830 RHA1_RS28395 (CasC) Nov2c221 (Scd4A) C211_RS11120 (Scd1B) CTCNB1_RS06835...”
iaaH / GB|AAA17679.1 indoleacetamide hydrolase; EC 3.5.1.- from Pseudomonas syringae pv. syringae (see paper)
P52831 Indoleacetamide hydrolase from Pseudomonas syringae pv. syringae
31% identity, 97% coverage
- Characterization of Four Bifunctional Plant IAM/PAM-Amidohydrolases Capable of Contributing to Auxin Biosynthesis
Sánchez-Parra, Plants (Basel, Switzerland) 2014 - “...(Medtr1g082750.1); Nt: Nicotiana tabacum (AB457638); Os: Oryza sativa (AMI1: Os04g02780.1, AMI2: Os04g02754.1); Psy: Pseudomonas syringae (P52831); Ppe: Prunus persica (ppa005982m); Pt: Populus trichocarpa (AMI1: Potri.013g024100.1, AMI2: Potri.013g024200.1); Pvi: Panicum virgatum (AMI1: Pavirv00043873m, AMI2: Pavirv00038995m); Pvu: Phaseolus vulgaris (Phvul.007G180900.1); Rco: Ricinus communis (30128.m008759); Sb: Sorghum bicolor (Sb02g039510.1);...”
- Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp. strain ADP
Shapir, Journal of bacteriology 2005 - “...IAAH, indoleacetamide hydrolase from Pseudomonas syringae, P52831; GatA, glutamyl-tRNA amidotransferase subunit A from Streptococcus pyogenes, Q99YC0; AtzF,...”
W6QRS4 Allophanate hydrolase from Pseudomonas pseudoalcaligenes (strain CECT 5344)
34% identity, 66% coverage
- Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344
Olaya-Abril, Frontiers in microbiology 2020 - “...). Proteins exclusive of the wild-type strain were the acetylornithine deacetylase (W6QQU2), the allophanate hydrolase (W6QRS4), a hydrogen peroxide-inducible activator (W6R3L3), and a LuxR family transcriptional regulator (W6R7G4), among others ( Figure 2 and Supplementary Table S1 ). Another protein exclusive of the wild-type strain of...”
- “...metabolism, as well as the acetylornithine deacetylase (W6QQU2, Figure 2 ) and the allophanate hydrolase (W6QRS4, Figure 4 ), which were exclusive of the wild-type strain. Allophanate hydrolase is conserved in many organisms and converts allophanate to ammonium and carbon dioxide, allowing the utilization of urea...”
R4SWV0 Amidase from Amycolatopsis keratiniphila
34% identity, 97% coverage
RGM3321_01475 amidase family protein from Pseudomonas sp. RGM 3321
32% identity, 92% coverage
LOC113823280 epidermal growth factor receptor-like from Penaeus vannamei
35% identity, 25% coverage
- Structure and function analyses of the Mmd2 gene in pacific white shrimp Litopenaeus vannamei
Si, Frontiers in genetics 2023 - “...alpha-1(I) chain-like 1.0131205 Up LOC113815446 chondroitin proteoglycan-2-like 1.187366726 Up LOC113815782 chondroitin proteoglycan 2-like 1.018277715 Up LOC113823280 Epidermal growth factor receptor 2.008971472 Up LOC113815384 Peritrophin-1 1.457802192 Up structural protein related genes LOC113816928 Peritrophin-1 1.09799355 Up LOC113824427 trypsin-like 1.451603354 Up protein digestion, absorption and transport LOC113814621 solute carrier...”
XAC4327 urea amidolyase from Xanthomonas axonopodis pv. citri str. 306
31% identity, 79% coverage
NCU04092 N-acylethanolamine amidohydrolase from Neurospora crassa OR74A
28% identity, 67% coverage
- A user-friendly CRISPR/Cas9 system for mutagenesis of Neurospora crassa
Grüttner, Scientific reports 2024 - “...a non-selectable gene with CRIPSR/Cas9 Next, a non-selectable gene encoding N-acylethanolamine amidohydrolase-2 ( naa-2 ; NCU04092) involved in the auxin biosynthesis pathway in N. crassa 19 , was targeted. Again, two different gRNAs (see Fig. 4 a and b) were designed: gRNA-n1 (targeting sequence position 211233...”
LOC101204792 probable amidase At4g34880 from Cucumis sativus
30% identity, 93% coverage
SPO2938 amidase family protein from Silicibacter pomeroyi DSS-3
28% identity, 93% coverage
- Ecological genomics of marine Roseobacters
Moran, Applied and environmental microbiology 2007 - “...S. pomeroyi and Silicibacter sp. strain TM1040 (SPO2938, -1314, and -1315 and TM1040_1578, TM1040_1971, and TM1040_1972) and arylacetone-specific nitrilase (33)...”
Rv2363 amidase from Mycobacterium tuberculosis H37Rv
Mb2384 PROBABLE AMIDASE AMIA2 (AMINOHYDROLASE) from Mycobacterium bovis AF2122/97
34% identity, 94% coverage
- Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms
The, PLoS biology 2022 - “...Bedaquiline Oligonucleotides situated in the region of overlap at the 3 ends of amiA2 ( Rv2363 ) and era ( Rv2364c ) were significantly associated with bedaquiline MIC (minimum p -value p < 10 10.5 , S13 Fig ). These genes encode an amidase and a...”
- Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis
Phong, Indian journal of microbiology 2015 - “...7 4.1 3.5 D Rv3257c Phosphomannomutase manB-1 7 Rv2363 Putative amidase amiA2 7 2.3 Rv0814c Rv3118 Conserved protein Uncharacterized protein sseC1 sseC1 7 7...”
- Disruption of cell wall fatty acid biosynthesis in Mycobacterium tuberculosis using a graph theoretic approach
Baths, Theoretical biology & medical modelling 2011 - “...11.5 RV3799C 11.5 RV0974C 11.5 RV2247 11.5 RV2888C 10 RV3375 10 RV3011C 10 RV1263 10 RV2363 10 RV1384 9 package nearnessindex; import java.util.Scanner; import java.util.regex .*; import java.io .*; /** * * @author Veeky */ public class Main { static double i,iT = 0; static String...”
- Mutually exclusive genotypes for pyrazinamide and 5-chloropyrazinamide resistance reveal a potential resistance-proofing strategy
Baughn, Antimicrobial agents and chemotherapy 2010 - “...between PzaA and predicted protein homolog) Rv1263 (30%), Rv2363 (35%), Rv2888c (29%), Rv3011c (33%), Rv3175 (44%), and Rv3375 (35%). Although, this basal level...”
- Feedback for the Seventh International AIDS conference, Florence 1991
, Genitourinary medicine 1991
FOXG_11632 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
36% identity, 49% coverage
Sb05g020350 No description from Sorghum bicolor
28% identity, 74% coverage
PSPTO_4204 amidase family protein from Pseudomonas syringae pv. tomato str. DC3000
32% identity, 85% coverage
FGSG_10913 hypothetical protein from Fusarium graminearum PH-1
32% identity, 22% coverage
C3UWD1 aryl-acylamidase (EC 3.5.1.13) from bacterium CSBL00001 (see 2 papers)
30% identity, 93% coverage
BC1G_09997 hypothetical protein from Botrytis cinerea B05.10
28% identity, 77% coverage
Saro_3057 Amidase from Novosphingobium aromaticivorans DSM 12444
33% identity, 93% coverage
H16_B1874 Amidase from Ralstonia eutropha H16
41% identity, 45% coverage
K3ZSH2 Amidase domain-containing protein from Setaria italica
38% identity, 54% coverage
- Comparative proteomic investigation of drought responses in foxtail millet
Pan, BMC plant biology 2018 - “...methionine sulfoxide reductase B3, chloroplastic-like 0.6 K3YQA0 primary amine oxidase-like 0.6 K4A6W5 Asparagine synthetase 0.6 K3ZSH2 putative amidase C869.01-like 0.6 K3XH80 UDP-glycosyltransferase 88A1-like 0.6 K4A3F8 UDP-glycosyltransferase 90A1-like 0.6 G Cell organization-related proteins K4A9U8 tubulin alpha-1 chain-like 2.8 K3XWX5 tubulin beta-1 chain-like 2.8 H Others K3XME6 ADP-ribosylation...”
4yjiA / C3UWD1 The crystal structure of a bacterial aryl acylamidase belonging to the amidase signature (as) enzymes family (see paper)
30% identity, 94% coverage
- Ligand: n-(4-hydroxyphenyl)acetamide (tylenol) (4yjiA)
ABUW_1948 indoleacetamide hydrolase from Acinetobacter baumannii
27% identity, 96% coverage
- Comparative Transcriptomic Profiling of Pellicle and Planktonic Cells from Carbapenem-Resistant Acinetobacter baumannii
Ng, Antibiotics (Basel, Switzerland) 2023 - “...0.4501 0.3547 2 13 ABUW_1624 gabD2 ko00380 Tryptophan metabolism 0.4087 0.3902 2 14 - ABUW_1150, ABUW_1948 K09101 Carbohydrate metabolism ko00053 Ascorbate and aldarate metabolism 3.1606 0.0007 5 9 gudD , ABUW_2787, kdgD , garD ABUW_1150 ko00620 Pyruvate metabolism 0.3450 0.4518 4 36 ABUW_1624, ald1 , ABUW_0255...”
- An Unprecedented Tolerance to Deletion of the Periplasmic Chaperones SurA, Skp, and DegP in the Nosocomial Pathogen Acinetobacter baumannii
Birkle, Journal of bacteriology 2022 - “...deletion mutants failed. In contrast, we were able to delete a different gene, e.g., ABUW_1852, ABUW_1948, or ABUW_0607, in the surA , skp , and degP knockout strain, indicating that the triple mutant can be genetically manipulated. As the further deletion of DegS and PpiD is...”
DUR1_LACKL / A5H0J2 Urea amidolyase; Pyrimidine-degrading protein 13,15; Uracil catabolism protein 3,5; EC 6.3.4.6; EC 3.5.1.54 from Lachancea kluyveri (Yeast) (Saccharomyces kluyveri) (see paper)
30% identity, 24% coverage
- function: Involved in uracil catabolism. Hydrolysis of urea to ammonia and CO(2).
catalytic activity: urea + hydrogencarbonate + ATP = urea-1-carboxylate + ADP + phosphate + H(+) (RHEA:20896)
catalytic activity: urea-1-carboxylate + H2O + 3 H(+) = 2 NH4(+) + 2 CO2 (RHEA:19029)
cofactor: biotin
subunit: Monomer.
YI01_SCHPO / Q9URY4 Putative amidase C869.01; EC 3.5.1.4 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPAC869.01 amidase (predicted) from Schizosaccharomyces pombe
39% identity, 44% coverage
- catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
- Epigenome Mapping in Quiescent Cells Reveals a Key Role for H3K4me3 in Regulation of RNA Polymerase II Activity
Zeng, Epigenomes 2024 - “...Active SPAC2H10.01 transcription factor Active SPAC3C7.02c pil2/ meiotic eisosome Active SPAC3G9.11c pdc201/ pyruvate decarboxylase Active SPAC869.01 hydrolase, cellular detoxification Active SPAC869.03c urea transmembrane transporter Active SPAC869.04 formamidase, cellular detoxification Active SPAC869.06c hry1/ cation binding protein Active SPAC869.07c mel1/ alpha-galactosidase Active SPAC869.08 mel2/ isoaspartate methyltransferase Active SPAC869.09...”
- An essential role for the Ino80 chromatin remodeling complex in regulation of gene expression during cellular quiescence
Zahedi, Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2023 - “...0,00042619 SPAC869.04 I 5511137 5512369 SPAC869.04 9,23276947 6,5934E-22 SPAC869.03c I 5512757 5514865 SPAC869.03c 9,16835946 9,8841E-22 SPAC869.01 I 5521275 5523181 SPAC869.01 3,00278941 0,00011382 SPBPB21E7.02c II;II 60553;61119 61107;61205 SPBPB21E7.02c 10,5415628 0,00031848 SPBPB21E7.10 II;II 61362;61632 61526;62126 SPBPB21E7.10 10,3509696 0,00048232 SPBPB21E7.11 II;II;II 61526;62598;62944 62449;62885;63086 SPBPB21E7.11 4,55305877 2,1632E-06 SPBC1683.05 II 147915...”
- Cellular economy in fission yeast cells continuously cultured with limited nitrogen resources
Chikashige, Scientific reports 2015 - “...(predicted) 7.41 7.52 9.19 7.97 SPBPB2B2.01 induced amino acid permease (predicted) 4.47 4.80 5.96 5.04 SPAC869.01 induced amidase (predicted) 3.72 3.06 6.03 4.57 SPCC285.05 induced purine nucleoside transmembrane transporter (predicted) 2.46 2.46 3.34 2.72 SPBC800.11 induced inosine-uridine preferring nucleoside hydrolase (predicted) 1.84 1.91 3.50 2.70 SPAC11D3.03c...”
- The global transcriptional response of fission yeast to hydrogen sulfide
Jia, PloS one 2011 - “...upregulated gene Mug46 hpm1 4.25 up homologous Pmf1p factor 1 SPCC550.07 3.72 up acetamidase (predicted) SPAC869.01 2.29 up amidase (predicted) SPBPB2B2.05 2.92 up GMP synthase [glutamine-hydrolyzing] (predicted) SPAC1039.08 2.25 up serine acetyltransferase (predicted) SPAC1002.17c 3.46 up uracil phosphoribosyltransferase (predicted) SPAC4F10.17 2.08 up conserved fungal protein SPCC584.16c...”
- Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation
Nugent, BMC genomics 2010 - “...are down-regulated in mst2 (SPAC186.06, SPAC186.05 and SPBCPT2R1.02 respectively), while at 47 kb telomere distal (SPAC869.01), there is no change in expression levels. This suggests a gradient effect on transcription of genes in these regions. The few genes that are down-regulated in gcn5 are localized near...”
LOC110029361 putative amidase C869.01 from Phalaenopsis equestris
36% identity, 56% coverage
TERG_00010 uncharacterized protein from Trichophyton rubrum CBS 118892
35% identity, 50% coverage
XP_011529069 fatty-acid amide hydrolase 2 isoform X2 from Homo sapiens
27% identity, 89% coverage
- Defects in fatty acid amide hydrolase 2 in a male with neurologic and psychiatric symptoms.
Sirrs, Orphanet journal of rare diseases 2015 - GeneRIF: A male patient with neuropsychiatric disorders attributed to a FAAH2 missense mutation is described.
- Lipid droplets are novel sites of N-acylethanolamine inactivation by fatty acid amide hydrolase-2.
Kaczocha, The Journal of biological chemistry 2010 - GeneRIF: results establish FAAH-2 as a bone fide N-acylethanolamine-catabolizing enzyme and suggest that inactivation is spatially separated in cells of higher mammals
- Biochemical and biological properties of 4-(3-phenyl-[1,2,4] thiadiazol-5-yl)-piperazine-1-carboxylic acid phenylamide, a mechanism-based inhibitor of fatty acid amide hydrolase.
Karbarz, Anesthesia and analgesia 2009 (PubMed)- GeneRIF: Biochemical and biological properties of 4-(3-phenyl-[1,2,4] thiadiazol-5-yl)-piperazine-1-carboxylic acid phenylamide, a mechanism-based inhibitor of fatty acid amide hydrolase.
- A second fatty acid amide hydrolase with variable distribution among placental mammals.
Wei, The Journal of biological chemistry 2006 (PubMed)- GeneRIF: FAAH2 is the second membrane-associated AS enzyme in humans that displays FAAH activity
KR76_17995 amidase from Pimelobacter simplex
34% identity, 91% coverage
bll0246 indoleacetamide hydrolase from Bradyrhizobium japonicum USDA 110
P59385 Indoleacetamide hydrolase from Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)
29% identity, 90% coverage
SMc02881 PUTATIVE AMIDASE PROTEIN from Sinorhizobium meliloti 1021
35% identity, 88% coverage
Q9ALV2 allophanate hydrolase (EC 3.5.1.54) from Enterobacter cloacae (see 2 papers)
32% identity, 71% coverage
MT3264 amidase from Mycobacterium tuberculosis CDC1551
44% identity, 39% coverage
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...2019 2.51 1.65E-33 1.69 1.21E-06 MT3263 Rv3174 Putative dehydrogenase/reductase Bacon et al., 2004 1.80 4.70E-03 MT3264 Rv3175 Possible amidase (aminohydrolase) 1.44 5.28E-03 MT3266 Rv3177 Putative peroxidase Reyes et al., 2012 2.78 4.78E-08 MT3301 * Rv3206c moeZ Molybdenum cofactor biosynthesis and cysteine biosynthesis Voss et al., 2011...”
Rv3175 amidase from Mycobacterium tuberculosis H37Rv
44% identity, 39% coverage
- Aldehyde accumulation in Mycobacterium tuberculosis with defective proteasomal degradation results in copper sensitivity
Limón, mBio 2023 - “...regulatory protein (probable TetR/AcR family) 3.66 1.48E-20 Rv3174 Probable short-chain dehydrogenase or reductase 27.58 0 Rv3175 Possible amidase 2.31 1.11E-11 mesT Probable epoxide hydrolase 7.52 3.85E-80 Rv3177 Possible peroxidase 7.07 4.08E-86 Rv3178 Conserved hypothetical protein 5.48 1.41E-51 Rv0195-Rv0197 Rv0195 Possible two-component transcriptional regulatory protein (LuxR family)...”
- Hit Compounds and Associated Targets in Intracellular Mycobacterium tuberculosis
Tsui, Molecules (Basel, Switzerland) 2022 - “...relatively low-abundance genes such as Rv0370c , Rv3629 , Rv1948 , Rv1825 , Rv0585c , Rv3175 , and Rv3327 is unclear; these mutations may be random or involved in compensating for resistance mutations or providing an additional level of resistance [ 60 ]. Fitness costs caused...”
- Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains
Ullah, Pathogens (Basel, Switzerland) 2021 - “...Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS strain. In addition, lprF, mce2R, mce2B, and Rv2627c were specifically expressed in the three DR strains, and 41...”
- “...and XDR strains all showed low expression of 5 proteins: fadE9, espB, espL, esxK, and Rv3175 ( Figure 1 E). Among them, espB, espL, and esxK were involved in cell wall and cell processes. fadE9 and Rv3175 were involved in lipid metabolism and intermediary metabolism and...”
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...2.51 1.65E-33 1.69 1.21E-06 MT3263 Rv3174 Putative dehydrogenase/reductase Bacon et al., 2004 1.80 4.70E-03 MT3264 Rv3175 Possible amidase (aminohydrolase) 1.44 5.28E-03 MT3266 Rv3177 Putative peroxidase Reyes et al., 2012 2.78 4.78E-08 MT3301 * Rv3206c moeZ Molybdenum cofactor biosynthesis and cysteine biosynthesis Voss et al., 2011 1.16...”
- Mutually exclusive genotypes for pyrazinamide and 5-chloropyrazinamide resistance reveal a potential resistance-proofing strategy
Baughn, Antimicrobial agents and chemotherapy 2010 - “...Rv1263 (30%), Rv2363 (35%), Rv2888c (29%), Rv3011c (33%), Rv3175 (44%), and Rv3375 (35%). Although, this basal level of amidase activity was sufficient for...”
- Genetic requirements for the survival of tubercle bacilli in primates
Dutta, The Journal of infectious diseases 2010 - “...1, amiB1, amiB2 , glgP , Rv1393c, epiA , Rv1526c, Rv1869c, amiA2 , Rv3049c, Rv3085, Rv3175, Rv3224), isoniazid resistance ( iniA ), heat shock ( htpX ), regulation ( kdpE , sirR , mox R3, sigJ ), starvation, cell division, DNA degradation and transport and some...”
- Natural transposon mutagenesis of clinical isolates of Mycobacterium tuberculosis: how many genes does a pathogen need?
Yesilkaya, Journal of bacteriology 2005 - “...Rv2336 plcC plcA 3 3 3 Rv2435c Rv2435c 3 Rv2807 Rv2817c Rv3175 Rv3189 Rv2807 Rv2817c Rv3175 Rv3189 3 3 3 3 sertions in these genes may indicate that IS6110 also...”
A2965_ARTBC / D4B3C8 Putative amidase ARB_02965; EC 3.5.1.- from Arthroderma benhamiae (strain ATCC MYA-4681 / CBS 112371) (Trichophyton mentagrophytes) (see 2 papers)
36% identity, 46% coverage
Q0BRB0 allophanate hydrolase (EC 3.5.1.54) from Granulibacter bethesdensis (see 2 papers)
34% identity, 72% coverage
4gysB / Q0BRB0 Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate (see paper)
34% identity, 87% coverage
- Ligand: malonate ion (4gysB)
AMI4G_ARATH / A0A1P8B760 Probable amidase At4g34880; EC 3.5.1.4 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_001329257 Amidase family protein from Arabidopsis thaliana
31% identity, 90% coverage
A9CMR9 Amidase homolog from Saccharomyces pastorianus
40% identity, 42% coverage
BTH_II1476 6-aminohexanoate-cyclic-dimer hydrolase from Burkholderia thailandensis E264
31% identity, 94% coverage
GRMZM2G111309 amidase precursor from Zea mays
38% identity, 51% coverage
SS1G_11068 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
36% identity, 49% coverage
BCAM0538 putative amidase from Burkholderia cenocepacia J2315
37% identity, 59% coverage
HMPREF0023_2956 amidase from Acinetobacter sp. ATCC 27244
34% identity, 50% coverage
C0J08_14135 amidase from Marinomonas sp. CT5
29% identity, 97% coverage
ESA_01767 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
34% identity, 71% coverage
PSHAa0910 putative allophanate hydrolase from Pseudoalteromonas haloplanktis TAC125
31% identity, 87% coverage
FQ188_09805 amidase from Rhodococcus sp. ANT_H53B
44% identity, 47% coverage
A0A077JIE7 acyl-homoserine-lactone acylase (EC 3.5.1.97) from Acinetobacter sp. Ooi24 (see paper)
40% identity, 40% coverage
N8UB59 Amidase domain-containing protein from Acinetobacter sp. CIP 102129
40% identity, 40% coverage
A0A1D8PDC6 allophanate hydrolase (EC 3.5.1.54) from Candida albicans (see paper)
XP_713590 bifunctional urea carboxylase/allophanate hydrolase from Candida albicans SC5314
32% identity, 23% coverage
DUR1,2 likely multifunctional urea amidolyase from Candida albicans (see paper)
32% identity, 23% coverage
- CharProtDB CGD description: Urea amidolyase, contains urea carboxylase and allophanate hydrolase activities needed to hydrolyze urea to CO2; required for utilization of urea as nitrogen source and for hyphal switch in macrophages; transcription is regulated by Nrg1p
FQ188_16180 amidase from Rhodococcus sp. ANT_H53B
31% identity, 92% coverage
Bphy_7768 amidase from Burkholderia phymatum STM815
BPHY_RS38320, Bphy_7768 amidase family protein from Paraburkholderia caribensis
38% identity, 42% coverage
- A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis
Bellés-Sancho, Frontiers in plant science 2022 - “...and the primers Bphy7768_dn_F_XhoI and Bphy7768_dn_R_ Eco RI for the 525 bp-length to get the Bphy_7768 downstream fragment. A trimethoprim cassette dhfr followed by a transcription terminator was digested with Nde I from the p34E-TpTer plasmid ( Shastri et al., 2017 ) and cloned in between...”
- Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA
Bellés-Sancho, Metabolites 2021 - “...hypothetical protein Bphy_7726 2.53 BPHY_RS38105 ATP-grasp domain-containing protein Bphy_7724 2.26 BPHY_RS36585 DNA-binding protein Bphy_7384 2.24 BPHY_RS38320 indoleacetamide hydrolase Bphy_7768 iaaH 1.69 Genes down-regulated in nifA mutant bacteroids BPHY_RS37800 branched-chain amino acid ABC transporter substrate-binding protein Bphy_7652 2.10 BPHY_RS37125 GntR family transcriptional regulator Bphy_7505 2.18 BPHY_RS37205 hypothetical...”
- “...heme oxygenase domain, respectively; Bphy_7816 (HP), Bphy_7384 encoding a histone family protein DNA-binding protein and Bphy_7768 ( iaaH ) coding for an indole acetamide (IAM) hydrolase ( Figure 3 c) ( Supplementary Figure S1b ). The up-regulation of P. phymatum iaaH expression strongly suggests that the...”
- “...and the increase in indole-acetamide (IAM) as well as the increase in transcript levels of Bphy_7768 coding for a IAM hydrolase ( iaaH ), suggested that P. phymatum NifA is involved in the regulation of auxin levels inside the nodule. In order to investigate a possible...”
1o9oA / Q9ZIV5 Crystal structure of the s131a mutant of malonamidase e2 complexed with malonamate from bradyrhizobium japonicum (see paper)
31% identity, 85% coverage
- Ligand: 3-amino-3-oxopropanoic acid (1o9oA)
atzF / Q936X2 allophanate hydrolase subunit from Pseudomonas sp. (strain ADP) (see 2 papers)
ATZF_PSESD / Q936X2 Allophanate hydrolase; EC 3.5.1.54 from Pseudomonas sp. (strain ADP) (see 2 papers)
Q936X2 allophanate hydrolase (EC 3.5.1.54) from Pseudomonas sp. ADP (see paper)
30% identity, 75% coverage
- function: Hydrolyzes allophanate to NH(3) and CO(2). Can also use malonamate, but with much lower efficiency.
catalytic activity: urea-1-carboxylate + H2O + 3 H(+) = 2 NH4(+) + 2 CO2 (RHEA:19029)
subunit: Homotetramer.
A6739_RS07555 amidase from Acinetobacter baumannii
31% identity, 81% coverage
- Transcriptome Analysis of Acinetobacter baumannii in Rapid Response to Subinhibitory Concentration of Minocycline
Gao, International journal of environmental research and public health 2022 - “...A6739_RS07175, A6739_RS15535, A6739_RS11675 and A6739_RS10785), TonB-dependent siderophore receptor (A6739_RS06520), ABC transporter ATP-binding protein (A6739_RS06535), amidase (A6739_RS07555), acyl-CoA dehydrogenase (A6739_RS07560), aromatic-ring-hydroxylating dioxygenase subunit beta (A6739_RS07580), and NAD(P) transhydrogenase subunit alpha (A6739_RS14015). 3.5. Genes Downregulated by Minocycline Treatment Genes encoding molecular chaperone GroES (A6739_RS03845), chaperonin GroL (A6739_RS03850), class...”
- “...protein ABC-type transporter, ATP binding, ATPase-coupled transmembrane transporter A6739_RS07175 - 1.715529743 up hypothetical protein - A6739_RS07555 amdA 1.461758079 up amidase amidase, indoleacetamide hydrolase A6739_RS07560 - 1.364873266 up acyl-CoA dehydrogenase oxidoreductase A6739_RS07580 - 1.127894768 up aromatic-ring-hydroxylating dioxygenase subunit beta dioxygenase A6739_RS08375 azr 1.071338077 down FMN-dependent NADH-azoreductase oxidoreductase...”
P13397 6-aminohexanoate-cyclic-dimer hydrolase from Pseudomonas sp. (strain NK87)
37% identity, 49% coverage
G8E09_08615 amidase from Acinetobacter pittii
32% identity, 81% coverage
- Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii
Zhang, Frontiers in microbiology 2020 - “...Ring-hydroxylating dioxygenase ferredoxin reductase family protein 2.49 0.0000 0.0000 G8E09_10205 Hypothetical protein 2.45 0.0022 0.0488 G8E09_08615 Amidase 2.45 0.0010 0.0278 G8E09_08625 IacB protein 2.40 0.0001 0.0048 G8E09_14200 Hypothetical protein 2.39 0.0001 0.0044 G8E09_08105 Hypothetical protein 2.39 0.0001 0.0061 G8E09_08620 Acyl-CoA dehydrogenase 2.39 0.0004 0.0138 G8E09_08600 OprD...”
DUR1,2 / P32528 urea amidolyase (EC 6.3.4.6) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 6 papers)
DUR1_YEAST / P32528 Urea amidolyase; EC 6.3.4.6; EC 3.5.1.54 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
P32528 allophanate hydrolase (EC 3.5.1.54); urea carboxylase (EC 6.3.4.6) from Saccharomyces cerevisiae (see 3 papers)
YBR208C Dur1,2p from Saccharomyces cerevisiae
30% identity, 22% coverage
- function: Hydrolysis of urea to ammonia and CO(2)
catalytic activity: urea + hydrogencarbonate + ATP = urea-1-carboxylate + ADP + phosphate + H(+) (RHEA:20896)
catalytic activity: urea-1-carboxylate + H2O + 3 H(+) = 2 NH4(+) + 2 CO2 (RHEA:19029)
cofactor: biotin
subunit: Monomer - New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources
Engel, Genetics 2022 - “...unnecessary punctuation ORF Old gene name New gene name YGL234W ADE5,7 ADE57 YER069W ARG5,6 ARG56 YBR208C DUR1,2 DUR12 YIL154C IMP2 IMP21 Although nonstandard historical names are maintained in SGD, any new names for yeast genes must conform to the standard format. The SGD Gene Registry (...”
- Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica
Dahlin, Frontiers in genetics 2019 - “...well as the upregulation of enzymes involved in nitrogen metabolism such as DUR1,2 (urea amidolyase, YBR208C) and DAL1 (allantoinase, YIR027C). Table 3 GO term enrichment in differentially expressed genes. Go terms enriched more than 2.5-fold. Indented GO terms in brackets are a sub-group of the preceeding...”
- Developing a set of strong intronic promoters for robust metabolic engineering in oleaginous Rhodotorula (Rhodosporidium) yeast species
Liu, Microbial cell factories 2016 - “...b 105 b 14 639 YBR041W DUR1 4446 25 303 b 109 b 12 1239 YBR208C LDP1 1256 10 115 bc 230 b 7 261 RHTO-05627 a Genbank numbers used for BLAST search and gene annotation b Predicted by transcriptomic results c Containing the first intron...”
- Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability
Barbosa, PloS one 2015 - “...responsible for the major part of volatile acetate ester production during fermentation "DUR1 , 2" YBR208C 11.1 Urea amidolyase, contains both urea carboxylase and allophanate hydrolase activities, degrades urea to CO2 and NH3; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in...”
- An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme
Romagnoli, Molecular microbiology 2014 - “...putative amidase 14.7 KLLA0F04235g Conserved hypothetical protein/putative arginase 13.5 KLLA0E08119g Highly similar to S. cerevisiae YBR208C DUR1 2 urea amidolyase 6.1 KLLA0F14366g Similar to S. cerevisiae ARG3 ornithine carbamoyltransferase 4.1 KLLA0F00594g Highly similar to S. cerevisiae GDH3 NADP(+)-dependent glutamate dehydrogenase 3.9 KLLA0B05247g Highly similar to S....”
- Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Picotti, Cell 2009 - “...YKL150W, YEL031W, YGL202W, YDL017W, YGR080W, YPL049C, YGL248W, YEL011W YMR170C, YCL017C 5121024 11 10 YHR107C, YGL100W, YBR208C, YPR118W, YJL172W, YBR283C, YCR088W, YGR256W, YJL026W, YCL030C YOL116W 256512 12 10 YCL017C, YOL116W, YNL161W, YJR051W, YKL068W, YHR138C, YGR232W, YMR199W, YOR267C, YJR134C YGL248W 128256 13 10 YKL141W, YHR074W, YLR330W, YDR436W, YKL129C,...”
- Prediction of protein-protein interactions using protein signature profiling
Mahdavi, Genomics, proteomics & bioinformatics 2007 - “...(= 22421438) proteins may point out a direction for further experimental validation. For example, proteins YBR208C and YGL062W are found interacting using our approach but they are not reported in the experimental dataset. Note that YBR208C contains seven domains, six of which are shared by YGL062W....”
- Comprehensive analysis of co-occurring domain sets in yeast proteins
Cohen-Gihon, BMC genomics 2007 - “...carboxylase, pyruvate carboxylase 1 and 2, urea amidolyase and HFA1 (SwissProt IDs YNR016C, YGL062W, YBR218C, YBR208C and YMR207C). The proteins share four domains: Carbamoyl-phosphate synthase L chain, Carbamoyl-phosphate synthetase large chain N-terminal, Biotin carboxylase C-terminal and Biotin/lipoyl attachment (Interpro IDs IPR005479, IPR005481, IPR005482 and IPR000089). (B)...”
- More
- Altered proteome in translation initiation fidelity defective eIF5G31R mutant causes oxidative stress and DNA damage
Ram, Scientific reports 2022 - “...P40043 RGI1 1.6674 0.0044 13 Q01454 CTF4 1.7217 0.0309 14 P46992 TOH1 1.7233 0.0489 15 P32528 DUR1,2 1.7275 0.0011 16 Q02725 VTC3 1.7513 0.0068 17 P47075 VTC4 1.8045 0.0040 18 P40159 YNL208W 1.8591 0.0191 19 Q04432 HSP31 1.8778 0.0026 20 P22943 HSP12 1.8912 0.0252 21 P43585...”
- Solving the Conundrum: Widespread Proteins Annotated for Urea Metabolism in Bacteria Are Carboxyguanidine Deiminases Mediating Nitrogen Assimilation from Guanidine
Schneider, Biochemistry 2020 - “...(UAAP1): UniProtKB Q87XD7, NCBI WP_005764729.1 Ps CgdB (UAAP2): UniProtKB Q87XD6, NCBI WP_005764727.1 Sc UAL: UniProtKB P32528, NCBI NP_009767.1 Ca UAL: UniProtKB A0A1D8PDC6, NCBI AOW26140.1 ABBREVIATIONS AH allophanate hydrolase CdgAB carboxyguanidine deiminase UAAP urea amidolyase associated proteins UAL urea amidolyase UC urea carboxylase REFERENCES [1] Wyatt BN...”
- Molecular evolution of urea amidolyase and urea carboxylase in fungi
Strope, BMC evolutionary biology 2011 - “...using blastp (version 2.2.17 [ 28 ]). For urea amidolyase search, the S. cerevisiae sequence (P32528) was used as a query. Search was performed using both the full sequence as well as only the amidase domain of this sequence. To search for urea carboxylase sequences, A....”
BB1142 putative amidase from Bordetella bronchiseptica RB50
48% identity, 32% coverage
B7XBZ9 6-aminohexanoate-cyclic-dimer hydrolase (EC 3.5.2.12) from Cupriavidus sp. U124 (see 2 papers)
38% identity, 49% coverage
bll6733 bll6733 from Bradyrhizobium japonicum USDA 110
30% identity, 99% coverage
B5MF68 6-aminohexanoate-cyclic-dimer hydrolase (EC 3.5.2.12) from Rhodococcus sp. U-224 (see paper)
37% identity, 49% coverage
B7XBZ7 6-aminohexanoate-cyclic-dimer hydrolase (EC 3.5.2.12) from Cupriavidus sp. T7 (see 2 papers)
B7XBZ8 6-aminohexanoate-cyclic-dimer hydrolase (EC 3.5.2.12) from Acidovorax sp. T31 (see 2 papers)
38% identity, 49% coverage
nylA / P13398 6-aminohexanoate cyclic dimer hydrolase monomer (EC 3.5.2.12) from Paenarthrobacter ureafaciens (see 4 papers)
NYLA_PAEUR / P13398 6-aminohexanoate-cyclic-dimer hydrolase; Nylon oligomers-degrading enzyme EI; EC 3.5.2.12 from Paenarthrobacter ureafaciens (see paper)
37% identity, 49% coverage
- function: Specifically catalyzes the hydrolysis of 6-aminohexanoic acid cyclic dimer (1,8-diazacyclotetradecane-2,9-dione) to form the linear dimer 6-aminohexanoyl-6-aminohexanoic acid. Is inactive on 6- aminohexanoic acid oligomers (degree of polymerization 2 to 6), various other cyclic amides, cyclic diamides, linear amides, oligopeptides, and casein. Allows the bacterium to grow on a medium containing 6- aminohexanoic acid cyclic dimer as the sole carbon and nitrogen sources.
catalytic activity: 1,8-diazacyclotetradecane-2,9-dione + H2O = N-(6- aminohexanoyl)-6-aminohexanoate (RHEA:16225)
subunit: Homodimer. - Cotinine Hydroxylase CotA Initiates Biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195
Zhao, Applied and environmental microbiology 2021 (secret) - A metagenomic study highlights phylogenetic proximity of quorum-quenching and xenobiotic-degrading amidases of the AS-family.
Tannières, PloS one 2013 - “...Derivatives of QsdB, LibA and NylA The qsdB , libA (G3K3F8 UniProt KB) and nylA (P13398 UniProt KB) genes were synthezised by Eurofins (Germany). Codon usage was optimized for heterologous expression in E. coli . Appropriate restriction sites and six terminal His-codons were incorporated for cloning...”
LOC4335110 probable amidase At4g34880 from Oryza sativa Japonica Group
37% identity, 50% coverage
- Combined miRNA and mRNA sequencing reveals the defensive strategies of resistant YHY15 rice against differentially virulent brown planthoppers
Yu, Frontiers in plant science 2024 - “...LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156b-5p -1.28 -1.56 LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156c-3p -4.39 LOC4335110; LOC4335111; LOC9268400; LOC107278252; LOC107279186 miR156c-5p -1.28 -1.56 LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156d -1.02 -1.08 LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156e -1.28 -1.56 LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156f-3p -3.36...”
- “...LOC9269030; LOC4348312; LOC4332049; LOC9269785; LOC4335110 miR156f-5p -1.02 -1.08 LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156g-3p -4.39 LOC4335110; LOC4335111; LOC9268400; LOC107278252; LOC107279186 miR156g-5p -1.28 -1.56 LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156h-3p -3.36 LOC9269030; LOC4348312; LOC4332049; LOC9269785; LOC4335110 miR156h-5p -1.02 -1.08 LOC4338174; LOC4333935; LOC4333937; LOC4328870; LOC4332289 miR156i -1.28 -1.56...”
B7XC00 6-aminohexanoate-cyclic-dimer hydrolase (EC 3.5.2.12) from Sphingomonas sp. U238 (see 2 papers)
37% identity, 49% coverage
3a2qA / P13398 Structure of 6-aminohexanoate cyclic dimer hydrolase complexed with substrate (see paper)
37% identity, 50% coverage
- Ligand: 6-aminohexanoic acid (3a2qA)
A6A40_22755 amidase from Azospirillum humicireducens
30% identity, 96% coverage
Q87XD4 Amidase family protein from Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)
PSPTO_4244 amidase family protein from Pseudomonas syringae pv. tomato str. DC3000
33% identity, 67% coverage
CC1323 6-aminohexanoate-cyclic-dimer hydrolase, putative from Caulobacter crescentus CB15
29% identity, 88% coverage
Q6CP22 allophanate hydrolase (EC 3.5.1.54); urea carboxylase (EC 6.3.4.6) from Kluyveromyces lactis (see 3 papers)
XP_454317 uncharacterized protein from Kluyveromyces lactis
32% identity, 22% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 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