PaperBLAST
PaperBLAST Hits for reanno::pseudo5_N2C3_1:AO356_14225 5-aminopentanamidase (EC 3.5.1.30) (Pseudomonas fluorescens FW300-N2C3) (264 a.a., MRVALYQCPP...)
Show query sequence
>reanno::pseudo5_N2C3_1:AO356_14225 5-aminopentanamidase (EC 3.5.1.30) (Pseudomonas fluorescens FW300-N2C3)
MRVALYQCPPLPLDPAGNLHRLHQVALEARGADVLVLPEMFMTGYNIGVDAVNVLAEVYN
GEWAQQIGRIAKAANLAIVYGYPERGEDGQIYNAVQLIDAQGERLANYRKSHLFGDLDHA
MFSAGDSALPIVELNGWKLGLLICYDLEFPENARRLALAGAELILVPTANMQPYEFIADV
TVRARAIENQCFVAYANYCGHEAELQYCGQSSIAAPNGSRPALAGLDEALIVGELDRQLL
DDSRAAYNYLHDRRPELYDDLHKH
Running BLASTp...
Found 250 similar proteins in the literature:
AO356_14225 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas fluorescens FW300-N2C3
100% identity, 100% coverage
- mutant phenotype: Specifically important for: L-Lysine. this is an early step in the oxidation of lysine
Pf6N2E2_4777 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas fluorescens FW300-N2E2
98% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (5-AMINOPENTANAMIDASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
PfGW456L13_1170 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas fluorescens GW456-L13
82% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (5-AMINOPENTANAMIDASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Pf1N1B4_2504 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas fluorescens FW300-N1B4
82% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (5-AMINOPENTANAMIDASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
AO353_07425 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas fluorescens FW300-N2E3
77% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (5-AMINOPENTANAMIDASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
PSPTO0517 hydrolase, carbon-nitrogen family from Pseudomonas syringae pv. tomato str. DC3000
65% identity, 98% coverage
B3IVI7 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas putida (see 4 papers)
63% identity, 98% coverage
davA / Q88QV2 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
Q88QV2 5-aminopentanamidase (EC 3.5.1.30) from Pseudomonas putida (see paper)
PP0382 carbon-nitrogen hydrolase family protein from Pseudomonas putida KT2440
PP_0382 carbon-nitrogen hydrolase family protein from Pseudomonas putida KT2440
63% identity, 98% coverage
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
Puchałka, PLoS computational biology 2008 - “...putida . Extensive literature search and careful reannotation has provided considerable evidence that the genes PP0382 and PP5257, currently annotated as carbon-hydrogen hydrolase family protein and oxidoreductase, FAD binding respectively, most probably code for a 5-aminopentamidase and l -pipecolate oxidase, respectively [36] . Another example is...”
- “...Glutarate-semialdehyde; dehydrogenase EC 1.2.1.20 [36] PP0214 4-Aminobutyrate aminotransferase; EC:2.6.1.19, EC:2.6.1.22 5-Aminovalerate transaminase; EC 2.6.1.48 [36] PP0382 Carbon-nitrogen hydrolase family protein 5-Aminopentanamidase; EC 3.5.1.30 [36] PP0383 Tryptophan 2-monooxygenase, putative Lysine 2-monooxygenase; EC 1.13.12.2 [36] PP2336 Aconitate hydratase, putative; EC:4.2.1.3 2-Methylisocitrate dehydratase; EC 4.2.1.99 a PP2432 Oxygen-insensitive NAD(P)H...”
- Multiple and interconnected pathways for L-lysine catabolism in Pseudomonas putida KT2440
Revelles, Journal of bacteriology 2005 - “...which corresponded to the ORF that encodes protein PP0382. The sequence of PP0382 was compared with Downloaded from http://jb.asm.org/ on February 12, 2017 by...”
- “...analysis of the P. putida KT2440 genome revealed that PP0382 forms a cluster with three other genes transcribed in the same direction. The stop codon of PP0382...”
- Systems metabolic engineering of Corynebacterium glutamicum for the production of the carbon-5 platform chemicals 5-aminovalerate and glutarate
Rohles, Microbial cell factories 2016 - “...] C. glutamicum AVA-1 LYS-12+genome-based integration of the P. putida genes davB (PP_0383) and davA (PP_0382) encoding lysine monooxygenase and aminovaleramide amidase, into the bioD genelocus (NCgl2516), encoding dithiobiotin synthetase This work C. glutamicum AVA-2 AVA-1+deletion of lysE gene (NCgl1214), encoding the lysine exporter This work...”
- “...of the structural tuf gene (NCgl0480), and (iii) the biosynthetic genes davB (PP_0383) and davA (PP_0382), which were separated by a 20-bp sized ribosomal binding site as inter-genic region (Fig. 1 ). The putative gabT gene (NCgl0462) was fully deleted from the genome. All DNA fragments...”
- Differential proteomics and physiology of Pseudomonas putida KT2440 under filament-inducing conditions
Crabbé, BMC microbiology 2012 - “...domain protein PP_0322 GlyA-1 gi|26987064 0.44 Serine hydroxymethyltransferase PP_0328 FdhA gi|26987070 0.38* Formaldehyde dehydrogenase, glutathione-independent PP_0382 gi|26987124 0.41 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase PP_0395 gi|26987137 0.19 Hypothetical protein PP_0395 PP_0397 gi|26987139 0.28* Putative serine protein kinase, PrkA PP_0541 gi|26987279 0.28 Acetyltransferase PP_0545 gi|26987283 0.43* Aldehyde dehydrogenase...”
SGR_6069 / B1W481 4-guanidinobutanamidase (EC 3.5.1.4) from Streptomyces griseus subsp. griseus (strain JCM 4626 / NBRC 13350) (see 2 papers)
50% identity, 98% coverage
A0A088BHP3 aryl-acylamidase (EC 3.5.1.13); amidase (EC 3.5.1.4) from Streptomyces sp. (see paper)
43% identity, 97% coverage
C6K3Z5 amidase (EC 3.5.1.4) from Nesterenkonia sp. (see paper)
37% identity, 98% coverage
YP_184329 carbon-nitrogen hydrolase from Thermococcus kodakaraensis KOD1
35% identity, 98% coverage
- The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase
Gagen, Archaea (Vancouver, B.C.) 2016 - “...criteria used, Table 3 for results). Of the proteins classified as being associated with lipids, YP_184329 (annotated as a class 9 apolipoprotein N-acyltransferase) may interact with lipids in the manner that other class 9 acyltransferases interact in, transferring the 1-carbonyl of a phospholipid to the amino...”
- “...a lipoprotein precursor (for mechanism, see [ 95 , 96 ]). However, despite its annotation, YP_184329 was more similar to class 13 nitrilases than to class 9 nitrilases and the substrates of this class are unknown [ 42 ]. YP_184329 was predicted to have transmembrane helices...”
PP3846, PP_3846 carbon-nitrogen hydrolase family protein from Pseudomonas putida KT2440
38% identity, 97% coverage
- Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system
Sun, Microbial cell factories 2018 - “...4033 18/18 5/5 KT2440 harboring pCAS-RK2T pSEVA-gR3939-3940T PP_3939PP_3940 2743 9/10 5/5 KT2440 harboring pCAS-RK2T pSEVA-gR3846T PP_3846 816 10/10 ND KT2440 harboring pCAS-RK2T pSEVA-gR1706T PP_1706 363 15/16 ND KT2440 harboring pCAS-RK2T pSEVA-gR5301T PP_5301 264 10/10 ND KT2440 harboring pCpf1-RK2K pSEVA-gcR3361T PP_3361 3048 4/4 ND KT2440 harboring pCpf1-RK2K...”
- “...mutations of nicC gene, nine other target sites, PP_0552, PP_3361, PP_3733, PP_3889, PP_3939PP_3940, PP_3947PP_3948, PP_1706, PP_3846 and PP_5301, were used to further examine the mutation rate of the CRISPR/Cas9 system. PP_0552, PP_3361, PP_3733 and PP_3889 were selected as genome editing sites in KT2440 harboring pCAS-RK2K. After...”
- A novel R-stereoselective amidase from Pseudomonas sp. MCI3434 acting on piperazine-2-tert-butylcarboxamide
Komeda, European journal of biochemistry 2004 (PubMed)- “...exhibits homology to a carbon-nitrogen hydrolase protein (PP3846) from Pseudomonas putida strain KT2440 (72.6% identity) and PA3598 protein from P. aeruginosa...”
- “...RamA, R-amidase from Pseudomonas sp. MCI3434; PP3846, carbon-nitrogen hydrolase PP3846 from Pseudomonas putida strain KT2440; PA3598, conserved hypothetical...”
4iztA / D0VWZ1 The e41q mutant of the amidase from nesterenkonia sp. An1 showing covalent addition of the acetamide moiety of fluoroacetamide at the active site cysteine
36% identity, 98% coverage
- Ligand: 2-fluoroacetamide (4iztA)
PA3598 hypothetical protein from Pseudomonas aeruginosa PAO1
35% identity, 97% coverage
ramA / Q75SP7 (R)-amidase (EC 3.5.1.100) from Pseudomonas sp. (see paper)
RSAM_PSESP / Q75SP7 (R)-stereoselective amidase; EC 3.5.1.100 from Pseudomonas sp. (see paper)
Q75SP7 (R)-amidase (EC 3.5.1.100) from Pseudomonas sp. (see paper)
36% identity, 96% coverage
- function: Hydrolyzes (R)-piperazine-2-carboxamide and (R)-piperazine-2- tert-butylcarboxamide with strict R-stereoselectivity. Also active towards beta-alaninamide, piperidine-3-carboxmide, D-glutaminamide and slightly active towards L-glutaminamide and piperidine-4-carboxamide.
catalytic activity: (R)-piperazine-2-carboxamide + H2O = (R)-piperazine-2- carboxylate + NH4(+) (RHEA:26542)
catalytic activity: beta-alaninamide + H2O = beta-alanine + NH4(+) (RHEA:26546)
subunit: Monomer.
MSMEG_6733 hydrolase, carbon-nitrogen family protein from Mycobacterium smegmatis str. MC2 155
36% identity, 86% coverage
WH5701_10155 hypothetical protein from Synechococcus sp. WH 5701
35% identity, 76% coverage
F8AEP0 amidase (EC 3.5.1.4) from Pyrococcus yayanosii (see paper)
34% identity, 98% coverage
sll1640 hypothetical protein from Synechocystis sp. PCC 6803
33% identity, 72% coverage
- Widespread Antisense Transcription in Prokaryotes
Georg, Microbiology spectrum 2018 (secret) - Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...Tlr0112, Tll0920 n.d Tlr0221 Synechocystis sp. PCC 6803 Sll1683, Slr0662, Slr1312 Sll1077, Sll0228 n.d Sll0601, Sll1640 n.d Sll1495, Slr0370 Gloeobacter violaceus PCC 7421 Gll4070, Gll3478 n.d Glr1681 Glr1682, Glr2043 n.d Gll2207, Gll1504, Glr3848, Gll2805 Nostoc sp. PCC 7120 All3401, All4887 Alr2310 n.d Alr2001 n.d Alr2826, Alr3771,...”
YCU9_SCHPO / O59829 Probable nitrilase C965.09; EC 3.5.-.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
33% identity, 95% coverage
ZP_01666349 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Thermosinus carboxydivorans Nor1
34% identity, 98% coverage
3klcA / Q9UYV8 Crystal structure of hyperthermophilic nitrilase (see paper)
33% identity, 98% coverage
- Ligand: bromide ion (3klcA)
NITR_PYRAB / Q9UYV8 Nitrilase; PaNit; EC 3.5.5.1 from Pyrococcus abyssi (strain GE5 / Orsay) (see 2 papers)
33% identity, 98% coverage
- function: Nitrilase that hydrolyzes preferentially aliphatic nitriles like malononitrile and fumaronitrile in vitro. These dinitriles are converted to the corresponding monoacid mononitriles, showing the enzyme is regioselective. Cannot hydrolyze compounds with a nitrile group bound to an aromatic ring or amino acid. Its biological role is unknown.
catalytic activity: a nitrile + 2 H2O = a carboxylate + NH4(+) (RHEA:21724)
subunit: Homodimer.
mtnU / O31664 2-oxoglutaramate:glutamine aminotransferase (EC 3.5.1.3) from Bacillus subtilis (strain 168) (see 4 papers)
MTNU_BACSU / O31664 2-oxoglutaramate amidase; EC 3.5.1.111 from Bacillus subtilis (strain 168) (see 2 papers)
33% identity, 92% coverage
pydC / Q846U4 3-amino-isobutyrate synthase (EC 3.5.1.6) from Brevibacillus agri (see paper)
32% identity, 79% coverage
Ta1208 nitrilase related protein from Thermoplasma acidophilum DSM 1728
33% identity, 97% coverage
ZMO1439 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Zymomonas mobilis subsp. mobilis ZM4
35% identity, 96% coverage
- Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4
Chang, Biotechnology for biofuels 2018 - “...and transport proteins. These proteins like ZMO0166, ZMO1207, and ZMO1701 were up-regulated, while ZMO0908 and ZMO1439 were down-regulated. Bacterial ABC transporters which can transport various substrates across cellular membranes are essential in cell viability, virulence, and pathogenicity. The ABC transporter-related proteins were differentially expressed under different...”
- “...9.53-fold change (Fig. 4 ). Furthermore, 13 DEPs (ZMO1408, ZMO1422, ZMO0937, Rho, ZMO0127, ZMO0794, Hcp, ZMO1439, ZMO1167, ZMO0912, RplY, ZMO1593, and ZMO1522) were simultaneously down-regulated; wherein, ZMO1522 exhibited the highest fold change with an average value of 0.10, followed by RplY with average 0.27-fold change and...”
PH0642 hypothetical protein from Pyrococcus horikoshii OT3
32% identity, 98% coverage
- Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis
Aguirre-Sampieri, Journal of structural biology 2024 - “...al., 2022 ). Therefore, it may be necessary to reclassify PaNit and the hypothetical protein PH0642 (PDB 1J31) ( Sakai et al., 2004 ) from P. horikoshii as amidases in the nitrilase superfamily. On the other hand, the asymmetric unit of Nit6803 is a dimer that...”
- “...Sakai N Tajika Y Yao M Watanabe N Tanaka I Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution Proteins 2004 57 869 873 15390259 Schindelin J Arganda-Carreras I Frise E Kaynig V Longair M Pietzsch T Preibisch S Rueden C Saalfeld S...”
- Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway
Kim, Proceedings of the National Academy of Sciences of the United States of America 2016 - “...diagrams comparing overall structures of yNta1 (A), PH0642, putative CN hydrolase from Pyrococcus horikoshii (B), hyperthermophilic nitrilase (C), putative...”
- “...score > 25) with the putative CN hydrolase protein PH0642 (PDB ID code 1J31) (31), a hyperthermophilic nitrilase (PDB ID code 3IVZ) (29), a putative...”
- The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase
Gagen, Archaea (Vancouver, B.C.) 2016 - “...Sakai N. Tajika Y. Yao M. Watanabe N. Tanaka I. Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6 resolution Proteins: Structure, Function and Genetics 2004 57 4 869 873 10.1002/prot.20259 2-s2.0-10344224511 43 Pace H. C. Brenner C. The nitrilase superfamily: classification, structure and...”
- “...enzyme is unknown YP_184329 Apolipoprotein N-acyltransferase 4.31 0.30 Function unknown Shows strong identity to protein Ph0642 (accession 1J31) within class 13 of the nitrilase superfamily, therefore potentially a carbon-nitrogen hydrolase [ 42 , 43 ] YP_182427 Oxetanocin 8.93 4.22 Function unknown Belongs to superfamily of metal-dependent...”
- Protein engineering of a nitrilase from Burkholderia cenocepacia J2315 for efficient and enantioselective production of (R)-o-chloromandelic acid
Wang, Applied and environmental microbiology 2015 - “...identity) from Pyrococcus abyssi (15), hypothetical protein Ph0642 (PDB accession number 1J31, 41% similarity and 25% identity) from Pyrococcus horikoshii (16),...”
- “...2004. Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution. Proteins 57:869 - 873....”
- Unique aliphatic amidase from a psychrotrophic and haloalkaliphilic nesterenkonia isolate
Nel, Applied and environmental microbiology 2011 - “...was the A chain of the hypothetical protein PH0642 from Pyrococcus horikoshii (Protein Data Bank [PDB] code 1j31) (34). This protein has 24.4% identity...”
- “...29.9% (PDB code 2plq) (22); and the hypothetical protein PH0642 from P. horikoshii, 24.4% (PDB code 1j31) (34). In addition, the predicted fold of NitN...”
- Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10
Kaplan, BMC biotechnology 2011 - “...known structures: the NitFhit protein from Caenorhabditis elegans (pdb-code 1EMS) [ 21 ]; hypothetical protein Ph0642 from Pyrococcus horikoshii (1J31) [ 22 ]; Nit3 protein from Saccharomyces cerevisiae (a member of branch 10 of the nitrilase superfamily, pdb-code 1F89) [ 23 ]; the pyrimidine degrading enzyme...”
- “...Sakai N Tajika Y Yao M Watanabe N Tanaka I Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6 A resolution Proteins 2004 57 869 873 10.1002/prot.20259 15390259 Kumaran D Eswaramoorthy S Gerchman SE Kycia H Studier FW Swaminathan S Crystal structure of a...”
- "Hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms
Paiardini, BMC structural biology 2008 - “...Pyrococcus horikoshii 1.60 1UF5 A a/b Agrobacterium sp . 1.60 0.00 31 Unknown Hypothetical Protein Ph0642 10 1JI0 A a/b Thermotoga maritima 2.00 1G6H A a/b Escherichia coli 1.60 0.40 31 Carrier Abc Transporter 11 1JVB A a/b Sulfolobus solfataricus 1.85 1M6H A a/b Homo sapiens...”
- “...Pyrococcus horikoshii 1.60 1UF5 A a/b Agrobacterium sp . 1.60 0.00 31 Unknown Hypothetical Protein Ph0642 14 1JI0 A a/b Thermotoga maritima 2.00 1G6H A a/b Escherichia coli 1.60 0.40 31 Carrier Abc Transporter 15 1JJI A a/b Archaeoglobus fulgidus 2.20 1JKM B a/b Bacillus subtilis...”
- Crystallization and preliminary X-ray data analysis of beta-alanine synthase from Drosophila melanogaster
Lundgren, Acta crystallographica. Section F, Structural biology and crystallization communications 2007 - “...Nakai et al., 2000) and of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31; 28% identity; Sakai et al., 2004) served as search models...”
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Q9XA70 Hydrolase from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
34% identity, 96% coverage
CD2737 putative carbon-nitrogen hydrolase from Clostridium difficile 630
30% identity, 89% coverage
- Characterization of the Clostridioides difficile 630Δerm putative Pro-Pro endopeptidase CD1597
Claushuis, Access microbiology 2024 - “...ClosTron effect CD0725 Bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase, subunit delta 1,80 1,52 Likely ClosTron effect CD2737 Putative nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 1,78 1,66 Possibly ClosTron effect CD0723 Dihydrolipoyl dehydrogenase 1,75 1,57 Likely ClosTron effect CD0777 Putative membrane protein 1,74 1,56 CD0772 sigF RNA polymerase sigma...”
CDR20291_2626 putative carbon-nitrogen hydrolase from Clostridium difficile R20291
29% identity, 95% coverage
6ypaB / O58376 The c146a variant of an amidase from pyrococcus horikoshii with bound glutaramide
32% identity, 96% coverage
- Ligand: pentanediamide (6ypaB)
PA2074 hypothetical protein from Pseudomonas aeruginosa PAO1
35% identity, 85% coverage
SCA_1544 carbon-nitrogen family hydrolase from Staphylococcus carnosus subsp. carnosus TM300
Sca_1544 hypothetical protein from Staphylococcus carnosus subsp. carnosus TM300
29% identity, 97% coverage
A3DHT2 nitrilase (EC 3.5.5.1) from Acetivibrio thermocellus (see paper)
31% identity, 99% coverage
LT85_RS01660 deaminated glutathione amidase from Collimonas arenae
33% identity, 87% coverage
- Identification of Collimonas gene loci involved in the biosynthesis of a diffusible secondary metabolite with broad-spectrum antifungal activity and plant-protective properties
Akum, Microbial biotechnology 2021 - “...family protein WP_038484499.1 LT85_RS01650 MarR family transcriptional regulator WP_038484502.1 LT85_RS01655 TCR/Tet family MFS transporter WP_052135471.1 LT85_RS01660 Deaminated glutathione amidase WP_172656931.1 LT85_RS01665 Hypothetical protein WP_156117398.1 LT85_RS01670 Polysaccharide pyruvyl transferase family protein WP_038484508.1 LT85_RS01675 4'phosphopantetheinyl transferase superfamily protein WP_052134537.1 LT85_RS01680 Thioesterase WP_052134540.1 LT85_RS01685 Polyunsaturated fatty acid/polyketide biosynthesis protein...”
- “...cplI and part of the same predicted operon as cplI are cplJ (LT85_RS01665) and cplK (LT85_RS01660), annotated as a hypothetical protein and a deaminated glutathione amidase respectively. Genetic characterization of 60C09 In mutant 60C09, the EZTn 5 transposon was found inserted into the sequence 5GTATAAGCA3, where...”
NIT1_MOUSE / Q8VDK1 Deaminated glutathione amidase; dGSH amidase; Nitrilase homolog 1; EC 3.5.1.128 from Mus musculus (Mouse) (see 7 papers)
Q8VDK1 deaminated glutathione amidase (EC 3.5.1.128) from Mus musculus (see paper)
33% identity, 72% coverage
- function: Catalyzes the hydrolysis of the amide bond in N-(4- oxoglutarate)-L-cysteinylglycine (deaminated glutathione), a metabolite repair reaction to dispose of the harmful deaminated glutathione. Possesses amidase activity toward deaminated ophthalmate in vitro (PubMed:28373563). Plays a role in cell growth and apoptosis: loss of expression promotes cell growth, resistance to DNA damage stress and increased incidence to NMBA-induced tumors. Has tumor suppressor properties that enhances the apoptotic responsiveness in cancer cells; this effect is additive to the tumor suppressor activity of FHIT. It is also a negative regulator of primary T-cells.
catalytic activity: N-(4-oxoglutaryl)-L-cysteinylglycine + H2O = L- cysteinylglycine + 2-oxoglutarate (RHEA:54532)
catalytic activity: N-(4-carboxy-4-oxobutanoyl)-L-ethylglycylglycine + H2O = N-(2- aminobutanoyl)glycine + 2-oxoglutarate (RHEA:17125)
disruption phenotype: Mice are normal at birth as well as during growth. Mammary glands exhibit an increase in ductal and alveolar structures as well as more cyclin-D1 positive cells in mid-pregnancy. In the basal layer of epidermis, the number of cyclin-D1 positive cells is also higher. No lymphoid malignancy is observed. Kidney cells lacking Nit1 exhibit round and compact shapes, loss of lobular structure, higher cell density with increased S and G2/M cell populations. Cyclin D1 expression is increased, whereas differences in the other cell cycle-associated proteins appeared minimal. T-cells lacking NIT-1 display enhanced proliferation, elevated activation marker expression, accelerated cell cycle progression and aberrant expression of some cell cycle proteins. - Pyruvate-Driven Oxidative Phosphorylation is Downregulated in Sepsis-Induced Cardiomyopathy: A Study of Mitochondrial Proteome.
Shimada, Shock (Augusta, Ga.) 2022 - “...HDHD3 0.602 32 tRNA methyltransferase 10 homolog C Q3UFY8 TRMT10C 1.503 33 Deaminated glutathione amidase Q8VDK1 NIT1 0.571 34 LETM1 domain-containing protein 1 Q924L1 LETMD1 0.656 35 Aurora kinase A-interacting protein Q9DCJ7 AURKAIP1 1.610 Table 2 Primer sequences for qRT-PCR Gene Primer sequence PDHE1 Forward 5-GGG...”
- How Reversible Are the Effects of Fumed Silica on Macrophages? A Proteomics-Informed View.
Torres, Nanomaterials (Basel, Switzerland) 2020 - “...response protein (P20108), a Krebs cycle protein (Q9D2G2), prohibitin (P67778), TMEM11 (Q8BK08), a mitochondrial deamidase (Q8VDK1), a subunit of respiratory complex I (Q9DCT2), and an ATP synthase subunit (P56480). This led us to test whether the mitochondrial transmembrane potential was altered upon exposure to pyrolytic silica....”
- “...ndus3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondria Q9DCT2 1.76/0.01 1.06/0.71 nit1 Nitrilase homolog 1 Q8VDK1 0.53/0.01 0.82/0.10 odo2 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial Q9D2G2 1.33/0.02 0.94/0.80 pdcd6 Programmed cell death protein 6 P12815 1.32/0.04 1.06/0.53 pddc1 Parkinson disease 7 domain-containing protein 1...”
Fisuc_2975 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Fibrobacter succinogenes subsp. succinogenes S85
30% identity, 87% coverage
- Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85
Wu, Scientific reports 2017 - “...lacks glutamate decarboxylases and the malolactic fermentation pathway, and the expression levels of arginine decarboxylases, Fisuc_2975 and Fisuc_2976, were not significantly altered at pH 6.10 and 5.65. Alternatively, we identified some significantly up-regulated genes that are involved in amino acid metabolism and those pathways possibly contribute...”
Q7TQ94 Deaminated glutathione amidase from Rattus norvegicus
33% identity, 71% coverage
ZMO1370 N-carbamoylputrescine amidase from Zymomonas mobilis subsp. mobilis ZM4
31% identity, 87% coverage
- Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis
Martien, mSystems 2021 - “...metabolic route from arginine to homospermidine via the enzymes encoded by ZMO1020, ZMO1019, ZMO1369, and ZMO1370. 1, arginine decarboxylase; 2, agmatine deiminase; 3, N -carbamoylputrescine amidase; 4, sym -homospermidine synthase. 10.1128/mSystems.00987-21.3 FIGS3 Relative protein abundance of arginine biosynthetic enzymes (A) and nucleotide biosynthetic enzymes (B) during...”
- “...in Z. mobilis is predicted to encode agmatine deiminase (ZMO1369) and N- carbamoyl putrescine amidase (ZMO1370). It has been demonstrated that the major polyamine produced in Z. mobilis is sym -homospermidine ( 73 ). The enzymes encoded by ZMO1020, ZMO1369, ZMO1370, and ZMO1019 form a feasible...”
- Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses
Yang, PloS one 2013 - “...hydrolase 2.7 1.10E-05 0.4 1.48E-16 1 ZMO1583 DNA topoisomerase (ATP-hydrolyzing) 2.6 3.40E-03 0.1 1.74E-02 1 ZMO1370 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 2.6 4.80E-03 0.4 7.08E-11 1 ZMO1722 S-(hydroxymethyl)glutathione dehydrogenase/class IIIalcohol dehydrogenase 2.6 4.80E-03 0.3 6.92E-09 1 ZMO1544 Cobaltochelatase 2.6 4.50E-05 0.5 2.75E-15 1 ZMO1576 putative short-chain...”
CG712_RS08380 carbon-nitrogen family hydrolase from Streptococcus thermophilus
30% identity, 98% coverage
XAC2303 beta-alanine synthetase from Xanthomonas axonopodis pv. citri str. 306
32% identity, 80% coverage
- The citrus plant pathogen Xanthomonas citri has a dual polyamine-binding protein
Cremonesi, Biochemistry and biophysics reports 2021 - “...S1 , Supplementary material). In the KEGG database, proteins XAC3923 (SpeA, arginine decarboxylase), XAC2302 (hypothetical), XAC2303 (N-carbamoylputrescine amidase), XAC3924 (SpeE, spermidine synthase), and XAC3002 (synthetase/amidase), are related to polyamine biosynthesis but their role in the bacterium is not clear. Considering that the X. citri polyamine transporter...”
D1O36_02385 carbon-nitrogen family hydrolase from Streptococcus thermophilus
30% identity, 98% coverage
NP_991174 omega-amidase NIT2 from Danio rerio
33% identity, 86% coverage
jhp0294 putative from Helicobacter pylori J99
30% identity, 87% coverage
YP_001306296 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Thermosipho melanesiensis BI429
30% identity, 99% coverage
Q4VBV9 Omega-amidase NIT2 from Danio rerio
33% identity, 88% coverage
- Proteomic analysis of zebrafish (Danio rerio) embryos exposed to benzyl benzoate
Kwon, Environmental science and pollution research international 2023 - “...13 Q6NWL6 Ubiquitin carboxyl-terminal hydrolase 1.52 3.5E-02 14 F1R184 Thioredoxin domain-containing 5 1.63 5.9E-03 15 Q4VBV9 Omega-amidase NIT2 1.53 3.0E-02 16 E7FE19 2,3-cyclic nucleotide 3 phosphodiesterase 1.85 1.3E-04 17 Q58EG2 Erlin-1 7.07 4.1E-16 18 I3ISS5 Ubiquitin-specific peptidase 7 (herpes virus-associated) 1.79 3.9E-04 19 Q6JWU9 Coatomer subunit...”
PAE2075 nitrilase, conjectural from Pyrobaculum aerophilum str. IM2
30% identity, 99% coverage
Q635P5 Hydrolase, carbon-nitrogen family from Bacillus cereus (strain ZK / E33L)
29% identity, 98% coverage
BAS3944 hydrolase, carbon-nitrogen family from Bacillus anthracis str. Sterne
BA4253 hydrolase, carbon-nitrogen family from Bacillus anthracis str. Ames
29% identity, 98% coverage
YP_001244336 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Thermotoga petrophila RKU-1
31% identity, 88% coverage
XIS1_460110 amidohydrolase from Xenorhabdus innexi
31% identity, 97% coverage
- The insect pathogenic bacterium Xenorhabdus innexi has attenuated virulence in multiple insect model hosts yet encodes a potent mosquitocidal toxin
Kim, BMC genomics 2017 - “...PKS), XIS1_460114 (beta- ketoacyl synthase), XIS1_460113 (PfaD family protein), XIS1_460112 (3-oxoacyl-ACP reductase), XIS1_460111 (thioester reductase), XIS1_460110 (amidohydrolase), XIS1_460107 (Type-I PKS) and XIS1_460105 (acyl-CoA thioesterase) and three had NRPS or NRPS-related functions: XIS1_460109 (NRPS), XIS1_460107 (NRPS) and XIS1_460106 (condensation protein). Table 7 Gene location, size and putative...”
- “...XIS1_460113 948 PfaD family proteinglutamate-1-semialdehyde 2,1-aminomutase XIS1_460112 255 3-oxoacyl-(acyl-carrier-protein) reductase XIS1_460111 412 Thioester reductase/polyketide synthase XIS1_460110 258 Amidohydrolase/NAD(P)-binding amidase with nitrilase XIS1_460109 4437 NRPS/glutamate racemase XIS1_460108 2301 NRPS XIS1_460107 1644 Type-I PKS/6-deoxyerythronolide-B synthase XIS1_460106 539 Condensation protein/peptide synthase XIS1_460105 142 Acyl-CoA thioesterase/acyl-CoA thioester hydrolase The arrangement...”
NIT1_HUMAN / Q86X76 Deaminated glutathione amidase; dGSH amidase; Nitrilase homolog 1; EC 3.5.1.128 from Homo sapiens (Human) (see paper)
32% identity, 71% coverage
HP0309 conserved hypothetical protein from Helicobacter pylori 26695
O25079 CN hydrolase domain-containing protein from Helicobacter pylori (strain ATCC 700392 / 26695)
29% identity, 88% coverage
- Carbon Fixation Driven by Molecular Hydrogen Results in Chemolithoautotrophically Enhanced Growth of Helicobacter pylori
Kuhns, Journal of bacteriology 2016 - “...Membrane proteins HP0402 HP0763 HP0576 HP0194 HP0380 HP0309 HP0632 HP0485 HP1454 HP0468 HP0204 HP0106 HP0492 HP1262 HP1346 Phenylalanyl-tRNA synthetase, beta...”
- Sequence divergence and conservation in genomes of Helicobacter cetorum strains from a dolphin and a whale
Kersulyte, PloS one 2013 - “...(HsdM) HP0104 HEL2216 2,3-cyclic-nucleotide 2-phosphodiesterase HP0105 HEL2077 S-ribosylhomocysteinase (LuxS) HP0106 HEL2078 Cystathionine gamma-synthase/cystathionine beta-lyase (MetB HP0309 HEL2219 N-carbomoyl-D-amino acid amidohydrolase (2) HP0311 HEL2220 Hypothetical protein HP0312 HEL2221 ATP-binding protein HP0338 HEL2222 Hypothetical protein HP0614 HEL2224 Hypothetical protein HP0630 HEL2096 NAD(P)H-quinone reductase (MdaB) HP0690 HEL2098 Acetyl Co...”
- Iron and pH homeostasis intersect at the level of Fur regulation in the gastric pathogen Helicobacter pylori
Gancz, Infection and immunity 2006 - “...3.2 2.5 3.1 3.2 2.0 0.5 HP0261-HP0260 MIL (HP0309, HP0310, HP0311) MIL (HP0589) EF (HP0260) Transcriptional unit genes identified in previous studiesc...”
- “...Fur box (HP0294, JHP0279) Theoretical Fur box (HP0309, JHP0294) Ni (HP0588) theoretical Fur box on (JHP0536) Downloaded from http://iai.asm.org/ on February...”
- Prediction of RNA-binding proteins from primary sequence by a support vector machine approach
Han, RNA (New York, N.Y.) 2004 - “...AF1917 (Archaeoglobus fulgidus) Hypothetical protein HP0309 Hypothetical protein PH0461 (Pyrococcus horikoshii) Hypothetical protein yhbY (Escherichia coli)...”
- Acid-adaptive genes of Helicobacter pylori
Wen, Infection and immunity 2003 - “...3.48 25.11 2.90 2.50 3.06 2.61 4.94 2.85 2.31 HP0309 HP0310 HP0312 HP0318 HP0693 HP0737 HP0891 HP0944 HP1020 HP1225 HP1240 HP0030 HP0078 HP0148 HP0152 HP0167...”
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25373 HP_0659 162 O24870 Omp2 163 Q09066 ureG 164 O25776 fldA 165 O25720 TktA 166 O25079 HP_0309 167 O24924 thrC 168 P56082 atpG 169 O25503 speE 170 P55972 infB 171 P56457 leuS 172 O25313 HP_0591 173 O25034 Omp7 174 P56155 pyrF 175 P64655 HP_0135 176 P55995...”
- “...O25530 RfaD 314 O25696 HP_1056 315 O25671 fur 316 O25144 YJR117W 317 P55995 lon 318 O25079 HP_0309 319 O25560 hypB 320 O26096 metN 321 O25509 HP_0838 322 O25612 HP_0958 323 P66119 rplW 324 O25512 CoaBC 325 O25296 apt 326 O25032 OppD 327 P56061 panC 328 O25281...”
NIT2_RAT / Q497B0 Omega-amidase NIT2; Nitrilase homolog 2; EC 3.5.1.3 from Rattus norvegicus (Rat) (see 2 papers)
NP_001029298 omega-amidase NIT2 from Rattus norvegicus
30% identity, 88% coverage
- function: Has omega-amidase activity. The role of omega-amidase is to remove potentially toxic intermediates by converting 2-oxoglutaramate and 2-oxosuccinamate to biologically useful 2-oxoglutarate and oxaloacetate, respectively.
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716)
catalytic activity: 2-oxoglutaramate + H2O = 2-oxoglutarate + NH4(+) (RHEA:32963)
catalytic activity: 2-oxosuccinamate + H2O = oxaloacetate + NH4(+) (RHEA:59412)
subunit: Homodimer. - Fermented food consumption modulates the oral microbiota
Ibarlucea-Jerez, NPJ science of food 2024 - “...Purine nucleoside phosphorylase 32301.9 5.58E04 2.10E02 3.1 P22283 Cystatin-related protein 2 21013.4 5.72E03 4.01E02 17.9 Q497B0 Omega-amidase NIT2 30700.9 7.48E03 4.52E02 5.7 Regulatory and structural activity P02401 60S acidic ribosomal protein P2 11691.9 4.52E07 2.41E04 17.1 D3ZAJ1 Cystatin A (Stefin A) 11034.5 6.41E03 4.17E02 5.0 F1LQM1...”
- PPAR beta/gamma mediates the antihypertensive activity of a synbiotic preparation of Bifidobacterium lactis and Lactobacillus acidophilus in spontaneous hypertensive rats
Huang, Heliyon 2024 - “...0.0152 0.8710 0.6664 14 Q5XI07 Lipoma-preferred partner homolog LPP 17 0.4325 0.0420 1.1272 0.8142 15 Q497B0 Omega-amidase NIT2 NIT2 11 0.4831 0.0090 0.8241 0.7662 16 Q9Z1Z9 PDZ and LIM domain protein 7 PDLI7 15 0.6081 0.0461 0.9727 0.5253 17 P07150 Annexin A1 OS=Rattus norvegicus ANXA1 15...”
- Proteomic analysis of rat colonic mucosa following acupuncture treatment for irritable bowel syndrome with diarrhea
Liu, PloS one 2022 - “...vs M FC P-value FC P-value Q9Z1N4 3(2),5-bisphosphate nucleotidase 1 Bpnt1 1.9 0.036 -2.3 0.017 Q497B0 Omega-amidase NIT2 Nit2 1.6 0.020 -2.0 0.019 P32551 Cytochrome b-c1 complex subunit 2, mitochondrial Uqcrc2 1.5 0.037 -1.5 0.0086 P15999 ATP synthase subunit alpha, mitochondrial Atp5a1 1.4 0.029 -1.5 0.0025...”
- “...0.025 P37397 Calponin-3 Cnn3 - 0.0021 Q5RK00 39S ribosomal protein L46, mitochondrial Mrpl46 - 0.030 Q497B0 Omega-amidase NIT2 Nit2 -2.0 0.019 P43527 Caspase-1; Caspase-1 subunit p20; Caspase-1 subunit p10 Casp1 -1.8 0.048 Q5XIN6 LETM1 and EF-hand domain-containing protein 1, mitochondrial Letm1 -1.6 0.00085 Q9JID2; P82471; P50148...”
- Brown Adipose Tissue Sheds Extracellular Vesicles That Carry Potential Biomarkers of Metabolic and Thermogenesis Activity Which Are Affected by High Fat Diet Intervention.
Camino, International journal of molecular sciences 2022 - “...MVP_RAT Q62667 Major vault protein 0.004 2.31 HYEP_RAT P07687 Epoxide hydrolase 1 0.011 2.30 NIT2_RAT Q497B0 Omega-amidase NIT2 0.012 2.30 GRIFN_RAT O88644 Grifin 0.006 2.29 SAP_RAT P10960 Prosaposin 0.009 2.29 5NTD_RAT P21588 5-Nucleotidase 0.019 2.27 PGAM1_RAT P25113 Phosphoglycerate mutase 1 0.001 2.24 DPP2_RAT Q9EPB1 Dipeptidyl peptidase...”
- Space Radiation-Induced Alterations in the Hippocampal Ubiquitin-Proteome System
Tidmore, International journal of molecular sciences 2021 - “...signature proteins. UniProt Accession Numbers B5DF41 P25093 P62890 * Q3ZB98 Q8K4M9 D3ZBM7 * P25809 P63029 Q497B0 Q91Z79 D4A6D8 P40329 P63088 Q4V882 Q99M64 O08557 P41123 * P69735 Q5M7U6 Q99PE7 O35821 * P46101 P83868 Q5PQN0 Q9ER24 O54922 P46844 P84087 Q5U2T3 Q9JLA3 O55043 P47987 P85970 Q5XHY5 Q9QVC8 P10686 *...”
- Proteomics Reveals the Potential Protective Mechanism of Hydrogen Sulfide on Retinal Ganglion Cells in an Ischemia/Reperfusion Injury Animal Model
Liu, Pharmaceuticals (Basel, Switzerland) 2020 - “...Cnga1 0.0175332 low Q8IX01 SUGP2 0.019042 low P97612 Faah 0.0195873 low P61203 Cops2 0.0208293 high Q497B0 Nit2 0.0211131 high P39069 Ak1 0.0216897 high P11506 Atp2b2 0.0227347 low Q7TP47 Syncrip 0.0239965 low Q8NCB2 CAMKV 0.0247766 low P14854 COX6B1 0.0270203 low P11167 Slc2a1 0.0276784 low P45479 Ppt1 0.0279009...”
- Modulation of the Liver Protein Carbonylome by the Combined Effect of Marine Omega-3 PUFAs and Grape Polyphenols Supplementation in Rats Fed an Obesogenic High Fat and High Sucrose Diet
Méndez, Marine drugs 2019 - “...33,390 53 27 (27) 20 P23457 3-alpha-hydroxysteroid dehydrogenase Akr1c9 Cytoplasm 37,028 40 20 (12) 21 Q497B0 Omega-amidase NIT2 Nit2 Cytoplasm 30,701 28 10 (10) marinedrugs-18-00034-t004_Table 4 Table 4 Carbonylation index calculated for each protein in high-fat and high-sucrose (HFHS) diets. Spot N refers to numbered spot...”
- Proteomic Expression Changes in Large Cerebral Arteries After Experimental Subarachnoid Hemorrhage in Rat Are Regulated by the MEK-ERK1/2 Pathway.
Müller, Journal of molecular neuroscience : MN 2017 - “...P63102 14-3-3 protein zeta/delta 1.03 Q60972 Histone-binding protein RBBP4 0.99 Q9DB16 Calcium-binding protein 39-like 0.96 Q497B0 Omega-amidase NIT2 0.96 B0BNA7 Eukaryotic translation initiation factor 3 subunit I 0.95 P47853 Biglycan 0.94 Q921M3 Splicing factor 3B subunit 3 0.93 O55126 Protein NipSnap homolog 2 0.93 Q8VHI3 GDP-fucose...”
- More
- Identification of the putative tumor suppressor Nit2 as omega-amidase, an enzyme metabolically linked to glutamine and asparagine transamination.
Krasnikov, Biochimie 2009 - GeneRIF: Data report that rat liver Nit2 is omega-amidase and in vivo amidase substrates are alpha-ketoglutaramate and alpha-ketosuccinamate, generated by transamination of glutamine and asparagine, respectively.
SCO6411 hydrolase from Streptomyces coelicolor A3(2)
32% identity, 73% coverage
ORF77 / Q93NG1 2-ketoglutaramate amidase monomer (EC 3.5.1.3) from Paenarthrobacter nicotinovorans (see 2 papers)
NIT_PAENI / Q93NG1 2-oxoglutaramate amidase; Omega-amidase; EC 3.5.1.111 from Paenarthrobacter nicotinovorans (Arthrobacter nicotinovorans) (see paper)
Q93NG1 2-oxoglutaramate amidase (EC 3.5.1.111) from Paenarthrobacter nicotinovorans (see paper)
30% identity, 82% coverage
y3324 hypothetical from Yersinia pestis KIM
YPO0938 putative carbon-nitrogen hydrolase from Yersinia pestis CO92
30% identity, 79% coverage
- Polyamines are essential for the formation of plague biofilm
Patel, Journal of bacteriology 2006 - “...1.2e106, and ypo0939 CO92, with an E value of 1.1e106; aguB, y3324 KIM10, with an E value of 7.1e102, and ypo0938 CO92, with an E value of 6.6e102). Thus, our...”
- Polyamines are essential for the formation of plague biofilm
Patel, Journal of bacteriology 2006 - “...aguB, y3324 KIM10, with an E value of 7.1e102, and ypo0938 CO92, with an E value of 6.6e102). Thus, our in silico analysis suggests that the Y. pestis polyamine...”
SCO6414 hypothetical protein from Streptomyces coelicolor A3(2)
29% identity, 87% coverage
- Quantitative Proteome and Phosphoproteome Analyses of <i>Streptomyces coelicolor</i> Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism
Rioseras, Molecular & cellular proteomics : MCP 2018 - “...4.7 SCO5443 5 Alpha-amylase n.s. 2.2 n.s. 4.7 SCO6411 5 Hydrolase - 2 - 4 SCO6414 4 Hydrolase 1.2 2.3 2.3 4.9 1 For cell division proteins, variations inside the 1 interval showing significant variations (q-value <0.01), are shown. Table III Averaged TMT phosphopeptide abundances (from...”
- Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
Yagüe, PloS one 2014 - “...SCO0740 Probable hydrolase 0.9 2.8 SCO6324 Putative hydrolase 2.2 0.4 SCO1509 Possible hydrolase 0.5 1.6 SCO6414 Possible hydrolase 1.2 0.4 SCO1643 20S proteasome alpha-subunit 0.5 2 SCO7205 Putative hydrolase 1.7 0 SCO3779 Probable nucleoside hydrolase 0.3 1.4 SCO7473 Phenylacetic acid degradation protein PaaC 0.7 3.3 SCO4108...”
- ArgR of Streptomyces coelicolor is a versatile regulator
Pérez-Redondo, PloS one 2012 - “..., forming succinate from arginine, have homologous genes scattered in S. coelicolor genome (SCO7311, SCO5527, SCO6414, SCO5655, SCO4913, SCO5676 and SCO7035) with e-value scores of 10 80 to 10 101 . These genes were not affected by arginine or by the ArgR regulator, with the exception...”
Nit2 / Q9JHW2 ω-amidase NIT2 monomer (EC 3.5.1.3) from Mus musculus (see 2 papers)
NIT2_MOUSE / Q9JHW2 Omega-amidase NIT2; Nitrilase homolog 2; EC 3.5.1.3 from Mus musculus (Mouse) (see 3 papers)
NP_075664 omega-amidase NIT2 from Mus musculus
30% identity, 87% coverage
- function: Has omega-amidase activity (PubMed:19596042, PubMed:28373563). The role of omega-amidase is to remove potentially toxic intermediates by converting 2-oxoglutaramate and 2-oxosuccinamate to biologically useful 2-oxoglutarate and oxaloacetate, respectively (PubMed:19596042). Can also hydrolyze gamma-monomethyl-alpha- ketoglutarate in vitro (PubMed:19596042).
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716)
catalytic activity: 2-oxoglutaramate + H2O = 2-oxoglutarate + NH4(+) (RHEA:32963)
catalytic activity: 2-oxosuccinamate + H2O = oxaloacetate + NH4(+) (RHEA:59412)
subunit: Homodimer. - A high-fat diet induces rapid changes in the mouse hypothalamic proteome.
McLean, Nutrition & metabolism 2019 - “...Omega-amidase NIT2 6.88 30,652 104,200 87,480 Amino acid metabolism Score: 45 Matches: 3(1) Sequences: 3(1) Q9JHW2 121 1.30E-02 1.5 Cytidine deaminase 5.63 15,212 32,230 47,840 Pyrimidine metabolism, Negative regulation of cell growth Score: 34 Matches: 1(1) Sequences: 1(1) P56389 59 1.70E-02 1.3 Haloacid dehalogenase-like hydrolase domain-containing...”
- Does reversible cysteine oxidation link the Western diet to cardiac dysfunction?
Behring, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2014 - Conserved sequence repeats of IQGAP1 mediate binding to Ezrin.
Liu, Journal of proteome research 2014 - “...Q99KP3 4 28 C Oxidoreducatse Inorganic pyrophosphatase Ppa1 Q9D819 3 34 C Hydrolase -amidase Nit2 Q9JHW2 2 12 C Hydrolase Bifunctional ATP-dependent dihydroxyacetone kinase /FAD-AMP lyase (cyclizing) Dak Q8VC30 7 23 C 2 Kinase/lyase/transferase Sedoheptulokinase Shpk Q9D5J6 2 5 C Kinase/transferase abhydrolase domain-containing protein 14B Abhd14b...”
- Proteome adaptations in Ethe1-deficient mice indicate a role in lipid catabolism and cytoskeleton organization via post-translational protein modifications.
Hildebrandt, Bioscience reports 2013 - “...1 3.01 Kidney 18 Q60866 Phosphotriesterase 0.34 19 P28825 Meprin A subunit alpha 0.37 20 Q9JHW2 Omega-amidase NIT2 0.41 21 Q9QUM9 Proteasome subunit alpha 0.42 22 Q9DBJ1 Phosphoglycerate mutase 1 0.42 23 Q9QYR9 Acyl-coenzyme A thioesterase 0.47 24 Q8CAQ8 Mitofilin 0.51 25 Q99J99 3-mercaptopyruvate sulfurtransferase 0.52...”
- Proteomic changes at 8 weeks after infection are associated with chronic liver pathology in experimental schistosomiasis
Manivannan, Journal of proteomics 2012 (secret) - Molecular identification of omega-amidase, the enzyme that is functionally coupled with glutamine transaminases, as the putative tumor suppressor Nit2.
Jaisson, Biochimie 2009 (PubMed)- GeneRIF: Data conclude that mammalian nitrilase 2 is omega-amidase.
VpaChn25_1373 N-carbamoylputrescine amidase from Vibrio parahaemolyticus
31% identity, 85% coverage
YAFV_STAA4 / P0DP65 Omega-amidase YafV; saYafV; EC 3.5.1.3 from Staphylococcus aureus (strain 04-02981) (see paper)
SA1841 hypothetical protein from Staphylococcus aureus subsp. aureus N315
32% identity, 83% coverage
- function: Hydrolyzes alpha-ketoglutaramate (a-KGM) to alpha- ketoglutarate (alpha-KG) and ammonia (specific activity 3.87 umol/min/mg), has weak activity on L-glutamine, almost no activity on deaminated glutathione (dGSH) and none on glutathione. May function as a metabolite repair enzyme.
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716) - 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 - “...MutT/nudix family protein sa_c3186s2733_a_at 3.6 2.5 5 SA1768 GAF domain-containing protein sa_c3455s2983_a_at 3.1 2.5 2.5 SA1841 MutT/nudix family protein sa_c3597s3080_at 2.6 2.5 15 SA1894 HIT family protein sa_c4896s4204_a_at * 7.1 2.5 2.5 SA2242 xanthine/uracil permease sa_c5009s4311_a_at 2.0 2.5 ND SA2276 inosine-uridine preferring nucleoside hydrolase Energy production...”
- A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
Geissmann, Nucleic acids research 2009 - “...). We have identified typical Rho-independent terminators located upstream of several genes (i.e. SA1002, SA1108, SA1841, splA and uppS ) suggesting that these genes might be regulated by a premature transcription termination event ( Supplementary Table S1 ). In agreement with this observation, cis -acting RNAs...”
P55177 Hydrolase in agr operon from Staphylococcus aureus
USA300HOU_2029 amidohydrolase from Staphylococcus aureus subsp. aureus USA300_TCH1516
WP_000867960 carbon-nitrogen family hydrolase from Staphylococcus aureus
32% identity, 83% coverage
- Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
Hiltunen, Microorganisms 2019 - “...Q6GHI2 CtpA-like serine protease Q6GGY8 HtrA-like serine protease Q6GI62 Hydrolase encoded by the agr operon P55177 Probable thiol peroxidase Q6GFZ4 Uncharacterized oxidoreductase SAR2567 Q6GDV6 Peptide methionine sulfoxide reductase MsrB Q6GGY4 Heme-dependent peroxidase (SAV0587) Q99W24 Thioredoxin reductase Q6GB66 NADPH-dependent oxidoreductase Q6GJR6 Multicopper oxidaseMco Q6GIX3 Nitric oxide synthase...”
- Identification of Genes Regulating Cell Death in Staphylococcus aureus
Yee, Frontiers in microbiology 2019 - “...wall synthesis ( n = 1). Two of the candidates were hypothetical proteins. Interestingly, two (USA300HOU_2029, gltT ) of the top four death-sensitive mutants (USA300HOU_0329, USA300HOU_2029, USA300HOU_2386, and gltT ) harbored mutations pertaining to glutamate metabolism. TABLE 2 Genes whose mutations resulted in more cell death...”
- “...USA300HOU_0649 ABC transporter ATP-binding protein USA300HOU_0329 ABC transporter ATP-binding protein USA300HOU_2386 Metabolism Isochorismatase USA300HOU_0200 Amidohydrolase USA300HOU_2029 Transcription Transcription regulator USA300HOU_0336 Cell wall capA Capsular polysaccharide biosynthesis protein USA300HOU_2664 Hypothetical proteins Unknown USA300HOU_1780 Unknown USA300HOU_2496 Death-Sensitive Strains Are Less Persistent in vitro ; Strains With Mutations Involved...”
- Association between the agr locus and the presence of virulence genes and pathogenesis in Staphylococcus aureus using a Caenorhabditis elegans model.
Thompson, International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2017 (PubMed)- GeneRIF: There was a strong association between the carriage of virulence genes and the presence of the agr operon in clinical strains of S. aureus.
NIT2_HUMAN / Q9NQR4 Omega-amidase NIT2; Nitrilase homolog 2; EC 3.5.1.3 from Homo sapiens (Human) (see 4 papers)
Q9NQR4 omega-amidase (EC 3.5.1.3) from Homo sapiens (see paper)
NP_064587 omega-amidase NIT2 from Homo sapiens
30% identity, 87% coverage
- function: Has omega-amidase activity (PubMed:19595734, PubMed:22674578). The role of omega-amidase is to remove potentially toxic intermediates by converting 2-oxoglutaramate and 2-oxosuccinamate to biologically useful 2-oxoglutarate and oxaloacetate, respectively (PubMed:19595734).
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716)
catalytic activity: 2-oxoglutaramate + H2O = 2-oxoglutarate + NH4(+) (RHEA:32963)
catalytic activity: 2-oxosuccinamate + H2O = oxaloacetate + NH4(+) (RHEA:59412)
subunit: Homodimer. - Downregulation of lncRNA APCDD1L-AS1 due to DNA hypermethylation and loss of VHL protein expression promotes the progression of clear cell renal cell carcinoma.
Yang, International journal of biological sciences 2022 - “...part 0.002548084 P68431, P62805, P16402, P16401 P10412, P16403, O00268, Q8IUE6 GO:0042581 specific granule 0.003470143 Q9NX76, Q9NQR4, Q5T4S7 GO:0000228 nuclear chromosome 0.004498937 P68431, P62805, P16402, P16401 P10412, P16403, O00268, Q8IUE6 GO:0044427 chromosomal part 0.006060522 P68431, P62805, Q5TEC6, P16402 P16401, P10412, B7Z7S9, P16403 O00268, Q8IUE6, Q9NVF7 GO:0090575 RNA...”
- “...P68431, P62805, Q5TEC6, P16402 P16401, P10412, B7Z7S9, P16403 O00268, Q8IUE6, Q9NVF7 GO:0070820 tertiary granule 0.01950291 Q9NQR4, Q5T9A4, Q5T4S7 GO:0005719 nuclear euchromatin 0.02006129 P16402, P16403 GO:0030667 secretory granule membrane 0.02145841 Q9NX76, O95716, Q5T9A4, Q5T4S7 GO:0048471 perinuclear region of cytoplasm 0.02266291 P04732, P16989, Q96J84, P15531 Q9BR76, P15121 GO:0101003...”
- A Proteomic Study Suggests Stress Granules as New Potential Actors in Radiation-Induced Bystander Effects
Tudor, International journal of molecular sciences 2021 - “...protein HSPD1 8.32 70.924 1.83 0.0186 P62917 60S ribosomal protein L8 11.15 32.789 1.79 0.0017 Q9NQR4 Omega-amidase NIT2 6.73 47.093 1.75 0.0335 P15880 40S ribosomal protein S2 10.37 34.399 1.67 0.0156 O75367 Core histone macro-H2A.1 9.75 68.531 1.67 0.0379 Q13126 S-methyl-5-thioadenosine phosphorylase 9.17 186.699 1.64 0.0031...”
- PERK-mediated expression of peptidylglycine α-amidating monooxygenase supports angiogenesis in glioblastoma
Soni, Oncogenesis 2020 - “...(SRS11) 2.16 1.43 Q15811 Intersectin-1 (ITSN1) 2.61 1.95 Q16666 Gamma-interferon-inducible protein 16 (IF16) 2.08 1.97 Q9NQR4 Omega-amidase NIT2 (NIT2) 2.19 1.71 a Fold-change protein expression level normalized to the respective normoxic conditions, as determined by mass spectrometry analysis. PERK regulates PAM at mRNA level independent of...”
- Identification of HO-1 as a novel biomarker for graft acute cellular rejection and prognosis prediction after liver transplantation
Jia, Annals of translational medicine 2020 - “...protein S23 RPS23 0.753 O75191 Xylulose kinase XYLB 0.755 P30613 Pyruvate kinase PKLR PKLR 0.758 Q9NQR4 Omega-amidase NIT2 NIT2 0.758 O94855 Protein transport protein Sec24D SEC24D 0.760 P83111 Serine beta-lactamase-like protein LACTB, mitochondrial LACTB 0.761 Q6UWY5 Olfactomedin-like protein 1 OLFML1 0.762 Q86SX6 Glutaredoxin-related protein 5, mitochondrial...”
- Salivary proteome signatures in the early and middle stages of human pregnancy with term birth outcome.
Dey, Scientific reports 2020 - “...0.000 0.000 2 O95274 Ly6/PLAUR domain-containing protein 3 LYPD3 1.13 0.87 0.77 0.006 0.024 2 Q9NQR4 Omega-amidase NIT2 NIT2 1.09 0.89 0.82 0.000 0.000 2 Q99497 Protein/nucleic acid deglycase DJ-1 PARK7 0.95 1.00 1.05 0.000 0.000 2 Q9ULZ3 Apoptosis-associated speck-like protein containing a CARD PYCARD 1.14...”
- Quantitative proteomics analysis of young and elderly skin with DIA mass spectrometry reveals new skin aging-related proteins.
Ma, Aging 2020 - “...form PYGL 0.020716 P00918 Carbonic anhydrase 2 CA2 0.005483 P23280 Carbonic anhydrase 6 CA6 0.003541 Q9NQR4 Omega-amidase NIT2 NIT2 0.015016 P55072 Transitional endoplasmic reticulum ATPase VCP 0.01621 Chaperone P10909 Clusterin CLU 0.001427 P50990 T-complex protein 1 subunit theta CCT8 0.04342 Apoptosis, proliferation and differentiation proteins Q15631...”
- Chronic Occupational Exposure to Ionizing Radiation Induces Alterations in the Structure and Metabolism of the Heart: A Proteomic Analysis of Human Formalin-Fixed Paraffin-Embedded (FFPE) Cardiac Tissue.
Azimzadeh, International journal of molecular sciences 2020 - “...2.82 10 2 O95182 NDUFA7 NADH dehydrogenase [ubiquinone] 1 alpha 7 0.59 8.36 10 3 Q9NQR4 NIT2 Omega-amidase NIT2 0.59 1.48 10 2 Q96ND0 FAM210A Protein FAM210A 0.58 3.74 10 2 P46109 CRKL Crk-like protein 0.58 2.56 10 2 Q13409 DYNC1I2 Cytoplasmic dynein 1 intermediate chain...”
- The human olfactory cleft mucus proteome and its age-related changes.
Yoshikawa, Scientific reports 2018 - “...7.7 8 P63208 18817 S-phase kinase-associated protein 1 25.2 1.6 7.1 0.6 3.5 >15 9 Q9NQR4 30988 Omega-amidase NIT2 14.7 0.9 4.3 0.3 3.4 4.7 10 P00325 40684 Alcohol dehydrogenase 1B 16.6 0.8 4.9 0.6 3.4 6.1 11 P02144 17230 Myoglobin 11.9 0.7 3.5 0.4 3.4...”
- More
- A novel efficient producer of human ω-amidase (Nit2) in Escherichia coli.
Epova, Analytical biochemistry 2021 (PubMed)- GeneRIF: A novel efficient producer of human omega-amidase (Nit2) in Escherichia coli.
- NIT2 overexpression predicts poor prognosis in tongue squamous cell carcinoma patients.
Chen, Molecular biology reports 2020 (PubMed)- GeneRIF: NIT2 overexpression predicts poor prognosis in tongue squamous cell carcinoma patients.
- Downregulation of NIT2 inhibits colon cancer cell proliferation and induces cell cycle arrest through the caspase-3 and PARP pathways.
Zheng, International journal of molecular medicine 2015 (PubMed)- GeneRIF: Downregulation of NIT2 inhibits colon cancer cell proliferation and induces cell cycle arrest through the caspase-3 and PARP pathways
- Human nitrilase-like protein does not catalyze the hydrolysis of vildagliptin.
Asakura, Drug metabolism and pharmacokinetics 2014 (PubMed)- GeneRIF: Human NIT1/2 are not involved in the metabolism of vildagliptin.
- Structural insights into the catalytic active site and activity of human Nit2/ω-amidase: kinetic assay and molecular dynamics simulation.
Chien, The Journal of biological chemistry 2012 - GeneRIF: The activity and substrate specificity of human Nit2 was determined with alpha-ketoglutaramate and succinamate as substrates.
- Growth inhibitory effect of the human NIT2 gene and its allelic imbalance in cancers.
Lin, The FEBS journal 2007 (PubMed)- GeneRIF: Genotype analysis in 4 types of tumor tissue showed allelic imbalance surrounding NIT2 locus; results show that NIT2 plays an important role in cell growth inhibition & links to malignancies, suggesting Nit2 may be a potential tumor suppressor candidate
B7Z410 cDNA FLJ50791, highly similar to Nitrilase homolog 1 from Homo sapiens
32% identity, 83% coverage
- miR-543 functions as a tumor suppressor in glioma in vitro and in vivo
Xu, Oncology reports 2017 - “...U87 glioma cells. Protein miR-543:miR-NC Upregulated ( 20 ) Q5LJA5 34.14326014 A0A024RDE8 26.47960363 GSLG1 20.15439479 B7Z410 19.53041636 ARK72 16.30160722 AN32B 10.8127484 B4DEX5 10.1040579 CKAP5 10.04365302 Q6IAX1 8.927064395 A0A024QZN8 7.504923236 F8W8R3 7.432445004 SYNJ2 7.16088658 POMP 6.727857068 IF4B 6.688933707 A0A0C4DFT3 6.599762499 EXOS3 6.591721953 B7ZM73 5.992988916 SSRD 5.988039064 Q53HS1...”
YP_003400513 Nitrilase/cyanide hydratase and apolipoprotein N- acyltransferase from Archaeoglobus profundus DSM 5631
32% identity, 86% coverage
tlr0112 ORF_ID:tlr0112~probable hydrolase from Thermosynechococcus elongatus BP-1
32% identity, 81% coverage
- Species-specific transcriptomic network inference of interspecies interactions
McClure, The ISME journal 2018 - “...amino acid metabolism genes (aguA, aguB, thrCII; tlr0111, tlr0112, tlr0982) and a sulfur metabolism gene (sir; tlr0339). Genes with positive edges were mainly...”
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...CYB_2779, CYB_0482 CYB_1744 n.d CYB_1181 n.d CYB_0715, CYB_1893 Thermosynechococcus elongatus BP-1 Tlr1866, Tll1807 n.d. Tlr0111 Tlr0112, Tll0920 n.d Tlr0221 Synechocystis sp. PCC 6803 Sll1683, Slr0662, Slr1312 Sll1077, Sll0228 n.d Sll0601, Sll1640 n.d Sll1495, Slr0370 Gloeobacter violaceus PCC 7421 Gll4070, Gll3478 n.d Glr1681 Glr1682, Glr2043 n.d Gll2207,...”
aguB / Q9I6J8 N-carbamoylputrascine amidohydrolase subunit (EC 3.5.1.53) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
PA14_03830 N-carbamoylputrescine amidohydrolase from Pseudomonas aeruginosa UCBPP-PA14
PA0293 N-carbamoylputrescine amidohydrolase from Pseudomonas aeruginosa PAO1
29% identity, 85% coverage
- Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist
Ueda, Microbial biotechnology 2009 - “...similarity PA14_00570 PA0045 4.6 1.1 3.7 Hypothetical protein PA14_00580 PA0046 4.6 1.1 4.3 Hypothetical protein PA14_03830 PA0293 aguB 10.6 1.1 9.8 N carbamoylputrescine amidohydrolase PA14_06420 PA0492 9.8 2.1 24.3 Conserved hypothetical protein PA14_06430 PA0493 7 1.6 10.6 Probable biotinrequiring enzyme PA14_06480 PA0496 6.5 1.6 8.6 Conserved...”
- Putrescine and Its Metabolic Precursor Arginine Promote Biofilm and c-di-GMP Synthesis in Pseudomonas aeruginosa
Liu, Journal of bacteriology 2022 (secret) - Increased ParB level affects expression of stress response, adaptation and virulence operons and potentiates repression of promoters adjacent to the high affinity binding sites parS3 and parS4 in Pseudomonas aeruginosa
Kawalek, PloS one 2017 - “...abundance of ParB. Majority of them seem to be involved in the stress adaptation. Only PA0293 , PA1894 , PA2113 and PA2792 showed opposite trends of the response. These four genes are downregulated in parB - deficient cells and upregulated in response to ParB excess, hence...”
- Common ancestry and novel genetic traits of Francisella novicida-like isolates from North America and Australia as revealed by comparative genomic analyses
Siddaramappa, Applied and environmental microbiology 2011 - “...PAO1 AguA (PA0292; E value, 1e58) and AguB (PA0293; E value, 8e94), respectively. These proteins are key components in the biosynthesis of polyamines in...”
- Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist
Ueda, Microbial biotechnology 2009 - “...PA14_00570 PA0045 4.6 1.1 3.7 Hypothetical protein PA14_00580 PA0046 4.6 1.1 4.3 Hypothetical protein PA14_03830 PA0293 aguB 10.6 1.1 9.8 N carbamoylputrescine amidohydrolase PA14_06420 PA0492 9.8 2.1 24.3 Conserved hypothetical protein PA14_06430 PA0493 7 1.6 10.6 Probable biotinrequiring enzyme PA14_06480 PA0496 6.5 1.6 8.6 Conserved hypothetical...”
- Transcriptome analysis of agmatine and putrescine catabolism in Pseudomonas aeruginosa PAO1
Chou, Journal of bacteriology 2008 - “...by University of California, Berkeley PA0265 PA0266d PA0292 PA0293 PA0295 PA0296 PA0297 PA0298 PA0299 PA0321 PA0322 PA0534 PA0535 PA1178d PA1179d PA1180d PA1409...”
- Chlorella viruses contain genes encoding a complete polyamine biosynthetic pathway
Baumann, Virology 2007 - “...CPA 299 33.5 5.93 At2g27450 100/63 Pa CPA 292 32.7 5.92 PA0293 63/100 PBCV-1 CPA 298 33.2 5.70 A78R 49/50 NY-2A CPA 298 33.2 5.42 B116R 49/51 MT325 CPA 296 32.9...”
- Molecular characterization and regulation of the aguBA operon, responsible for agmatine utilization in Pseudomonas aeruginosa PAO1
Nakada, Journal of bacteriology 2001 - “...this DNA region contains three putative genes, PA0292, PA0293, and PA0294, of unknown function (accession no. AE004467) (Fig. 2). Knockout mutations of genes...”
- “...Materials and Methods, yielding strains PAO5003 (PA0294), PAO5002 (PA0293), and PAO5001 (PA0292). Utilization of agmatine by these mutants as the sole C and N...”
F1SKY2 Omega-amidase NIT2 from Sus scrofa
30% identity, 85% coverage
5h8iC / G7ITU5 Crystal structure of medicago truncatula n-carbamoylputrescine amidohydrolase (mtcpa) in complex with n-(dihydroxymethyl)putrescine (see paper)
28% identity, 78% coverage
- Ligand: (4-azanylbutylamino)methanediol (5h8iC)
AGUB_SOLLC / Q9XGI9 N-carbamoylputrescine amidase; EC 3.5.1.53 from Solanum lycopersicum (Tomato) (Lycopersicon esculentum) (see paper)
30% identity, 79% coverage
- function: Involved in polyamine biosynthesis.
catalytic activity: N-carbamoylputrescine + H2O + 2 H(+) = putrescine + NH4(+) + CO2 (RHEA:22284)
subunit: Homooctamer.
PG0143 hydrolase, carbon-nitrogen family from Porphyromonas gingivalis W83
28% identity, 90% coverage
- Growth of Porphyromonas gingivalis on human serum albumin triggers programmed cell death
Ghods, Journal of oral microbiology 2023 - “...of genes encoding enzymes involved in arginine metabolism and polyamine synthesis, including PG0144 (agmatine deiminase), PG0143 (amidohydrolase), and PG0152 (carboxyspermidine decarboxylase). This finding aligns with the higher expression levels (2.0 logFC in W83 at 12.5h when compared to W50 at 20h) of PG1424 the porphyromonas peptidylarginine...”
- “...require further study. Results also indicated a high degree of variability in the expression of PG0143 (amidohydrolase). While this variability was consistent throughout repeat experiments, the expression was consistently higher in strain W83 than W50. Lastly, the analysis confirmed higher levels of expression of the ppGpp...”
- A Novel Regulation of K-antigen Capsule Synthesis in Porphyromonas gingivalis Is Driven by the Response Regulator PG0720-Directed Antisense RNA
Kim, Frontiers in oral health 2021 - “...AI-2/quorum sensing. In contrast, a few genes involved in signaling and metabolism, including PG0707, PG0719, PG0143, PG0497, PG0629, and PG1310 were up-regulated in the PG0720 mutant. Altogether, expression of genes involved in heme acquisition, transcriptional regulation, signaling and metabolism showed significant changes in the PG0720 mutant...”
- “...T9SS type A sorting domain-containing protein 0.65 Enzyme/metabolism PG0135 rsmA 16S rRNA [adenine(1518)-N(6)/adenine(1519)-N(6)]-dimethyltransferase RsmA 1.01 PG0143 Carbon-nitrogen hydrolase 0.87 PG0343 megL Methionine gamma-lyase 0.59 PG0445 pepT Peptidase T 0.75 PG0497 5'-methylthioadenosine/adenosylhomocysteine nucleosidase 0.82 PG0583 Cell division protein FtsA 0.59 PG0629 NAD kinase 0.81 PG1310 queC 7-cyano-7-deazaguanine...”
YP_002730079 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Persephonella marina EX-H1
30% identity, 83% coverage
Q10166 Hydrolase C26A3.11 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
30% identity, 75% coverage
G1TXN1 Omega-amidase NIT2 from Oryctolagus cuniculus
30% identity, 88% coverage
At2g27450 / Q8VYF5 At2g27450-monomer (EC 3.5.1.53) from Arabidopsis thaliana (see paper)
NILP1_ARATH / Q8VYF5 N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G27450 NLP1 (NITRILASE-LIKE PROTEIN 1); N-carbamoylputrescine amidase/ hydrolase, acting on carbon-nitrogen (but not peptide) bonds from Arabidopsis thaliana
29% identity, 78% coverage
- function: Involved in polyamine biosynthesis (PubMed:12435743). Catalyzes the hydrolysis of N-carbamoylputrescine to produce putrescine and ammonia (PubMed:12435743).
catalytic activity: N-carbamoylputrescine + H2O + 2 H(+) = putrescine + NH4(+) + CO2 (RHEA:22284)
subunit: Homooctamer (isoform 2). - Genome-wide analysis of polyamine biosynthesis genes in wheat reveals gene expression specificity and involvement of STRE and MYB-elements in regulating polyamines under drought
Ebeed, BMC genomics 2022 - “...378 42.0 5.31 40.78 TaAIH5 TraesCS5D02G198300 5D:301125775301129288 reverse 424 46.8 5.9 40.55 N-carbamoyl putrescine amidohydrolase AT2G27450 TaNLP11 TraesCS5B02G022300 5B:2082991620833469 forward 242 27.1 5.57 29.1 TaNLP12 TraesCS5A02G024500 5A:1922304519227613 forward 241 27.0 5.57 28.38 S-adenosylmethionine decarboxylase AT3G02470 TaSAMDC1 TraesCS6A02G219500 6A:407085609407086775 forward 443 48.3 5.11 44.57 AT5G15950 TaSAMDC2 TraesCS6D02G202500...”
- Responses of Polyamine-Metabolic Genes to Polyamines and Plant Stress Hormones in Arabidopsis Seedlings
Yariuchi, Cells 2021 - “...1.36 0.74 ARGAH2 AT4G08870 1.51 1.10 1.04 1.18 AIH AT5G08170 1.89 1.13 1.21 1.27 CPA AT2G27450 1.33 1.20 1.21 0.89 SPDS1 AT1G23820 1.77 1.04 1.01 1.61 SPDS2 AT1G70310 1.17 1.85 1.20 0.91 SPMS AT5G53120 1.49 1.90 1.49 0.85 ACL5 AT5G19530 1.10 2.33 1.34 0.28 ** SAMDC1...”
- “...2.31 31.78 ** 0.97 AIH AT5G08170 1.66 0.59 5.24 * 1.34 1.65 3.23 * CPA AT2G27450 1.74 0.74 3.84 * 1.82 1.23 1.49 SPDS1 AT1G23820 1.14 1.72 1.55 1.36 1.07 1.40 SPDS2 AT1G70310 1.85 1.43 2.81 * 1.07 0.89 1.15 SPMS AT5G53120 1.70 0.90 20.25 **...”
- Arabidopsis aldehyde dehydrogenase 10 family members confer salt tolerance through putrescine-derived 4-aminobutyrate (GABA) production
Zarei, Scientific reports 2016 (no snippet) - Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria
Wintermans, Plant molecular biology 2016 - “...At1G58330 ZW2, unknown protein Similarities with RESPONSE TO ABA AND SALT 1 (RAS1) LRF 6.06 At2G27450 Nitrilase-like protein 1 (NLP1) N-carbamoylputrescine amidohydrolase; Involved in polyamine biosynthesis, nitrogen compound metabolic process LRF 5.14 At3G14075 Mono-/di-acylglycerol lipase Involved in lipid metabolic process LRF 5.24 At5G26780 Serine hydroxymethyltransferase 2...”
- Physiological implications of arginine metabolism in plants
Winter, Frontiers in plant science 2015 - “...by agmatine iminohydrolase (AIH, At5g08170, Janowitz et al., 2003 ) and N -carbamoylputrescine amidase (NLP, At2g27450, Piotrowski et al., 2003 ) producing putrescine. Subsequently spermidine and spermine are formed by two different aminopropyltransferases, spermidine synthase (SPDS, At1g23820, At1g70310) and spermine synthase (SPMS, At1g23820, At1g70310, At5g53120; reviewed...”
- Chlorella viruses contain genes encoding a complete polyamine biosynthetic pathway
Baumann, Virology 2007 - “...363 41.1 5.42 M766L 45/51 CPA At CPA 299 33.5 5.93 At2g27450 100/63 Pa CPA 292 32.7 5.92 PA0293 63/100 PBCV-1 CPA 298 33.2 5.70 A78R 49/50 NY-2A CPA 298 33.2...”
glr1682 probable hydratase from Gloeobacter violaceus PCC 7421
31% identity, 86% coverage
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...Sll0228 n.d Sll0601, Sll1640 n.d Sll1495, Slr0370 Gloeobacter violaceus PCC 7421 Gll4070, Gll3478 n.d Glr1681 Glr1682, Glr2043 n.d Gll2207, Gll1504, Glr3848, Gll2805 Nostoc sp. PCC 7120 All3401, All4887 Alr2310 n.d Alr2001 n.d Alr2826, Alr3771, All3556, All5022 Nostoc punctiforme PCC 73102 Npun02000556, Npun02000612 Npun02002114 n.d Npun02002053 n.d...”
MSMEG_0571 hydrolase, carbon-nitrogen family protein from Mycobacterium smegmatis str. MC2 155
31% identity, 80% coverage
D7B8P3 nitrilase (EC 3.5.5.1) from Nocardiopsis dassonvillei ATCC 23218 (see paper)
33% identity, 68% coverage
C5XTG0 CN hydrolase domain-containing protein from Sorghum bicolor
29% identity, 86% coverage
- Identifying differentially expressed proteins in sorghum cell cultures exposed to osmotic stress
Ngara, Scientific reports 2018 - “...123 C5XFH6 Fructose-bisphosphate aldolase OS= Sorghum bicolor GN=SORBI_003G393900 4.01 0.53 2.75E-05 Fructose-bisphosphate aldolase, class-I 130 C5XTG0 Uncharacterized protein OS= Sorghum bicolor GN=SORBI_004G166500 6.10 0.45 5.54E-07 N-carbamoylputrescine amidase 132 C5X9N2 Uncharacterized protein OS= Sorghum bicolor GN=SORBI_002G039000 4.15 0.38 4.03E-06 + ML domain 139 C5YRS3 Purple acid phosphatase...”
W6QZD7 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Pseudomonas pseudoalcaligenes (strain CECT 5344)
32% identity, 91% coverage
STM0308 putative amidohydrolase from Salmonella typhimurium LT2
33% identity, 97% coverage
SerAS9_4277 amidohydrolase from Serratia plymuthica AS9
32% identity, 83% coverage
lpl0007 hypothetical protein from Legionella pneumophila str. Lens
30% identity, 83% coverage
- The Legionella pneumophila Siderophore Legiobactin Is a Polycarboxylate That Is Identical in Structure to Rhizoferrin
Burnside, Infection and immunity 2015 - “...lpp0007 (98, 99) lpg0007 (98, 99) lpa00008 (99, 99) lpl0007 (100, 100) lpc0007 (99, 99) lpw13341 (100, 100) lpp1280 (98, 99) lpg1325 (98, 99) lpa01955 (98, 98)...”
H2MN42 omega-amidase from Oryzias latipes
32% identity, 89% coverage
Syncc9902_1323 possible nitrilase from Synechococcus sp. CC9902
32% identity, 84% coverage
Q93XI4 N-carbamoylputrescine amidase from Oryza sativa subsp. japonica
28% identity, 85% coverage
- Overexpression of EiKCS confers paraquat-resistance in rice (Oryza sativa L.) by promoting the polyamine pathway
Luo, Pest management science 2022 - “...of the key proteins involved in regulating polyamines synthesis also increased, which were Q7X7N2 (1.12fold), Q93XI4 (1.32fold), and Q9SMB1 (1.10fold). This directly promoted the formation of putrescine and its conversion to spermidine and spermine. The expression levels of the proteins Q69P84 (1.15fold), Q9FRX7 (1.20fold), B9F3B6 (1.24fold),...”
- “...osa00330 Arginine and proline Q6ZG77 LYSA Chloroplast Ornithine decarboxylase EC 4.1.1.20 K01586 osa00300 Lysine biosynthesis Q93XI4 CPA Cytoplasm Ncarbamoyl putrescine amidase EC 3.5.1.53 K12251 osa00330 Arginine and proline metabolism Q9SMB1 SPDSYN1 Cytoskeleton Spermidine synthase 1 EC 2.5.1.16 K00797 osa00330 Arginine and proline metabolism Q69P84 OJ1344_B01.271 Chloroplast...”
CG8132 uncharacterized protein from Drosophila melanogaster
30% identity, 83% coverage
- Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration
Doyle, Molecular ecology 2022 - “...EBAG2002106 CG14687 4.71 2.69E28 Muscle function EBAG0002152 CG6409 3.56 4.44E28 Unknown Top by log2fold EBAG0000970 CG8132 (Omegaamidase) 26.93 1.06E27 Metabolic processes EBAG2001904 CG4830 (LongchainfattyacidCoA ligase) 22.22 2.76E11 Metabolic processes EBAG0003336 CG17191 (Triacylglycerol lipase) 21.33 1.67E19 Metabolic processes EBAG0005851 Lsp1alpha 20.08 5.49E22 Muscle function EBAG0004000 CG9522 18.89...”
- “...Hanson & Patel, 2006 ). We also detected genes involved in protein metabolic processes ( CG8132 and CG6428 ) in our top upregulated gene lists suggesting that amino acids may form part of the fuel mix for flight, as seen in some Hymenoptera and in tsetse...”
- An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue
Rotelli, G3 (Bethesda, Md.) 2019 - “...CG3568 I mild altered planar polarity CG4459 I - III enlarged girth of base, disordered CG8132 I - II mild disorder, hair tufts CG9547 II mild disorder, denser anterior CG12171 II - III mild disorder CG34174 II - III disorder CG34177 I - III Mild disorder...”
- “...? ? CG4459 Organic ion transporter; drug / toxin metabolism; hormonal signaling; neurotransmission. SLC22A15? (2) CG8132 Omega Amidase; converts toxic oxoglutaramate to alpha-ketoglutarate NIT2 (14) Tumor Suppressor? CG9547 Glutaryl-CoA dehydrogenase; mitochondrial matrix; lysine and tryptophan metabolism GCDH (15) Glutaric Acidemia CG12171 Steroid dehydrogenase HSD17B14 (4) CG34174...”
- A Genetic Screen Using the Drosophila melanogaster TRiP RNAi Collection To Identify Metabolic Enzymes Required for Eye Development
Pletcher, G3 (Bethesda, Md.) 2019 - “...development. Abbreviations: D-glucosamine-6-phosphate (GLCN-6-P) and 5-phosphoribosylamine (PRA). (B) Bb8 , targeted using BDSC 57484. (C) CG8132 , targeted using BDSC 38321. (D) Gs1 , targeted using BDSC 40836. (E) Gfat2 , targeted using BDSC 34740. For all images, eya composite-GAL4 is abbreviated eya comp . big...”
- “...study in Drosophila has implicated bb8 in promoting spermatogenesis ( Vedelek et al. 2016 ). CG8132 (FBgn0037687; BDSC 57794) encodes an omega-amidase that is homologous to the human nitrilase family member 2 (NIT2) enzyme, which converts -ketoglutaramate into a-ketoglutarate and ammonia ( Jaisson et al. 2009...”
WP_003405206 carbon-nitrogen hydrolase family protein from Clostridium botulinum
31% identity, 83% coverage
lpp0007 hypothetical protein from Legionella pneumophila str. Paris
30% identity, 83% coverage
- The Legionella pneumophila Siderophore Legiobactin Is a Polycarboxylate That Is Identical in Structure to Rhizoferrin
Burnside, Infection and immunity 2015 - “...lpl0005 (99, 99) lpc0005 (98, 99) lpw00061 (100, 100) lpp0007 (98, 99) lpg0007 (98, 99) lpa00008 (99, 99) lpl0007 (100, 100) lpc0007 (99, 99) lpw13341 (100,...”
TERTU_1871 N-carbamoylputrescine amidase from Teredinibacter turnerae T7901
30% identity, 77% coverage
W6QQS6 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Pseudomonas pseudoalcaligenes (strain CECT 5344)
28% identity, 78% coverage
MSMEG_3555 hydrolase from Mycobacterium smegmatis str. MC2 155
29% identity, 73% coverage
YBEM_ECOBD / A0A140NCB4 Deaminated glutathione amidase; dGSH amidase; Nitrilase homolog 1; ecYbeM; EC 3.5.1.128 from Escherichia coli (strain B / BL21-DE3) (see paper)
30% identity, 84% coverage
- function: Hydrolyzes deaminated glutathione (dGSH) to 2-oxoglutarate and L-cysteinylglycine (specific activity 40.63 umol/min/mg), very little activity against alpha-ketoglutaramate (a-KGM, specific activity 0.178 umol/min/mg) and no activity on glutathione or L-glutamine. May function as a metabolite repair enzyme.
catalytic activity: N-(4-oxoglutaryl)-L-cysteinylglycine + H2O = L- cysteinylglycine + 2-oxoglutarate (RHEA:54532)
UTI89_C0629 putative amidase from Escherichia coli UTI89
30% identity, 84% coverage
- High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division
Mediati, BMC genomics 2018 - “...R 361,550364,162 UTI89_C0348 yahD R 2613 17.1 935.0 UTI89_C0349 yahE S UTI89_C0350 yahF C 640,717641,788 UTI89_C0629 ybeM R 1072 4.3 112.5 UTI89_C0630 tatE U UTI89_C0631 lipA H 690,222691,856 UTI89_C0684 glnS J 1635 79.2 8504.0 1,016,1701,016,793 UTI89_C1021 matP MD 624 9.1 575.5 UTI89_C1022 ompA M 1,139,7041,141,232 UTI89_C1147...”
RS9917_11395 possible nitrilase from Synechococcus sp. RS9917
34% identity, 90% coverage
VP0634 hypothetical protein from Vibrio parahaemolyticus RIMD 2210633
31% identity, 45% coverage
- Genetic Relationship, Virulence Factors, Drug Resistance Profile and Biofilm Formation Ability of Vibrio parahaemolyticus Isolated From Mussel
Ashrafudoulla, Frontiers in microbiology 2019 - “...isolates 16S rRNA toxR tox-RS/ Old L-tdh trh VP 0950 VP 0952 VP 0962 VPaI-2 VP0634 VPaI-2 VP0636 VPal-3 VP1094 VPaI-6 VP1263 VPaI-6 VP1253 T6SS VP1409 T6SS VP1418 VP1506 Type 1 pilus VP1510 Type I pilus T3SS VP1690 T3SS VP1677 ATCC17802 + + + + +...”
- Galleria mellonella as an infection model to investigate virulence of Vibrio parahaemolyticus
Wagley, Virulence 2018 - “...T024 PSU 3565 PSU 3384 G35 Reference Chromosome 1 VP0218 VP0234 LPS VP0380 VP0403 VPaI-1 VP0634 VP0643 VPaI-2 P P P P P P VP1071 VP1095 VPaI-3 P P P P P P VP1386 VP1414 T6SS1 VP1549 VP1590 phage f237 P P P P P P...”
- Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
Boyd, BMC microbiology 2008 - “...40 - Present This study VP0380 VP0403 VPaI-1 24 42 Int Absent [ 26 ] VP0634 VP0643 VPaI-2 10 45 Int Absent [ 26 ] VP1071 VP1095 VPaI-3 32 42 Int Partial [ 26 ] VP1386 VP1420 T6SS 57 43 - Absent This study VP1549 VP1590...”
- “...are empty (see Additional file 3 ). Two VPaIs were rearranged. One, the VPaI-2 region (VP0634 to VP0643), is present at the tmRNA gene ( ssrA ) in RIMD2210633, a gene that encodes both tRNA and mRNA properties. In AQ3810, at this same locus, the first...”
tll0920 ORF_ID:tll0920~nitrilase homolog from Thermosynechococcus elongatus BP-1
33% identity, 83% coverage
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...CYB_0482 CYB_1744 n.d CYB_1181 n.d CYB_0715, CYB_1893 Thermosynechococcus elongatus BP-1 Tlr1866, Tll1807 n.d. Tlr0111 Tlr0112, Tll0920 n.d Tlr0221 Synechocystis sp. PCC 6803 Sll1683, Slr0662, Slr1312 Sll1077, Sll0228 n.d Sll0601, Sll1640 n.d Sll1495, Slr0370 Gloeobacter violaceus PCC 7421 Gll4070, Gll3478 n.d Glr1681 Glr1682, Glr2043 n.d Gll2207, Gll1504,...”
lpg0007 probable hydrolase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
29% identity, 82% coverage
- New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila
Ge, Molecular & cellular proteomics : MCP 2022 - “...LegD1 lpg2694 33 5.73 3.69 Phytanoyl-CoA dioxygenase Lpg0567 lpg0567 53.7 10.01 2.32 Peptidase, M23/M37 family Lpg0007 lpg0007 31.9 5.78 1.76 Probable hydrolase MreC lpg0812 33.4 8.25 5.38 2.11 3.06 Cell shapedetermining protein MreC Lpg1446 lpg1446 22.6 5.07 2.54 3.16 Segregation and condensation protein B ProQm lpg0133...”
- The Legionella pneumophila Siderophore Legiobactin Is a Polycarboxylate That Is Identical in Structure to Rhizoferrin
Burnside, Infection and immunity 2015 - “...lpc0005 (98, 99) lpw00061 (100, 100) lpp0007 (98, 99) lpg0007 (98, 99) lpa00008 (99, 99) lpl0007 (100, 100) lpc0007 (99, 99) lpw13341 (100, 100) lpp1280 (98,...”
NIT3_YEAST / P49954 Omega-amidase NIT3; Nitrilase homolog 2; EC 3.5.1.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
YLR351C Nit protein, one of two proteins in S. cerevisiae with similarity to the Nit domain of NitFhit from fly and worm and to the mouse and human Nit protein which interacts with the Fhit tumor suppressor; nitrilase superfamily member from Saccharomyces cerevisiae
29% identity, 91% coverage
- function: Possesses omega-amidase activity (PubMed:28373563). The role of omega-amidase is to remove potentially toxic intermediates by converting 2-oxoglutaramate and 2-oxosuccinamate to biologically useful 2-oxoglutarate and oxaloacetate, respectively.
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716)
subunit: Homodimer. - Structural genomics: a pipeline for providing structures for the biologist
Chance, Protein science : a publication of the Protein Society 2002 - “...cerevisiae s. cerevisiae Human B. subtilis E. coli SP Q01518 SP P49954 SP Q58497 SP P40363 SP P53889 SP P40165 GI 2198534 GI 9966777 SP P20964 SP P52097 157 291...”
- Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages
Fischer, PLoS genetics 2006 - “...YCR011c, YDL031w, YDR140w, YDR449c, YER068w, YER110c, YER141w, YGR096w, YGR235c, YIL043c, YJR010w, YJR096w, YKL184w, YKL134c, YKL103c, YLR351c, YNL062c, YNR007c, and YPR051w ), and another using 16 ubiquitous ribosomal proteins. Both trees had exactly the same topology. Trees were built from the distance matrix using BIONJ [ 27...”
- A modified Saccharomyces cerevisiae strain that consumes L-Arabinose and produces ethanol
Becker, Applied and environmental microbiology 2003 - “...by University of California, Berkeley YLR342w YLR348c YLR351c YLR354c YLR359w YLR370c Standard name (function)a VOL. 69, 2003 L-ARABINOSE 4149 reductase- and...”
- Structural genomics: a pipeline for providing structures for the biologist
Chance, Protein science : a publication of the Protein Society 2002 - “...cyclase-associated protein, human Hypothetical protein YLR351C Bacterial lysine biosynthesis enzyme Hypothetical esterase YJL068C Hypothetical protein YNL168C...”
- Tagging chromatin with retrotransposons: target specificity of the Saccharomyces Ty5 retrotransposon changes with the chromosomal localization of Sir3p and Sir4p
Zhu, Genes & development 1999 - “...VPS45 and PAN2 between YKR060W and KTR2 between YLR351C and YLR352W between PSD1 and YNL168C within YOR268C Nearby chromosomal features a (T) Targeted...”
Q8PXI9 nitrilase (EC 3.5.5.1) from Methanosarcina mazei (see paper)
30% identity, 80% coverage
PFLU5051 putative hydrolase from Pseudomonas fluorescens SBW25
32% identity, 85% coverage
NILP3_ARATH / Q8RUF8 Omega-amidase, chloroplastic; Nitrilase-like protein 3; EC 3.5.1.3 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q8RUF8 omega-amidase (EC 3.5.1.3) from Arabidopsis thaliana (see paper)
AT5G12040, NP_196765 carbon-nitrogen hydrolase family protein from Arabidopsis thaliana
30% identity, 62% coverage
- function: Omega-amidase involved in the metabolism of asparagine. Probably also closely coupled with glutamine transamination in the methionine salvage cycle. Can use alpha-ketosuccinamate and alpha- hydroxysuccinamate as substrates, producing respectively oxaloacetate and malate, or alpha-ketoglutaramate, producing alpha-ketoglutarate.
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716)
disruption phenotype: 2-fold higher levels of alpha-ketosuccinamate and 3-fold higher levels of alpha-hydroxysuccinamate. - The intermediate in a nitrate-responsive ω-amidase pathway in plants may signal ammonium assimilation status
Unkefer, Plant physiology 2023 - “...A. thaliana , At1g77670.1) revealed only 20.3% identity, 33.4% similarity, and 38.2% gaps. A sequence (At5g12040) had been identified as an -amidase in the KEGG database and Zhang and Marsolais (2014) confirmed that this sequence encodes -amidase and uses 2OGM as a substrate. With this sequence...”
- “...analysis to find sequences in other plants and organisms with high homology. The Arabidopsis -amidase (At5g12040, AY093711.1) was used for a BLAST-X analysis for sequences in other plants and organisms with high homology. The GTK or -amidase gene sequences were codon optimized and synthesized commercially and...”
- To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana
Willems, Frontiers in plant science 2021 - “.../Ac-MK AT1G77670 Pyridoxal phosphate-dependent transferase Met41 Ac-T AT5G13050 5-Formyltetrahydrofolate cycloligase (5-FCL) Met43 NH 2 /Ac-S AT5G12040 -amidase Met63 Ac-A AT4G08790 Deaminated glutathione amidase Met29 Ac-A AT5G03370 Acylphosphatase family Met66 NH 2 /Ac-T AT5G15870 Glycosyl hydrolase family 81 protein Met45 Ac-S AT5G41970 Metal-dependent protein hydrolase Met28 NH...”
- “...exonic region of [ (A) , top] IPP1 (AT5G16440) and [ (B) , left] -amidase (AT5G12040). Genome view showing CHX and LTM strand-specific positional Ribo-seq data (red). Vertical lines indicate identified dTIS (orange) and the cTP predicted cleavage site (dark green, dotted line) (Almagro Armenteros et...”
- Downregulation of the E2 Subunit of 2-Oxoglutarate Dehydrogenase Modulates Plant Growth by Impacting Carbon-Nitrogen Metabolism in Arabidopsis thaliana
Condori-Apfata, Plant & cell physiology 2021 - “...isoforms from Arabidopsis were shown to interact with a signal transduction-related protein described as omega-amidase (At5g12040) ( Zhang et al. 2018 ), also known to be associated with amino acid metabolism ( Zhang and Marsolais 2014 ). Such interactions are able to form transient complexes allowing...”
- A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea
Granados, BMC evolutionary biology 2015 - “...outgroup taxa. Primer pairs producing multiple PCR products corresponded to the AT2G17975, AT5G48470, AT3G54170 and AT5G12040 A. thaliana orthologs. Among the regions that amplified a single band, only three produced clear sequences, and were therefore selected for further tests using the extended taxon sampling. The amplified...”
- “...loci were randomly selected from the pool for primer design: AT1G10840, AT1G63900, AT2G17975, AT3G54170, AT4G35850, AT5G12040, AT5G13030, AT5G48470, AT5G57410 and AT5G64860. These genes were subsequently aligned to the A. thaliana full length genomic sequence obtained from TAIR ( http://www.arabidopsis.org/ ). Alignments were screened for regions with...”
- Pre-symptomatic transcriptome changes during cold storage of chilling sensitive and resistant peach cultivars to elucidate chilling injury mechanisms
Pons, BMC genomics 2015 - “...Cyanide detoxification PP1000E01 Cyanate hydratase AT3G23490 CYN PPN066B01 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase family protein AT5G12040 Flavonoid metabolism PPN050G05 Dihydroflavonol 4-reductase-like AT5G58490 Flavonoid/PA biosynthesis PPN052H09 Chalcone synthase 2 AT5G13930 CHS/TT4 Negative regulation of AUX transport Signal transduction pathway Cytoplasmic TOR signaling PPN076G10 Protein lethal with sec...”
- Synergistic use of plant-prokaryote comparative genomics for functional annotations
Gerdes, BMC genomics 2011 - “...enzyme The Methanocaldococcus jannaschii ortholog is a pseudouridine-N1-specific methyltransferase. 31 [ 91 ] (2010) 19 At5g12040 0388 Omega-amidase Omega amidase in methionine salvage pathway Biochemical characterization of the rat and mouse orthologs 113 [ 92 ] (2009) [ 93 ] (2009) Table 3 Status of the...”
- “...fatty acid metabolic process (2.06); photosynthesis, light reaction (1.99); sulfate assimilation (1.98); lignin biosynthesis (1.87) AT5g12040 YafV Omega amidase in methionine salvage pathway Predicted C-N hydrolase family amidase, NAD(P)-binding indoleacetic acid biosynthesis (4.27), cellular response to sulfate starvation, cyanide metabolic process, glucosinolate catabolic process, detoxification of...”
- Proteomic characterization of iron deficiency responses in Cucumis sativus L. roots
Donnini, BMC plant biology 2010 - “...40.7/5.3 43.2/5.7 17 1341 AAT40304 Medicago sativa S-adenosylmethionine synthase 2.5.1.6 SAMs 40.6/5.3 42.8/5.7 28 1760 NP_196765 Arabidopsis thaliana carbon-nitrogen hydrolase family protein 3.5.-.- CNH 33.3/6.0 40.3/8.8 14 2607 P51118 Vitis vinifera glutamine synthetase cytosolic isozyme 1 6.3.1.2 GS1 36.0/5.5 39.2/5.8 29 Redox-related and other proteins 724...”
NP_649732 pyd3 from Drosophila melanogaster
29% identity, 54% coverage
CJJ81176_0971 hydrolase, carbon-nitrogen family from Campylobacter jejuni subsp. jejuni 81-176
Cj0947c putative hydrolase from Campylobacter jejuni subsp. jejuni NCTC 11168
25% identity, 91% coverage
- Novel components of the flagellar system in epsilonproteobacteria
Gao, mBio 2014 - “...CetA Methyl-accepting chemotaxis protein 51156 14 1 11 CJJ81176_0473 Methyl-accepting chemotaxis protein 40562 9 4 CJJ81176_0971 Carbon-nitrogen family hydrolase 34107 5 6 CJJ81176_1272 Hypothetical protein 25530 4 6 CJJ81176_0412 SerS Seryl-tRNA synthetase 46900 2 1 2 CJJ81176_0199 Hypothetical protein 7859 22 12 51 CJJ81176_0359 MotA Flagellar...”
- Aerotolerancy of <i>Campylobacter</i> spp.: A Comprehensive Review
Delaporte, Pathogens (Basel, Switzerland) 2024 - “...oxidative stress was observed in C . jejuni with mutations in cj0062c , cj0344 , cj0947c , and cj1388 [ 111 ]. Identification of the mechanisms and genes involved in aerotolerance is important for understanding how aerotolerance develops and how it might be prevented or attenuated....”
- “...[ 21 ] cj1371 , cj1476c , cj0012c [ 103 ] cj0062c , cj0344 , cj0947c , cj1388 [ 111 ] Mutating these genes appears to result in an increase in aerotolerance rather than a decrease....”
- Structural and Functional Basis for Targeting Campylobacter jejuni Agmatine Deiminase To Overcome Antibiotic Resistance
Shek, Biochemistry 2017 - “...a peptidyl-arginine deiminase (PAD; NCBI Gene database). Cj0949c is located in the same operon as Cj0947c, which encodes an N-carbamoyl putrescine amidohydroylase (NCP). Thus, similar to the recently characterized Heliobacter pylori agmatine deiminase 14 , we believe that Cj0949c encodes an agmatine deiminase and does not...”
- Phenotypic screening of a targeted mutant library reveals Campylobacter jejuni defenses against oxidative stress
Flint, Infection and immunity 2014 - “...cj1484c cj0062c Miscellaneous acs cj0295 cj0494 cj0561c cj0672 cj0947c cj0949c cj1036c cj1167 cj1209 cj1241 cj1255 cj1340c cj1388 cj1406c cj1623 dprA folP pstC...”
- “...to both H2O2 and menadione sodium bisulfite (flgH and cj0947c), and 1 was hypersensitive to both H2O2 and cumene hydroperoxide (pstC). The remaining 6 mutants...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “...cj0767c, cj0795c, cj0798c, cj0806, cj0813, cj0821, cj0822, cj0847, cj0853c, cj0858c, cj0862c, cj0891c, cj0905c, cj0918c, cj0932c, cj0947c, cj0949c, cj0955c, cj0992c, cj0995c, cj1039, cj1044c, cj1046c, cj1048c, cj1067, cj1080c, cj1081c, cj1088c, cj1096c, cj1104, cj1114c, cj1133, cj1149c, cj1150c, cj1151c, cj1152c, cj1177c, cj1183c, cj1196c, cj1198, cj1202, cj1213c, cj1238, cj1243, cj1248, cj1364c,...”
SERP1488 hydrolase, carbon-nitrogen family from Staphylococcus epidermidis RP62A
28% identity, 87% coverage
WH5701_10020 Possible nitrilase from Synechococcus sp. WH 5701
32% identity, 84% coverage
PADG_11833 uncharacterized protein from Paracoccidioides brasiliensis Pb18
30% identity, 84% coverage
- Characterization of Aspartic Proteases from Paracoccidioides brasiliensis and Their Role in Fungal Thermo-Dimorphism
Silva, Journal of fungi (Basel, Switzerland) 2023 - “...analysis of metabolic pathways carried out in FungiDB showed that proteins identified as PADG_05225, PADG_08047, PADG_11833, and PADG_03562 proteins might be involved with the pathways of the pyrimidine metabolism and UMP (uridine 5-monophosphate) biosynthesis, which are the precursors of the pyrimidine nucleotide ( Table 4 )....”
- “...of aspartic proteases in important cellular processes, such as nucleic acid metabolisms. Notably, PADG_08047 and PADG_11833 proteins may be involved in drug metabolism, suggesting an important role of aspartic proteases in antifungal resistance. 3.3. Inhibition of Aspartic Protease Proteins Causes a Delay in the Mycelium-to-Yeast Transition...”
W6QQZ6 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Pseudomonas pseudoalcaligenes (strain CECT 5344)
36% identity, 67% coverage
BFP66_RS06520 N-carbamoylputrescine amidase from Streptococcus suis
28% identity, 80% coverage
- A novel aquaporin Aagp contributes to Streptococcus suis H2O2 efflux and virulence
Zhu, Virulence 2023 - “...same methodology to construct deletions of exodeoxyribonuclease III ( exo III, BFP66_RS05940 ), AguB ( BFP66_RS06520 ), metQ ( BFP66_RS08225 ) in strain GZ0565 background, as well as Aagp in serotype 2 strain P1/7 background ( Aagp P1/7 ). Supplementary Table S2 contains a list of...”
- “...under H 2 O 2 stress, including BFP66_RS05940 encoding an exodeoxyribonuclease III (exo III) and BFP66_RS06520 encoding an N-carbamoylputrescine amidase (AguB). The gene expression of enzymes encoded by BFP66_RS01580, BFP66_RS05715, BFP66_RS06935, BFP66_RS07745, BFP66_RS04160 ( LDH ) was upregulated under H 2 O 2 condition, and these...”
YAFV_ECOBD / A0A140NDS5 Omega-amidase YafV; ecYafV; EC 3.5.1.3 from Escherichia coli (strain B / BL21-DE3) (see paper)
31% identity, 95% coverage
- function: Hydrolyzes alpha-ketoglutaramate (a-KGM) to alpha- ketoglutarate (alpha-KG) and ammonia (specific activity 6.65 umol/min/mg), has weak activity on L-glutamine, almost no activity on deaminated glutathione (dGSH) and none on glutathione. May function as a metabolite repair enzyme.
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716)
SP_0922 carbon-nitrogen hydrolase family protein from Streptococcus pneumoniae TIGR4
29% identity, 90% coverage
- Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae
Ayoola, Frontiers in microbiology 2019 - “...Manganese ABC transporter substrate-binding lipoprotein 2.7 Polyamine biosynthesis aguA SP_0921 Putative agmatine deiminase 25.7 aguB SP_0922 Carbonnitrogen hydrolase family protein 19.7 nspC SP_0920 Carboxynorspermidine decarboxylase 27.5 speE SP_0918 Polyamine aminopropyltransferase 41.5 TABLE 4 Differentially expressed two component system genes in cadA . Fold Gene Locus change...”
- Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
Jiménez-Munguía, PeerJ 2018 - “...SP_0768, SP_0770 2/4 Downregulated 38627 SP_0785, SP_0786, SP_0787 3/3 Downregulated 38655 SP_0918, SP_0919, SP_0920, SP_0921, SP_0922 5/5 Downregulated 38665 SP_0963, SP_0964 2/2 Downregulated 38674 SP_1013, SP_1014 2/2 Downregulated 38682 SP_1069, SP_1070, SP_1071 3/6 Downregulated 38684 SP_1079, SP_1080 2/2 Downregulated 38726 SP_1276, SP_1277, SP_1278 3/3 Downregulated 38731...”
Q84FR7 N-carbamoyl-D-amino-acid hydrolase (EC 3.5.1.77) from Arthrobacter crystallopoietes (see paper)
28% identity, 73% coverage
Q19437 beta-ureidopropionase (EC 3.5.1.6) from Caenorhabditis elegans (see paper)
29% identity, 52% coverage
P60327 N-carbamoyl-D-amino acid hydrolase from Agrobacterium sp. (strain KNK712)
28% identity, 76% coverage
- Structural Analysis and Substrate Specificity of D-Carbamoylase from <i>Pseudomonas</i>
Paronyan, Biotech (Basel (Switzerland)) 2024 - “...considered an advantage. Multiple sequence analysis of the mentioned enzymes with Agrobacterium sp. KNK712 (GenBank: P60327) and Arthrobacter crystallopoietes DSM 20117 (GenBank: AAO24770.1) carbamoylases revealed highly conserved regions ( Figure S6 ). High similarity was observed between four aligned sequences, especially in the regions responsible for...”
NIT1_SYNYG / P0DP66 Deaminated glutathione amidase; dGSH amidase; Nitrilase homolog 1; syNit1; EC 3.5.1.128 from Synechocystis sp. (strain PCC 6803 / GT-S) (see paper)
P0DP66 deaminated glutathione amidase (EC 3.5.1.128) from Synechocystis sp. PCC 6803 (see paper)
sll0601 hypothetical protein from Synechocystis sp. PCC 6803
30% identity, 82% coverage
- function: Hydrolyzes deaminated glutathione (dGSH, 2-oxoglutaramate) to alpha-ketoglutarate (alpha-KG) and cysteinylglycine (specific activity 7.77 umol/min/mg), hydrolyzes alpha-ketoglutaramate (a-KGM, specific activity 2.13 umol/min/mg), has no activity on glutathione or L- glutamine. May function as a metabolite repair enzyme.
catalytic activity: N-(4-oxoglutaryl)-L-cysteinylglycine + H2O = L- cysteinylglycine + 2-oxoglutarate (RHEA:54532) - Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione
Peracchi, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...(ybl23) yafV y0194 No gene symbol PA4475 PA3797 sll0601 mmNit1 mmNit2 scNit1 scNit2 ecYbeM ecYafV yeNit1 yeYafV paNit1 paYafV syNit1 2650840504 No gene symbol...”
- ClpB1 overproduction in Synechocystis sp. strain PCC 6803 increases tolerance to rapid heat shock
Gonzalez-Esquer, Applied and environmental microbiology 2013 - “...regions around slr0646 (bases 2676067 to 2676566) and sll0601 (bases 2676567 to 2677047), the psbA2 promoter (bases 6666 to 7227), and the kanamycin selection...”
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...Tlr0111 Tlr0112, Tll0920 n.d Tlr0221 Synechocystis sp. PCC 6803 Sll1683, Slr0662, Slr1312 Sll1077, Sll0228 n.d Sll0601, Sll1640 n.d Sll1495, Slr0370 Gloeobacter violaceus PCC 7421 Gll4070, Gll3478 n.d Glr1681 Glr1682, Glr2043 n.d Gll2207, Gll1504, Glr3848, Gll2805 Nostoc sp. PCC 7120 All3401, All4887 Alr2310 n.d Alr2001 n.d Alr2826,...”
aguB / A0A1J6PBK3 N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) from Campylobacter jejuni (see paper)
25% identity, 91% coverage
YafV / b0219 2-oxoglutaramate amidase (EC 3.5.1.3; EC 3.5.1.111) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
yafV / Q47679 2-oxoglutaramate amidase (EC 3.5.1.3) from Escherichia coli (strain K12) (see paper)
31% identity, 95% coverage
Syncc9605_1134 possible nitrilase from Synechococcus sp. CC9605
32% identity, 85% coverage
WH7805_01902 Possible nitrilase from Synechococcus sp. WH 7805
31% identity, 90% coverage
PMN2A_0052 Possible nitrilase from Prochlorococcus marinus str. NATL2A
29% identity, 86% coverage
spr0823 Beta-alanine synthase or beta-ureidopropionase from Streptococcus pneumoniae R6
29% identity, 90% coverage
PMT0395 Possible nitrilase from Prochlorococcus marinus str. MIT 9313
32% identity, 86% coverage
cg3093 carbon-nitrogen hydrolase from Corynebacterium glutamicum ATCC 13032
29% identity, 94% coverage
- In silico analysis of nitrilase-3 protein from Corynebacterium glutamicum for bioremediation of nitrile herbicides
Amrutha, Journal, genetic engineering & biotechnology 2022 - “...( https://www.ebi.ac.uk/Tools/msa/clustalo/ ) [ 12 ]. Phylogenetic analysis The evolutionary history of the target sequence (cg3093) was generated using the Neighbour-Joining method of MEGA (Molecular Evolutionary Genetics Analysis) X version ( https://www.megasoftware.net/ ) [ 13 ]. The protein sequences can be used to generate the phylogenetic...”
- “...hydrolase protein (Accession: CAF20814.1) was identified and confirmed by different in-silico tools. The identified gene (cg3093) consists of 266 amino acids in length and it comes under the nitrilase superfamily. The respective protein sequence (FASTA format) was retrieved from the NCBI database for further analysis. Multiple...”
SF0269 putative EC 3.5. amidase-type enzyme from Shigella flexneri 2a str. 301
S0290 putative EC 3.5. amidase-type enzyme from Shigella flexneri 2a str. 2457T
31% identity, 95% coverage
RL4288 putative amidohydrolase from Rhizobium leguminosarum bv. viciae 3841
38% identity, 60% coverage
LOC100162330 beta-ureidopropionase from Acyrthosiphon pisum
27% identity, 52% coverage
- A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont
Price, BMC biology 2014 - “...ACYPI004747 LOC100163680 1.3.1.2 dihydropyrimidine dehydrogenase (DPD) DHPase a ACYPI002925 LOC100161725 3.5.2.2 dihydropyrimidinase (DHPase) BUP ACYPI003488 LOC100162330 3.5.1.6 beta-ureidopropionase (BUP) ADC ACYPI009960 LOC100169332 4.1.1.11 L-aspartate--decarboxylase (ADC) a Alternative splice forms are annotated in National Center for Biotechnology Information (NCBI) A. pisum RefSeq (Acyr_2.0) gene models. Gene identification...”
NFT1_DROME / O76464 Nitrilase and fragile histidine triad fusion protein NitFhit; NFT-1 protein; EC 3.6.1.29; EC 3.5.-.- from Drosophila melanogaster (Fruit fly) (see paper)
31% identity, 53% coverage
- function: Cleaves A-5'-PPP-5'A to yield AMP and ADP.
catalytic activity: P(1),P(3)-bis(5'-adenosyl) triphosphate + H2O = AMP + ADP + 2 H(+) (RHEA:13893)
cofactor: Mn(2+)
subunit: Homotetramer.
D2VT95 Predicted protein from Naegleria gruberi
28% identity, 44% coverage
C0NHD9 Amidohydrolase from Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)
29% identity, 84% coverage
NFT1_CAEEL / O76463 Nitrilase and fragile histidine triad fusion protein NitFhit; EC 3.6.1.29; EC 3.5.-.- from Caenorhabditis elegans (see 2 papers)
30% identity, 52% coverage
- function: Cleaves A-5'-PPP-5'A to yield AMP and ADP.
catalytic activity: P(1),P(3)-bis(5'-adenosyl) triphosphate + H2O = AMP + ADP + 2 H(+) (RHEA:13893)
cofactor: Mn(2+)
subunit: Homotetramer.
VV1_1455 Predicted amidohydrolase from Vibrio vulnificus CMCP6
31% identity, 73% coverage
DCAS_ENSAD / Q5S260 N-carbamoyl-D-amino acid hydrolase; D-carbamoylase; EC 3.5.1.77 from Ensifer adhaerens (Sinorhizobium morelense) (see paper)
Q5S260 N-carbamoyl-D-amino-acid hydrolase (EC 3.5.1.77) from Ensifer adhaerens (see paper)
27% identity, 76% coverage
- function: Catalyzes the hydrolysis of N-carbamoyl-D-amino acids to the corresponding D-amino acids. Hydrolyzes aromatic and aliphatic N- carbamoyl-D-amino acids in vitro. Effectively hydrolyzes N-carbamoyl-D- p-hydroxyphenylglycine and N-carbamoyl-DL-p-hydroxyphenylglycine, and to a lesser extent N-carbamoyl-D-methionine. No activity for N- carbamoyl-L-amino acids, N-carbamoyl-beta-alanine or (RS)-alpha-ethyl- N-carbamoylphenylglycine in vitro.
catalytic activity: an N-carbamoyl-D-amino acid + H2O + 2 H(+) = a D-alpha-amino acid + NH4(+) + CO2 (RHEA:11000)
subunit: Homotetramer.
SYNW1008 Possible nitrilase from Synechococcus sp. WH 8102
32% identity, 86% coverage
8hpcC / P60327 Crystal structure of c171a mutant of n-carbamyl-d-amino acid amidohydrolase complexed with n-carbamyl-d-hydroxyphenylglycine
28% identity, 76% coverage
- Ligand: (2~{r})-2-(aminocarbonylamino)-2-(4-hydroxyphenyl)ethanoic acid (8hpcC)
M1C5D1 Nitrilase and fragile histidine triad fusion protein from Solanum tuberosum
29% identity, 80% coverage
TERTU_3348 hydrolase, carbon-nitrogen family from Teredinibacter turnerae T7901
29% identity, 45% coverage
AS588_RS10830 bifunctional GNAT family N-acetyltransferase/carbon-nitrogen hydrolase family protein from Bacillus amyloliquefaciens
29% identity, 46% coverage
RCF35_09895, V529_08860 bifunctional GNAT family N-acetyltransferase/carbon-nitrogen hydrolase family protein from Bacillus velezensis
29% identity, 46% coverage
- Whole genome sequencing data of the submerged macrophytes growth promoting and aerobic denitrifying bacterium Bacillus velezensis NBNZ-0060
Chen, Data in brief 2024 - “...RCF35_01945, RCF35_07080, RCF35_07085 ( bsdC ) indole-3-acetaldehyde dehydrogenase RCF35_04555, RCF35_14870, RCF35_08890, RCF35_18825 indole-3-acetonitrile pathway nitrilase RCF35_09895 Others tryptophan acetyltransferase RCF35_03780 Table 4 Secondary metabolite clusters of Bacillus velezensis NBNZ-0060 as determined by antiSMASH. Table 4 Region Genes Type The most similar known cluster Similarity Functions Controlling...”
- Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9
Shao, Microbial cell factories 2015 - “...Not detected IAAld dehydrogenase aldX (V529_39560), dhaS (V529_19360), yfmT (V529_06950), ywdH (V529_29500) IAN Nitrilase yhcX (V529_08860) Other pathway Tryptophan acetyltransferase ysnE (V529_38080) a Accession number was shown in bracket. IPyA , IAM , IAN and TAM are abbreviates of indole-3-pyruvic acid, indole-3-acetamide, indole-3-acetonitrile, and tryptamine pathways,...”
ctu / Q5NHL7 citrullinase (EC 3.5.1.20) from Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (see paper)
CTU_FRATT / Q5NHL7 Citrullinase; Citrulline ureidase; CTU; EC 3.5.1.20 from Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (see paper)
Q5NHL7 citrullinase (EC 3.5.1.20) from Francisella tularensis subsp. tularensis (see paper)
FTT_0435 carbon-nitrogen hydrolase family protein from Francisella tularensis subsp. tularensis SCHU S4
31% identity, 67% coverage
- function: Catalyzes the degradation of citrulline into ornithine, carbon dioxide and ammonia (PubMed:19502406, Ref.3). Contributes to intramacrophage survival, in vivo growth and pathogenesis (PubMed:19502406).
catalytic activity: L-citrulline + H2O + 2 H(+) = L-ornithine + NH4(+) + CO2 (RHEA:11940)
disruption phenotype: Deletion of the gene results in loss of CTU activity (PubMed:19502406). Loss of the gene does not affect acellular growth, but it impairs intramacrophage survival in resting as well as gamma interferon-stimulated macrophages (PubMed:19502406). Mice infected intranasally with the mutant show significantly reduced bacterial burden in the lungs, liver and spleen compared to wild-type Schu S4-infected mice (PubMed:19502406). Mice infected with the mutant succumb to infection, but they survive longer and show significantly extended median time to death compared to that shown by wild-type Schu S4-infected mice (PubMed:19502406). - The francisella tularensis proteome and its recognition by antibodies
Kilmury, Frontiers in microbiology 2010 - “...this study were only detected in 2DE of subspecies tularensis ; FTT_0607, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, FTT_0435, a carbonnitrogen hydrolase and FTT_1157, a type IV pili lipoprotein. Type IV pilin proteins, such as PilA have been shown to play a significant role as virulence factors of Francisella...”
- “...2004 ) FTT_0389 NAD-specific glutamate dehydrogenase Increased expression No Pavkova et al. ( 2006 ) FTT_0435 Putative carbonnitrogen hydrolase Unique No Hubalek et al. ( 2004 ) FTT_0607 4-Hydroxy-3-methylbut-2-en-1-yl diphosphate synthase Unique No Hubalek et al. ( 2004 ) FTT_0611/0681 B-lactamase precursor Increased expression No Hubalek...”
PMM0615 Possible nitrilase from Prochlorococcus marinus sp. MED4
30% identity, 65% coverage
- Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp
Kamennaya, Applied and environmental microbiology 2011 - “...The reference genes in the RT-PCR analyses were PMM0615 of Prochlorococcus sp. MED4 (cell wall hydrolase/autolysin [COG0388]) and orf0250 of Synechococcus sp....”
- “...February 12, 2017 by University of California, Berkeley PMM0615 Sequence (5-3) VOL. 77, 2011 CYANASE IN MARINE UNICELLULAR CYANOBACTERIA F Sstime Sstime type/2...”
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...PMT1066, PMT2150 PMT2214 n.d PMT0395 n.d PMT0191 Prochlorococcus marinus MED 4 PMM1084, PMM0045 PMM1686 n.d PMM0615 n.d PMM1215, PMM0331 Prochlorococcus marinus NATL 2A PMN2A_0665, PMN2A_1378 PMN2A_1287 n.d PMN2A_0052 n.d PMN2A_1709 Synechococcus sp. CC 9605 Syncc9605_1621, Syncc9605_2513 Syncc9605_1082Syncc9605_2591 n.d Syncc9605_1134 n.d Syncc9605_0497 Synechococcus sp. CC 9902 Syncc9902_1380,...”
PSEEN1080 hydrolase, carbon-nitrogen hydrolase family from Pseudomonas entomophila L48
33% identity, 85% coverage
- Proteomic analysis of Pseudomonas putida reveals an organic solvent tolerance-related gene mmsB
Ni, PloS one 2013 - “...chain elongation factor EF-Ts, and isochorismatase superfamily hydrolase, which are encoded by arcA (GenBank: CAK17111), PSEEN1080 (GenBank: CAK13980), mmsB (GenBank: JC7926), tsf (GenBank: CAK16908), and PSEEN0851 (GenBank: CAK13762) respectively ( Table 2 ). 10.1371/journal.pone.0055858.t001 Table 1 MALDI-TOF/TOF analysis of peptides from 5 high-abundance proteins. SSP Protein...”
- “...a B b 3001 arginine deiminase arcA 21910.2174.6 36522.2298.7 2904 putative hydrolase, carbon-nitrogen hydrolase family PSEEN1080 6575.634.1 12626.5139.6 3202 3-hydroxyisobutyrate dehydrogenase mmsb 4699.546.4 11110.166.9 6302 proteinchain elongation factor EF-Ts tsf 8314.451.7 14962.7102.4 6101 Isochorismatase superfamily hydrolase PSEEN0851 8520.332.6 15962.782.2 a The expression level of P. putida...”
YP_001667192 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Pseudomonas putida GB-1
32% identity, 85% coverage
GM298_10355 amidohydrolase from Enterobacter sp. HSTU-ASh6
30% identity, 97% coverage
- Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses
Haque, Frontiers in microbiology 2022 - “...0.954, 1.63, 0.242, 0.981 33, 15, 51, 1 86.12 97.72 73.6, 22.1, 2.8, 1.6 Amidohydrolase (GM298_10355) 2e11A 0.984, 0.72, 0.467, 0.996 25, 32, 42, 1 84.55 87.50 75.9, 21.0, 1.3, 1.8 Amidohydrolase (GM298_00905) 4ewtA 0.989, 0.56, 0.334, 0.995 31, 24, 44, 0 89.04 95.17 78.1, 17.2,...”
- “...with phnL (8.8 kcal/mol), and the lowest negative score was found for demephion-O with amidohydrolase (GM298_10355) (3.1 kcal/mol). The box plot analysis revealed that each box with the bold line represents median values, and the square sign indicates mean values. Moreover, the upper and lower lines...”
YHCX_BACSU / P54608 Probable hydrolase YhcX; EC 3.5.-.- from Bacillus subtilis (strain 168) (see paper)
29% identity, 46% coverage
- disruption phenotype: No visible growth phenotype.
PMT9312_0615 nitrilase-like from Prochlorococcus marinus str. MIT 9312
29% identity, 86% coverage
CYB_1181 hydrolase, carbon-nitrogen family from Synechococcus sp. JA-2-3B'a(2-13)
30% identity, 82% coverage
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...CYA_0128 CYA_0859 n.d CYA_0558 n.d CYA_0364 Synechococcus Yellowstone sp. JA-2-3Ba (2-13) CYB_2779, CYB_0482 CYB_1744 n.d CYB_1181 n.d CYB_0715, CYB_1893 Thermosynechococcus elongatus BP-1 Tlr1866, Tll1807 n.d. Tlr0111 Tlr0112, Tll0920 n.d Tlr0221 Synechocystis sp. PCC 6803 Sll1683, Slr0662, Slr1312 Sll1077, Sll0228 n.d Sll0601, Sll1640 n.d Sll1495, Slr0370 Gloeobacter...”
F2DZ92 Predicted protein from Hordeum vulgare subsp. vulgare
29% identity, 74% coverage
Pro1045 Nitrilase homolog from Prochlorococcus marinus str. SS120
30% identity, 84% coverage
B8A0E5 omega-amidase (EC 3.5.1.3) from Zea mays (see paper)
30% identity, 63% coverage
B8C1M9 nitrilase (EC 3.5.5.1) from Thalassiosira pseudonana (see paper)
XP_002290043 nitrilase from Thalassiosira pseudonana CCMP1335
27% identity, 80% coverage
B8A2V8 omega-amidase (EC 3.5.1.3) from Zea mays (see paper)
29% identity, 65% coverage
PP0859 carbon-nitrogen hydrolase family protein from Pseudomonas putida KT2440
30% identity, 94% coverage
A4I2F5 Putative nitrilase from Leishmania infantum
29% identity, 88% coverage
VV2_0920 Predicted amidohydrolase from Vibrio vulnificus CMCP6
28% identity, 40% coverage
NILP2_ARATH / Q94JV5 Deaminated glutathione amidase, chloroplastic/cytosolic; dGSH amidase; Nitrilase-like protein 2; Protein nitrilase 1 homolog; AtNit1; Protein Nit1 homolog; EC 3.5.1.128 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q94JV5 deaminated glutathione amidase (EC 3.5.1.128) from Arabidopsis thaliana (see paper)
AT4G08790 nitrilase, putative from Arabidopsis thaliana
29% identity, 73% coverage
- function: Catalyzes the hydrolysis of the amide bond in N-(4- oxoglutarate)-L-cysteinylglycine (deaminated glutathione), a metabolite repair reaction to dispose of the harmful deaminated glutathione (PubMed:30692244). Possesses amidase activity toward deaminated ophthalmate in vitro (PubMed:30692244).
catalytic activity: N-(4-oxoglutaryl)-L-cysteinylglycine + H2O = L- cysteinylglycine + 2-oxoglutarate (RHEA:54532)
catalytic activity: N-(4-carboxy-4-oxobutanoyl)-L-ethylglycylglycine + H2O = N-(2- aminobutanoyl)glycine + 2-oxoglutarate (RHEA:17125)
disruption phenotype: No visible phenotype under normal growth conditions, but the accumuluation of N-(4-oxoglutarate)-L- cysteinylglycine (deaminated glutathione) in mutant plants is up to 70- fold higher than in the wild type. - Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome
Luklová, International journal of molecular sciences 2022 - “...is involved in cytokinesis, vesicular trafficking, and endocytosis, [ 56 ]); and an amidase NILP2 (AT4G08790, which catalyzes the removal of a damaged deamidated glutathione, [ 57 ]). A lower nightday ratio was found for 37 lhy-specific regulations, including Cinnamyl alcohol dehydrogenase CADH5 (AT4G34230, which is...”
- To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana
Willems, Frontiers in plant science 2021 - “...transferase Met41 Ac-T AT5G13050 5-Formyltetrahydrofolate cycloligase (5-FCL) Met43 NH 2 /Ac-S AT5G12040 -amidase Met63 Ac-A AT4G08790 Deaminated glutathione amidase Met29 Ac-A AT5G03370 Acylphosphatase family Met66 NH 2 /Ac-T AT5G15870 Glycosyl hydrolase family 81 protein Met45 Ac-S AT5G41970 Metal-dependent protein hydrolase Met28 NH 2 -A AT3G10620 Nudix...”
- The metabolite repair enzyme Nit1 is a dual-targeted amidase that disposes of damaged glutathione in Arabidopsis
Niehaus, The Biochemical journal 2019 (PubMed)- “...Nit1 amidase. We show that recombinant Arabidopsis Nit1 (At4g08790) has high and specific amidase activity towards dGSH. Ablating the Arabidopsis Nit1 gene...”
- “...insertion in the sixth exon of the Nit1 gene (At4g08790) was identified in the Salk collection (SALK_108849C). Seeds from this line and the Columbia-0 wild-type...”
- Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Voutsina, BMC genomics 2016 - “..., 45 , 67 ]. We identified two genes involved in cadmium ion response ( AT4G08790 & AT4G10320 ) that were DE between the high and low GLS plants. Watercress GLS content has also been shown to respond to light [ 62 ] and our list...”
- Proteomic analysis of early-responsive redox-sensitive proteins in Arabidopsis
Wang, Journal of proteome research 2012 - “...D/I AT5G48480 lactoylglutathione lyase 4 27.0 B/I AT3G44300 nitrilase 2 (NIT2) 5 15.0 D/B B/B AT4G08790 nitrilase, putative 2 6.8 D/I AT1G63000 nucleotide-rhamnose synthase/epimerase-reductase 4 14.0 D/I D/B AT3G62530 PBS lyase, HEAT-like repeat-containing protein 3 13.0 B/I AT3G07090 PPPDE putative thiol peptidase family protein 3 13.0...”
- A temporal precedence based clustering method for gene expression microarray data
Krishna, BMC bioinformatics 2010 - “...12 3824 9.0400E-4 4.2857E-2 10/15 Catalytic activity AT2G17420, AT3G15020, AT5G04590, AT3G13235, AT1G23190, AT3G53160, AT3G48090, AT4G23600, AT4G08790, AT1G51680 Figure 13 6950 7.0271E-10 6.6055E-8 14/37 Response to stress AT5G20230, AT5G61900, AT4G16845, AT3G22370, AT2G04030, AT1G55490, AT3G11820, AT4G12400, AT4G34990, AT4G23100, AT4G20260, AT3G49910, AT5G09810, AT5G05410 Figure 14 44464 2.6470E-3 1.8771E-2 25/36...”
EHI_035680 hydrolase, carbon-nitrogen family from Entamoeba histolytica HM-1:IMSS
27% identity, 82% coverage
BCAL3280 putative carbon-nitrogen hydrolase protein from Burkholderia cenocepacia J2315
31% identity, 89% coverage
PP0939 carbon-nitrogen hydrolase family protein from Pseudomonas putida KT2440
32% identity, 85% coverage
XP_415242 beta-ureidopropionase from Gallus gallus
27% identity, 68% coverage
PXO_06060 hydrolase, carbon-nitrogen family from Xanthomonas oryzae pv. oryzae PXO99A
33% identity, 80% coverage
EY04_RS03865 carbon-nitrogen hydrolase family protein from Pseudomonas chlororaphis
33% identity, 81% coverage
- Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23
Shah, PloS one 2020 - “...82 cgaaCCGGCCTGAGCGGCCAGAacca Hypothetical protein cl01077 - EY04_RS03745 - -2.16 474 ttctCCGACCTGTTCGGCAAGGgcct Carbon-nitrogen hydrolase COG0388 R EY04_RS03865 3.14 1.90 397 Protease TldD EY04_RS03870 1.80 - ttcgGCTGCCTGACCGCCATGGcggg N-acetylmuramoyl-L-alanine amidase COG3023 M EY04_RS05345 -2.52 -3.81 265 caggGCGGCATGGGCGGCCAAGtcgt Hypothetical protein - - EY04_RS05505 -4.80 -4.52 260 tacaACGGCCAGCGCTGGGTATcggt Hypothetical protein -...”
YP_920845 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Thermofilum pendens Hrk 5
28% identity, 91% coverage
O25452 Beta-alanine synthetase homolog from Helicobacter pylori (strain ATCC 700392 / 26695)
HP0757 beta-alanine synthetase homolog from Helicobacter pylori 26695
27% identity, 66% coverage
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25564 HP_0906 268 P56039 rplN 269 P56084 atpC 270 O25673 HP_1029 271 O24949 HP_0137 272 O25452 HP_0757 273 O25553 HP_0893 274 O24865 HP_0020 275 O26035 RibG 276 O25949 HP_1399 277 O25255 HP_0518 278 O26083 CeuE 279 O25213 HP_0466 280 O25253 hslV 281 O25006 HP_0218 282 P55992...”
- “...O25574 FrpB 221 O24924 thrC 222 O25572 HP_0914 223 P56004 efp 224 P56032 rplD 225 O25452 HP_0757 226 P56455 hisS 227 O25508 HP_0837 228 P56137 purA 229 O25036 Omp8 230 O25925 mreB 231 O25594 YckK 232 P56459 aspS 233 O24949 HP_0137 234 O25999 HP_1463 235 P56018...”
- AI-2 Induces Urease Expression Through Downregulation of Orphan Response Regulator HP1021 in Helicobacter pylori
Yang, Frontiers in medicine 2022 - “...1.4140 HP1584 tRNA N6-adenosine threonylcarbamoyltransferase 1.4356 HP0640 tRNA nucleotidyltransferase/poly(A) polymerase 1.4423 HP1028 Hypothetical protein 1.4482 HP0757 N-carbamoylputrescine amidase 1.4625 HPt26 tRNA-Pro 1.471 HP0758 Sodium:proton antiporter 1.4774 HP0434 Pseudogene 1.4937 HP0937 Pseudogene 1.4976 HP1556 Cell division protein FtsI 1.5018 HP0754 5-formyltetrahydrofolate cyclo-ligase 1.5228 HP0073 Urease subunit alpha...”
- The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
Xu, Frontiers in microbiology 2021 - “...2.6091 HP0752 fliD 2.6449 HP0753 fliS 1.2148 HP0754 5-formyltetrahydrofolate cyclo-ligase 2.0228 HP0755 Predicted gene 1.3991 HP0757 Beta-alanine synthetase homolog 1.2021 HP0758 Membrane protein 1.8156 HP0759 Membrane protein 1.6024 HP0821 uvrC 1.3838 HP0846 hsdR 1.8459 HP0860 gmhB 1.369 HP0896 omp19 1.8089 HP0897 Predicted gene 1.124 HP0922 Membrane...”
- Targeted identification of glycosylated proteins in the gastric pathogen Helicobacter pylori (Hp)
Champasa, Molecular & cellular proteomics : MCP 2013 - “...Inner membrane 7 4 13.5 HP0026 P56062 gltA 50.9 Citrate synthase Cytoplasm 71 6 13.2 HP0757 AAD07805 34.9 Beta-alanine synthase Cytoplasm 6 2 12.4 HP0485 AAD07551 37.7 Catalase-like protein Periplasm 4 3 12.3 HP0201 AAD07269 plsX 38.4 Fatty acid phospholipid synthesis Cytoplasm 5 2 12.1 HP0183...”
- Characterization of the ArsRS regulon of Helicobacter pylori, involved in acid adaptation
Pflock, Journal of bacteriology 2006 - “...phospholipid metabolism Central intermediary metabolism Protein fate HP0757 JHP0649 0.41 HP1332* JHP1225 0.48 Transport and binding proteins HP0228 HP0889...”
- Genes of Helicobacter pylori regulated by attachment to AGS cells
Kim, Infection and immunity 2004 - “...HP1285, HP0222, HP0836, HP0582, infC, HP0906, HP0118, omp19, HP0757, HP1430, and HP0973) and for 14 down-regulated genes (omp11, flgM, flgG, HP0359, HP1548,...”
- “...intermediary metabolism), and a beta-alanine synthetase homolog (HP0757), were also up-regulated. A conserved gene, a gene encoding a predicted ATP/GTP binding...”
- pH-regulated gene expression of the gastric pathogen Helicobacter pylori
Merrell, Infection and immunity 2003 - “...HP1331 HP0228 HP1225 HP0318 HP1430 HP1507 HP0759 HP1020 HP0757 JHP1154 JHP1081 JHP1014 HP1021 HP0278 JHP0403 JHP0263 HP0550 HP1203 HP0123 HP1019 HP1171 HP1172...”
Q9HVU6 deaminated glutathione amidase (EC 3.5.1.128) from Pseudomonas aeruginosa (see paper)
PA4475 hypothetical protein from Pseudomonas aeruginosa PAO1
35% identity, 71% coverage
- The Pseudomonas aeruginosa RpoH (σ32) Regulon and Its Role in Essential Cellular Functions, Starvation Survival, and Antibiotic Tolerance
Williamson, International journal of molecular sciences 2023 - “...PA4472 pmbA Zn-dependent protease 15.5 5.2 10 5 PA4474 Zn-dependent protease 16.4 1.1 10 3 PA4475 Amidohydrolase 5.0 4.0 10 4 PA4542 clpB Protease 10.8 4.8 10 4 PA4751 ftsH Membrane-bound, ATP-dependent protease 3.0 1.1 10 4 +++ PA4756 carB Carbamoylphosphate synthase large subunit 2.2 1.7...”
- Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Rubio-Gómez, Frontiers in microbiology 2020 - “...0.005 PA4451 yrbA Uncharacterized protein 0.9 0.000 PA4462 rpoN RNA polymerase sigma-54 factor 0.9 0.000 PA4475 Uncharacterized protein 0.7 0.001 PA4520 Probable chemotaxis transducer 0.6 0.002 PA4525 pilA Type 4 fimbrial precursor 0.9 0.000 PA4541 lepA Large extracellular protease 1.0 0.000 PA4545 comL Outer membrane lipoprotein...”
- Two Regulators, PA3898 and PA2100, Modulate the Pseudomonas aeruginosa Multidrug Resistance MexAB-OprM and EmrAB Efflux Pumps and Biofilm Formation
Heacock-Kang, Antimicrobial agents and chemotherapy 2018 - “...hypothetical protein; PA4322, conserved 197 hypothetical protein; PA4475, conserved hypothetical protein; PA4636, hypothetical 198 protein. All of these genes...”
- Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione
Peracchi, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...NIT3 ybeM (ybl23) yafV y0194 No gene symbol PA4475 PA3797 sll0601 mmNit1 mmNit2 scNit1 scNit2 ecYbeM ecYafV yeNit1 yeYafV paNit1 paYafV syNit1 2650840504 No...”
YE3235 putative regulatory protein (methionine salvage) from Yersinia enterocolitica subsp. enterocolitica 8081
31% identity, 98% coverage
- The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081
Thomson, PLoS genetics 2006 - “...YE3231), MtnC (bifunctional enolase/phosphatase, YE3232), MtnB (dehydratase, YE3233), MtnE (transaminase, YE3234), and MtnU (possible regulator, YE3235). In addition, there is a second unlinked locus encoding a nuclease (MtnN, YE0739). Therefore, the Y. enterocolitica methionine salvage pathway is similar to that of Klebsiella pneumoniae, with a two-stage...”
SS1G_09546 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
26% identity, 75% coverage
BAbS19_I17580 nitrilase/cyanide hydratase/apolipoprotein N-acyltransferase from Brucella abortus S19
37% identity, 58% coverage
- Comparative proteomic and genomic analyses of Brucella abortus biofilm and planktonic cells
Tang, Molecular medicine reports 2020 - “...activity [GO:0016301]; metal ion binding [GO:0046872]; phosphoenolpyruvate carboxykinase (ATP) activity [GO:0004612] gluconeogenesis [GO:0006094] 3.5 4.59 BAbS19_I17580 Nitrilase/cyanide hydratase/apolipoprotein N-acyltransferase hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [GO:0016810]; transferase activity, transferring acyl groups [GO:0016746] nitrogen compound metabolic process [GO:0006807] 5.3 2.02 BAbS19_I14530 MaoC-like dehydratase Butanoate...”
CNAG_02920 hydrolase from Cryptococcus neoformans var. grubii H99
28% identity, 73% coverage
Q16TC0 Uncharacterized protein from Aedes aegypti
25% identity, 52% coverage
A0A023XI92 N-carbamoyl-D-amino-acid hydrolase (EC 3.5.1.77) from Bradyrhizobium japonicum (see paper)
27% identity, 69% coverage
YAFV_YEREN / P0DP67 Omega-amidase YafV; yeYafV; EC 3.5.1.3 from Yersinia enterocolitica (see paper)
31% identity, 98% coverage
- function: Hydrolyzes alpha-ketoglutaramate (a-KGM) to alpha- ketoglutarate (alpha-KG) and ammonia (specific activity 21 umol/min/mg), has very weak activity on L-glutamine, and no activity on deaminated glutathione (dGSH) or glutathione. May function as a metabolite repair enzyme.
catalytic activity: a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+) (RHEA:11716)
Q7T395 Beta-ureidopropionase from Danio rerio
28% identity, 49% coverage
- Proteomic analysis of zebrafish (Danio rerio) embryos exposed to benzyl benzoate
Kwon, Environmental science and pollution research international 2023 - “...4.1E-16 28 F1R5M2 Kinesin-like protein 1.71 1.7E-03 29 Q4QRE2 Acyl-coenzyme A oxidase 1.52 3.4E-02 30 Q7T395 Upb1 protein 1.51 3.7E-02 31 Q6P0V6 60S ribosomal protein L8 1.51 3.9E-02 32 Q8QGV4 Lipocalin-type prostaglandin D synthase-like protein 1.78 4.7E-04 33 Q566Z0 LOC553381 protein >10 4.1E-16 34 E7FD14 Protein...”
K4AC07 CN hydrolase domain-containing protein from Setaria italica
29% identity, 55% coverage
- Comparative proteomic investigation of drought responses in foxtail millet
Pan, BMC plant biology 2018 - “...K4A868 alanine aminotransferase 2-like 1.7 K4A1C4 alanine aminotransferase 2 1.5 K3XK90 chorismate mutase 3 1.6 K4AC07 omega-amidase NIT2-A-like 1.9 K3YRS9 allene oxide synthase (AOS), chloroplastic-like 1.7 K3ZV70 1-aminocyclopropane-1-carboxylate oxidase (ACO) 1-like 1.6 K3XV98 Lipoxygenase 2.8 K3ZI80 patatin 2.4 K4A844 3-ketoacyl-CoA synthase 2.0 K3ZQL2 cyclopropane fatty acid...”
YP_425830 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Rhodospirillum rubrum ATCC 11170
30% identity, 80% coverage
A4HF72 Nitrilase from Leishmania braziliensis
29% identity, 88% coverage
RLO149_c040080 formamidase from Roseobacter litoralis Och 149
26% identity, 70% coverage
A8HPY4 Uncharacterized protein from Chlamydomonas reinhardtii
28% identity, 44% coverage
PA3797 hypothetical protein from Pseudomonas aeruginosa PAO1
30% identity, 80% coverage
- Cell division factor ZapE regulates <i>Pseudomonas aeruginosa</i> biofilm formation by impacting the <i>pqs</i> quorum sensing system
Liu, mLife 2023 - “...of candidate biofilm determinants with unknown function We selected five hypothetical genes (PA0222, PA1112, PA2345, PA3797, and PA4438) with the highest fold changes between input and output mutant pools for experimental validation (Table 1 ). Clean knockout mutants for these five genes were constructed, and the...”
- “...PAO1 wildtype strain, PA0222 showed similar biofilm structures with slightly smaller microcolonies; PA1112, PA2345, and PA3797 formed tiny microcolonies with significantly less biofilm biomass; and PA4438 formed loose biofilm aggregates with decreased amounts of biomass (Figures 2A and S2F ). To further compare the biofilm formation...”
- Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione
Peracchi, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...ybeM (ybl23) yafV y0194 No gene symbol PA4475 PA3797 sll0601 mmNit1 mmNit2 scNit1 scNit2 ecYbeM ecYafV yeNit1 yeYafV paNit1 paYafV syNit1 2650840504 No gene...”
BUP1_RAT / Q03248 Beta-ureidopropionase; Beta-alanine synthase; N-carbamoyl-beta-alanine amidohydrolase; EC 3.5.1.6 from Rattus norvegicus (Rat) (see 2 papers)
27% identity, 48% coverage
- function: Catalyzes a late step in pyrimidine degradation. Converts N- carbamoyl-beta-alanine (3-ureidopropanoate) into beta-alanine, ammonia and carbon dioxide. Likewise, converts N-carbamoyl-beta- aminoisobutyrate (3-ureidoisobutyrate) into beta-aminoisobutyrate, ammonia and carbon dioxide.
catalytic activity: 3-(carbamoylamino)propanoate + H2O + 2 H(+) = beta-alanine + NH4(+) + CO2 (RHEA:11184)
catalytic activity: 3-(carbamoylamino)-2-methylpropanoate + H2O + 2 H(+) = (R)-3- amino-2-methylpropanoate + NH4(+) + CO2 (RHEA:37339)
subunit: Homodimer, homotetramer, homooctamer; can also form higher homooligomers. - Modulation of the Liver Protein Carbonylome by the Combined Effect of Marine Omega-3 PUFAs and Grape Polyphenols Supplementation in Rats Fed an Obesogenic High Fat and High Sucrose Diet
Méndez, Marine drugs 2019 - “...Mitochondria 47,873 36 24 (24) P32755 4-hydroxyphenylpyruvate dioxygenase Hpd Endoplasmic reticulum 45,112 45 24 (24) Q03248 Beta-ureidopropionase Upb1 Cytoplasm 44,042 28 12 (12) 13 P09034 Argininosuccinate synthase Ass1 Cytosol 46,496 54 48 (48) 14 P16617 Phosphoglycerate kinase 1 Pgk1 Cytoplasm 44,538 20 7 (7) P13437 3-ketoacyl-CoA...”
- Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
Ayyar, Journal of proteomics 2017 - “...Got2 Aspartate aminotransferase, mitochondrial Catalyzes interconversion of aspartate and -ketoglutarate to oxaloacetate and glutamate UP Q03248 Bup1 Beta-ureidopropionase Converts N-carbamoyl-beta-alanine (3-ureidopropanoate) to beta-alanine UP P25093 Fah Fumarylacetoacetate hydrolase Synthesizes acetoacetate and fumarate from L-phenylalanine degradation UP P10860 Glud1 Glutamate dehydrogenase 1, mitochondrial Converts L-glutamate into alpha-ketoglutarate...”
- Proteomic characterization of early changes induced by triiodothyronine in rat liver
Severino, Journal of proteome research 2011 - “...PH/T3 65a P10111 Peptidyl prolyl cis trans isomerase (Ppia) 17.731/8.3 84 16 100 PH/T3 42 Q03248 Beta ureidopropionase (Ubp1) 44.013/6.5 53.7 25 100 Control 62 P14669 Annexin III - Lipocortin III (Anxa3) 36.299/6.0 54.6 17 84 Control Table 3 Relative mRNA levels after T3 treatment. Ratios...”
- Potential application of N-carbamoyl-beta-alanine amidohydrolase from Agrobacterium tumefaciens C58 for beta-amino acid production
Martínez-Gómez, Applied and environmental microbiology 2009 - “...no. NP_057411; Rattus norvegicus, GenBank accession no. Q03248; Arabidopsis thaliana, GenBank accession no. BAB09868) (10, 15, 27, 39). The highest sequence...”
- Protein targets of reactive metabolites of thiobenzamide in rat liver in vivo.
Ikehata, Chemical research in toxicology 2008 - Purine and pyrimidine nucleotide synthesis and metabolism.
Moffatt, The arabidopsis book 2002
YP2544 putative glutamine-dependent NAD from Yersinia pestis biovar Medievalis str. 91001
32% identity, 39% coverage
E1Q554 Aliphatic amidase from Helicobacter pylori (strain PeCan4)
34% identity, 45% coverage
MAB_2545c Hypothetical nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Mycobacterium abscessus ATCC 19977
27% identity, 72% coverage
CwatDRAFT_4111 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Crocosphaera watsonii WH 8501
29% identity, 82% coverage
jhp0694 putative from Helicobacter pylori J99
25% identity, 66% coverage
jhp0279 ALIPHATIC AMIDASE from Helicobacter pylori J99
28% identity, 63% coverage
- Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system
Loh, Journal of bacteriology 2010 - “...Acid acclimation AmiE HypB RocF UreB UreG UreH jhp0279, jhp0837, jhp1427, jhp0067, jhp0063, jhp0062, HP0294 HP0900 HP1399 HP0072 HP0068 HP0067 0.27 0.63 0.001...”
- Iron and pH homeostasis intersect at the level of Fur regulation in the gastric pathogen Helicobacter pylori
Gancz, Infection and immunity 2006 - “...Theoretical Fur box (HP0261) Theoretical Fur box (HP0294, JHP0279) Theoretical Fur box (HP0309, JHP0294) Ni (HP0588) theoretical Fur box on (JHP0536) Downloaded...”
- “...Avg fold change Avg HP no. JHP0245 JHP0279 JHP0294 JHP0536 Ferredoxin oxidoreductase, alpha subunit, oorA Ferredoxin oxidoreductase, gamma subunit, oorC Nonheme...”
- Characterization of the ArsRS regulon of Helicobacter pylori, involved in acid adaptation
Pflock, Journal of bacteriology 2006 - “...HP0755 JHP0062 JHP0063 JHP0064 JHP0065 JHP0066 JHP0067 JHP0068 JHP0279 JHP1159 JHP0098 JHP1001 JHP0692 0.36 0.22 0.39 0.25 0.21 0.24 0.20 0.06 0.15 0.27 0.38...”
- Growth phase-dependent response of Helicobacter pylori to iron starvation
Merrell, Infection and immunity 2003 - “...2.8 2.2 3.0 2.7 2.3 JHP0018 JHP0022 JHP0279 JHP0537 JHP0586 JHP0716 JHP0837 JHP0878 JHP1112 JHP1159 JHP1428 JHP1427 #JHP0585 Carboxynorspermidine decarboxylase,...”
- “...*HP1399 HP1538 HP1539 JHP0022 JHP0162 JHP0262 JHP0279 JHP0637 JHP0636 JHP0878 JHP1159 JHP1427 JHP1461 JHP1460 Citrate synthase, gltA Fructose-bisphosphate...”
- pH-regulated gene expression of the gastric pathogen Helicobacter pylori
Merrell, Infection and immunity 2003 - “...1.2 3.5 5.5 3.0 3.0 6.9 7.2 1.6 JHP0279 JHP1159 JHP585 JHP0586 JHP0504 Aliphatic amidase energy metabolism, amiF Aliphatic amidase energy metabolism, amiE...”
AMIE_HELPY / O25067 Aliphatic amidase; Acylamide amidohydrolase; EC 3.5.1.4 from Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) (see 3 papers)
HPG27_RS01475 aliphatic amidase from Helicobacter pylori Hp A-11
HP0294 aliphatic amidase (aimE) from Helicobacter pylori 26695
HPG27_273 aliphatic amidase from Helicobacter pylori G27
33% identity, 45% coverage
- function: Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia. Hydrolyzes propionamide, acetamide and acrylamide, but has no activity with formamide or urea. The natural substrates of AmiE in its gastric environment are not known. Probably functions to ensure nitrogen supply to the bacteria
function: Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates. The highest level of acyl transfer activity is observed with acetamide
catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
subunit: Homotetramer. - Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Marcus, Helicobacter 2018 - “...HPG27_RS07635 HP1399 4.82 0.29 0.00 5.83 0.28 0.00 6.73 0.40 0.00 arginase ( rocF ) HPG27_RS01475 HP0294 1.91 0.10 0.04 1.25 0.16 0.28 1.02 0.16 0.47 aliphatic amidase ( amiE ) HPG27_RS06200 HP1238 1.92 0.03 0.00 1.76 0.04 0.01 1.46 0.03 0.01 formamidase ( amiF )...”
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25787 HP_1173 114 O25166 HP_0410 115 O25052 AddB 116 O25465 HP_0773 117 O25008 iscS 118 O25067 amiE 119 P56060 kdsA 120 O25658 HdhA 121 O25936 fbp 122 P55982 nrdA 123 O25089 HP_0322 124 P66928 trxA 125 P56047 rplV 126 O24990 fabI 127 P0A0R3 groS 128 O26104...”
- Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
Voss, Proteomics. Clinical applications 2015 - “...HP1248 P56123 nucleic acid phosphodiester bond hydrolysis 2.92 virulence associated protein homolog (VacB) HP0294 * O25067 nitrogen compound metabolic process 2.76 aliphatic amidase (AmiE) HP1464 * O26000 NA 2.58 conserved hypothetical secreted protein HP0908 ! O25566 NA 2.37 flagellar hook (FlgE2) HP0497 O25239 transmembrane transport 2.37...”
- Structural and functional aspects of the Helicobacter pylori secretome
Zanotti, World journal of gastroenterology 2014 - “...2JGQ 3QBU, 4LY4 P56062 P69996 P14916 P48285 P56076 O25025 O25067 O25080 O25090 P55990 O25153 February 14, 2014|Volume 20|Issue 6| Zanotti G et al . Structural...”
- Targeted identification of glycosylated proteins in the gastric pathogen Helicobacter pylori (Hp)
Champasa, Molecular & cellular proteomics : MCP 2013 - “...Cytoplasm 5 3 15.2 HP0974 P56196 pgm 57.7 Phosphoglycerate mutase Cytoplasm 5 4 18.1 HP0294 O25067 aimE 39.7 Aliphatic amidase Cytoplasm 31 3 17.9 HP0649 P56149 aspA 54.6 Aspartate ammonia lyase Cytoplasm 17 5 17.5 HP0865 O25536 dut 16.8 Nucleotidohydrolase Unknown 3 1 17.5 HP0020 AAD07088...”
- Regulation of Helicobacter pylori Urease and Acetone Carboxylase Genes by Nitric Oxide and the CrdRS Two-Component System
Allen, Microbiology spectrum 2023 - “...2 crdR ns 1.77 ** HP_RS04110 HP0842 Hypothetical protein 2 crdR ns 2.07 * HP_RS01450 HP0294 amiE 2 crdR ns 1.90 *** HP_RS01940 HP0394 Calcineurin-like phosphoesterase 2 crdR ns 1.94 *** HP_RS00465 HP0091 DpnII restriction endonuclease 2 crdR ns 1.85 *** HP_RS03520 HP0723 ansA 2 crdR...”
- AI-2 Induces Urease Expression Through Downregulation of Orphan Response Regulator HP1021 in Helicobacter pylori
Yang, Frontiers in medicine 2022 - “...hook-associated protein FlgK 2.7713 HP1120 Hypothetical protein 2.9003 HP0807 Iron(III) dicitrate transport protein FecA 2.928 HP0294 Acylamide amidohydrolase 3.9658 AI-2 Induces UreAB Expression and Bacterial Urease Activity in H . pylori From the transcriptomic analysis, we determined that UreA and UreB expression was lower in the...”
- Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System
Loh, Infection and immunity 2021 (secret) - The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
Xu, Frontiers in microbiology 2021 - “...1.9605 HP0289 ImaA 1.3117 HP0290 lysA 1.5474 HP0291 Predicted gene 1.2657 HP0292 Predicted gene 1.0587 HP0294 amiE 2.2148 HP0296 rplU 1.4814 HP0297 rpmA 1.4635 HP0298 dppA 4.9784 HP0299 dppB 1.4717 HP0300 dppC 2.088 HP0301 dppD 2.4619 HP0302 dppF 2.0374 HP0303 obgE A-3.1174 HP0304 Predicted gene 2.0838...”
- Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Marcus, Helicobacter 2018 - “...HP1399 4.82 0.29 0.00 5.83 0.28 0.00 6.73 0.40 0.00 arginase ( rocF ) HPG27_RS01475 HP0294 1.91 0.10 0.04 1.25 0.16 0.28 1.02 0.16 0.47 aliphatic amidase ( amiE ) HPG27_RS06200 HP1238 1.92 0.03 0.00 1.76 0.04 0.01 1.46 0.03 0.01 formamidase ( amiF ) F...”
- In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis
Thorell, Infection and immunity 2017 - “...HP1432 HP1204 Nic01_A_00859 HP1563 HP1427 tRNA-Ser(gct) HP0072 HP0875 HP0294 HP1161 HP0243 ssrA ureA hpn2 rpL33 HP0824 HP0835 HP0601 HP0129 trx1, trxA hup flaA...”
- Survival of Helicobacter pylori in gastric acidic territory
Ansari, Helicobacter 2017 - “...and HP1364 in the expression of other several genes, including those that encode urease, amidase (HP0294) and formamidase (HP1238) for acid resistance in H. pylori [ 120 ]. All these enzymes are involved in ammonia generation, are likely to play an important role in acid resistance...”
- The cag-pathogenicity island encoded CncR1 sRNA oppositely modulates Helicobacter pylori motility and adhesion to host cells
Vannini, Cellular and molecular life sciences : CMLS 2016 - “...(ccdA) HP0293 -1.7 Para-aminobenzoate synthetase (pabB) HP0294 -1.7 Acylamide amidohydrolase (amiE) HP0639 -1.5 7-Cyano-7-deazaguanine synthase (exsB) HP0773...”
- More
- Detailed analysis of Helicobacter pylori Fur-regulated promoters reveals a Fur box core sequence and novel Fur-regulated genes
Pich, Molecular microbiology 2012 - “...Candidate Fur boxes were also found in the intergenic regions containing the promoters of amiE (HPG27_273) and hpn2 (HPG27_1353), encoding an aliphatic amidase ( van Vliet et al. , 2003 ) and a histidine- and glutamine-rich protein involved in nickel storage and iron detoxification ( Seshadri...”
- “...< 0.01, Student's t-test). Figure 3 Analysis of Fur regulation of the promoters of amiE (HPG27_273), hpn2 (HPG27_1353), ribBA (HPG27_760) and pdxJ (HPG27_1519) using a gene reporter system. A) Promoter sequences that were fused to the cat coding region to create the aimed transcriptional fusions. Underlined...”
Afu6g13230 nitrilase family protein (Nit3), putative from Aspergillus fumigatus Af293
30% identity, 85% coverage
- Sub-telomere directed gene expression during initiation of invasive aspergillosis
McDonagh, PLoS pathogens 2008 - “...Afu3g01700 maltose permease 7.059699432 Afu1g17470 high affinity nitrate transporter NrtB 2.917548 Afu2g10910 maltose permease 0.55716766 Afu6g13230 Nit protein 2 2.6084555 Afu1g03280 maltose permease Secreted Proteins 3.2031907 Afu3g03380 maltose O-acetyltransferase 7.40411592 Afu5g14190 beta-glucanase 2.5614034 Afu8g07070 maltase 5.898216645 Afu1g17510 lipase/esterase 4.678081 Afu7g06380 maltase 5.644563577 Afu2g09380 cutinase 3.4802952 Afu4g00150...”
NP_598756 beta-ureidopropionase from Mus musculus
27% identity, 48% coverage
- Cloning, sequencing, and expression of a cDNA encoding beta-alanine synthase from rat liver.
Kvalnes-Krick, The Journal of biological chemistry 1993 (PubMed)- GeneRIF: cloning and characterization of rat ortholog
YPTB0872 putative amidase-type enzyme from Yersinia pseudotuberculosis IP 32953
32% identity, 76% coverage
BCAM1315 aliphatic amidase (acylamide amidohydrolase) from Burkholderia cenocepacia J2315
29% identity, 62% coverage
AMIE_PSEAE / P11436 Aliphatic amidase; Acylamide amidohydrolase; EC 3.5.1.4 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
P11436 amidase (EC 3.5.1.4) from Pseudomonas aeruginosa (see paper)
PA3366 aliphatic amidase from Pseudomonas aeruginosa PAO1
NP_252056 acylamide amidohydrolase from Pseudomonas aeruginosa PAO1
30% identity, 62% coverage
- function: Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia. Enables the organism to use acetamide as both carbon and nitrogen source
function: Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates.
catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
subunit: Homohexamer. - Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control
Sonnleitner, Frontiers in microbiology 2023 - “...regulator PA3364 7.74 2.61E-32 amiC Aliphatic amidase expression-regulating protein PA3365 10.84 1.42E-48 amiB Probable chaperone PA3366 9.76 4.52E-43 amiE Aliphatic amidase PA4022 3.00 2.41E-04 hdhA Hydrazone dehydrogenase, HdhA PA5168 2.41 1.29E-02 dctQ C(4)-dicarboxylate transport system protein DctQ PA5169 3.27 3.02E-04 dctM C(4)-dicarboxylate transport system protein DctM...”
- Architectural principles for Hfq/Crc-mediated regulation of gene expression
Pei, eLife 2019 - “...NA Pseudomonas genome database: PA5332 Gene ( P. aeruginosa ) amiE NA Pseudomonas genome database: PA3366 Strain, strain background ( P. aeruginosa ) PAO1 PMID: 111024 Strain, strain background ( P. aeruginosa ) PAO1crc PMID: 20080802 Strain, strain background ( Escherichia coli ) XL1-Blue Stratagene Strain,...”
- The development of a new parameter for tracking post-transcriptional regulation allows the detailed map of the Pseudomonas aeruginosa Crc regulon
Corona, Scientific reports 2018 - “...two-component sensor 2,75 0,32 1,85 Catabolism pauA5 PA3356 Glutamylpolyamine synthetase 0,85 0,13 1,21 Catabolism amiE PA3366 Aliphatic amidase 1,95 1,72 2,95 Catabolism PA3579 Probable carbohydrate kinase 1,76 0,23 1,1 Catabolism glpK PA3582 Glycerol kinase 1,93 1,44 6,02 Catabolism glpD PA3584 Glycerol-3-phosphate dehydrogenase 2,87 0,16 3,31 Transport...”
- Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa
Sonnleitner, PloS one 2012 - “...+1) PA3190 7,43 7,81 probable binding protein component ofABC sugar transporter AAUAACAA (24 to 17) PA3366 amiE 4,65 2,04 aliphatic amidase AACAACAA (20 to 13) PA3452 mqoA 4,87 3,12 malate:quinone oxidoreductase PA3570 mmsA 2,23 methylmalonate-semialdehyde dehydrogenase AACAAUAA (37 to 30) PA3875 narG 6,01 4,46 4,79 respiratory...”
- Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients
D'Argenio, Molecular microbiology 2007 - “...CF5296/CF416a CF416lasR::Gm/CF416a PA0510b PA1913 PA2112b PA2625 PA3166 PA3366 PA3392 PA3976 PA4329 PA4442b PA4486b PA4726 PA5435 NirE 14.29 100 4.55 6.25 3.23...”
- The Pseudomonas aeruginosa proteome during anaerobic growth
Wu, Journal of bacteriology 2005 - “...PA3049 PA3195 PA3327 PA3328 PA3329* PA3331 PA3347 PA3365 PA3366 PA3481 PA3537 PA3569 PA3570 PA3842 PA3919* PA4015 PA4129* Proteine VOL. 187, 2005 NOTES 8189...”
- Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector
Rasmussen, Journal of bacteriology 2005 - “...PA3274 PA3316 PA3324 PA3332 PA3333 PA3336 PA3361 PA3365 PA3366 PA3369 PA3370 PA3371 PA3416 PA3451 PA3459 PA3460 PA3461 PA3466 PA3478 PA3479 PA3492 PA3500 PA3520...”
- Crystallization, diffraction data collection and preliminary crystallographic analysis of hexagonal crystals of Pseudomonas aeruginosa amidase.
Andrade, Acta crystallographica. Section F, Structural biology and crystallization communications 2007 - GeneRIF: It is possible that biologically active P. aeruginosa homohexameric amidase is made up of monomers in a spatial arrangement similar to the quaternary structure described for Geobacillus pallidus RAPc8 amidase.
- Support for a three-dimensional structure predicting a Cys-Glu-Lys catalytic triad for Pseudomonas aeruginosa amidase comes from site-directed mutagenesis and mutations altering substrate specificity
Novo, The Biochemical journal 2002 - “...from Pseudomonas aeruginosa (Swiss-prot accession number P11436) [3], Rhodococcus erythropolis (Swiss-Prot accession number Q01360) [4], Helicobacter pylori...”
- “...alignment of NitFhit (1EMS) with P. aeruginosa (P11436), R. erythropolis (Q01360) H. pylori (F64556) and B. stearothermophilus (AAF14257) amidases. Residues...”
- Cloning and heterologous expression of an enantioselective amidase from Rhodococcus erythropolis strain MP50
Trott, Applied and environmental microbiology 2002 - “...smegmatis NCTC 8159 (Q07838 [42]), Pseudomonas aeruginosa (P11436 [2]), Pseudomonas chlororaphis B23 (P27765 [49]); Pseudomonas putida 5B (O69768 [67]);...”
PSF113_2053 aliphatic amidase from Pseudomonas ogarae
29% identity, 62% coverage
- Secondary metabolites from plant-associated Pseudomonas are overproduced in biofilm
Rieusset, Microbial biotechnology 2020 - “...P. chlororaphis subsp. aureofaciens 3084 JV497_v1_320416 X JV395B_v1_1150001 X iaaM; amiE P. kilonensis F113 PSF113_5381; PSF113_2053 X Siderophore type compounds Pyridine2,6thiocarboxylic acid (PDTC) pdtCKPELMFGHIJON P. kilonensis F113 PSF113_26052618 X Pyoverdine pvdSL; pvdIJKDEONMP; fpvI; pvdA P. kilonensis F113 PSF113_17491750; PSF113_18361847; PSF113_18561860 X pvdSL; pvdLY; pvdAPMNOFEJID P. chlororaphis...”
XP_004248793 beta-ureidopropionase from Solanum lycopersicum
25% identity, 57% coverage
C289_2552 carbon-nitrogen hydrolase family protein from Anoxybacillus ayderensis
26% identity, 80% coverage
Q0PIV8 nitrilase (EC 3.5.5.1) from Aeribacillus pallidus (see 2 papers)
25% identity, 80% coverage
A0QQY9 D-inositol-3-phosphate glycosyltransferase (EC 2.4.1.250) from Mycolicibacterium smegmatis (see paper)
MSMEG_0924 hydrolase, carbon-nitrogen family protein from Mycobacterium smegmatis str. MC2 155
28% identity, 95% coverage
PYD3 / Q8H183 β-ureidopropionase (EC 3.5.1.6) from Arabidopsis thaliana (see 2 papers)
BUP1_ARATH / Q8H183 Beta-ureidopropionase; N-carbamoyl-beta-alanine amidohydrolase; Protein PYRIMIDINE 3; EC 3.5.1.6 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
Q8H183 beta-ureidopropionase (EC 3.5.1.6) from Arabidopsis thaliana (see paper)
AT5G64370 BETA-UP (beta-ureidopropionase); beta-ureidopropionase from Arabidopsis thaliana
27% identity, 51% coverage
- function: Catalyzes a late step in pyrimidine degradation. Converts N- carbamoyl-beta-aminoisobutyrate and N-carbamoyl-beta-alanine (3- ureidopropanoate) to, respectively, beta-aminoisobutyrate and beta- alanine, ammonia and carbon dioxide. Involved in the recycling of nitrogen from nucleobases to general nitrogen metabolism.
catalytic activity: 3-(carbamoylamino)propanoate + H2O + 2 H(+) = beta-alanine + NH4(+) + CO2 (RHEA:11184)
catalytic activity: 3-(carbamoylamino)-2-methylpropanoate + H2O + 2 H(+) = (R)-3- amino-2-methylpropanoate + NH4(+) + CO2 (RHEA:37339)
subunit: Homodimer, homotetramer, homooctamer; can also form higher homooligomers.
disruption phenotype: No visible phenotype, but unable to grow on uracil as sole nitrogen source. - Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis
Bellin, Molecules (Basel, Switzerland) 2023 - “...catabolism AT3G17810 PYD1 0.53 0.44 1.00 1.50 1.18 catabolism AT5G12200 PYD2 0.41 1.19 0.90 catabolism AT5G64370 PYD3 0.42 1.17 0.69 catabolism AT2G26230 UOX 0.37 1.01 1.25 0.53 catabolism AT1G80050 APT2 1.58 1.89 1.02 salvage AT4G22570 APT3 0.74 2.90 2.66 1.29 1.75 salvage AT5G11160 APT5 1.13 1.54...”
- Exploiting breakdown in nonhost effector-target interactions to boost host disease resistance
McLellan, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...low sulfur 2 Pi15287 No Yes 3 AT5G28770 bZIP protein BZO2H3 Pi07555 No No 4 AT5G64370 AtPYD3 encodes a -ureidopropionase Pi15278 Yes No 1 AT5G65430 ATMIN10, general regulatory factor 8 Pi02860 Yes No 1 Expression of AtPUB33 Reduces P. infestans Colonization of Host Plants. AtPUB33 is...”
- Molecular mechanisms of resistance to Myzus persicae conferred by the peach Rm2 gene: A multi-omics view
Le, Frontiers in plant science 2022 - “...semialdehyde synthase Beta-alanine and Beta-aminosiobutyrate biosynthesis Prupe_4G264100 AT5G12200 81 No 1.8 8.40E-12 PYD2; Dihydropyrimidinase Prupe_8G070200 AT5G64370 84 Yes 2.0 1.30E-08 PYD3; Beta-ureidopropionase Shikimate pathway Prupe_2G143700 AT2G45300 77 Yes -1.8 2.50E-07 EPSPS; 3-phosphoshikimate 1-carboxyvinyltransferase Prupe_1G393400 AT5G10870 67 Yes 2.2 4.30E-09 CM2; Chorismate mutase 2 Prupe_1G281400 AT1G69370 66...”
- The Synthesis and Role of β-Alanine in Plants
Parthasarathy, Frontiers in plant science 2019 - “...( Campbell, 1960 ; Traut and Loechel, 1984 ); the A. thaliana accession IDs are At5g64370 and At5g64370.1. The degradation of uracil and thymine to produce carbon dioxide, ammonia, -alanine, and -aminoisobutyrate has been shown to occur in seedlings of Brassica napus (rapeseed), while the -ureidopropionase...”
- Combined Proteomic and Metabolomic Profiling of the Arabidopsis thaliana vps29 Mutant Reveals Pleiotropic Functions of the Retromer in Seed Development
Durand, International journal of molecular sciences 2019 - “...A possible cause for the -alanine decrease might be the low abundance of -ureidopropionase (PYD3, At5g64370, 2.4), the enzyme that produces -alanine. It is noteworthy that increased abundance of alanine is considered as a universal stress signal [ 36 ]. Gluconate (5.6), which results from the...”
- A functional analysis of the pyrimidine catabolic pathway in Arabidopsis
Zrenner, The New phytologist 2009 - “...pyd2-1 ) + 11% GABI_114F11 ( pyd2-2 ) + nd -ureidopropionase -UPase PYD3 EC 3.5.1.6 At5g64370 SALK_016594 ( pyd3 ) + 9% nd, not determined. Although T-DNA insertions within genes frequently result in a complete loss of function associated with the protein product, our initial determination...”
- Dynamic evolution at pericentromeres
Hall, Genome research 2006 - “...At5g67350 At2g03330 At2g26610 At5g06480 At5g06480 At3g42150 At4g10080 At5g35695 At5g64370 At2g20120 cDNA EST, ma cDNA cDNA cDNA ma cDNA ma, mpss MPSS cDNA cDNA...”
UPB1 / Q9UBR1 β-ureidopropionase (EC 3.5.1.6) from Homo sapiens (see 2 papers)
BUP1_HUMAN / Q9UBR1 Beta-ureidopropionase; BUP-1; Beta-alanine synthase; N-carbamoyl-beta-alanine amidohydrolase; EC 3.5.1.6 from Homo sapiens (Human) (see 7 papers)
27% identity, 49% coverage
- function: Catalyzes a late step in pyrimidine degradation (PubMed:22525402, PubMed:24526388). Converts N-carbamoyl-beta-alanine (3-ureidopropanoate) into beta-alanine, ammonia and carbon dioxide (PubMed:10415095, PubMed:10542323, PubMed:11508704, PubMed:22525402, PubMed:24526388, PubMed:29976570). Likewise, converts N-carbamoyl-beta- aminoisobutyrate (3-ureidoisobutyrate) into beta-aminoisobutyrate, ammonia and carbon dioxide (Probable).
catalytic activity: 3-(carbamoylamino)propanoate + H2O + 2 H(+) = beta-alanine + NH4(+) + CO2 (RHEA:11184)
catalytic activity: 3-(carbamoylamino)-2-methylpropanoate + H2O + 2 H(+) = (R)-3- amino-2-methylpropanoate + NH4(+) + CO2 (RHEA:37339)
subunit: Homodimer, homotetramer, homooctamer; can also form higher homooligomers. - Dynamic Changes of Urine Proteome in Rat Models Inoculated with Two Different Hepatoma Cell Lines.
Zhang, Journal of oncology 2021 - “...O00161 Synaptosomal-associated protein 23 2.22 P49189 4-Trimethylaminobutyraldehyde dehydrogenase 2.21 Q9Y6I3 Epsin-1 2.20 2.18 Prostate cancer Q9UBR1 Beta-ureidopropionase 2.17 Serum Q14847 LIM and SH3 domain protein1 2.16 Tissue Gastric cancer O43704 Sulfotransferase family cytosolic 1B member 1 2.15 Q9UNQ0 ATP-binding cassette subfamily G member 2 2.15 Tissue...”
- Bioinformatic analysis of 302 reactive metabolite target proteins. Which ones are important for cell death?
Hanzlik, Toxicological sciences : an official journal of the Society of Toxicology 2013 - Pan-pathway based interaction profiling of FDA-approved nucleoside and nucleobase analogs with enzymes of the human nucleotide metabolism.
Egeblad, PloS one 2012 - “...gi|4507835 P11172 1.17.4.1 792 75742 De novo purine + pyrimidine 48.8 22 UPB1 Beta-ureidopropionase gi|17373540 Q9UBR1 2.7.1.48 277 22243 Salvage pyrimidine 56.4 23 UPP1 Uridine phosphorylase 1 gi|13938418 Q16831 2.4.2.10 480 7203 De novo pyrimidine 42.6 24 UPP2 Uridine phosphorylase 2 gi|27597096 O95045 4.1.1.23 480 224479...”
- Identification of protein targets of reactive metabolites of tienilic acid in human hepatocytes.
Koen, Chemical research in toxicology 2012 - “...P02763 4 22 34.1 Alpha-1-acid glycoprotein 1 P02763 3 17 22 Beta-ureidopropionase (UPB1 protein Fragment) Q9UBR1 2 6 BB, TB 1 Cathepsin D (heavy chain,169412) P07339 8 32 5 Cathepsin D (heavy chain,169412) P07339 8 31 7 Dihydropteridine reductase P09417 2 11 22 DnaJ homolog subfamily...”
- Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus
Vieira, BMC genomics 2011 - “...1.394 0.015 O60566 Mitotic checkpoint serine/threonine-protein kinase BUB1 beta Mitotic checkpoint protein. SAPD17118 1.393 0.041 Q9UBR1 Beta-ureidopropionase (BUP-1) Amino acid biosynthesis. SAPD13849 1.390 0.021 Q9H7X7 Rab-like protein 5 Regulator of haematopoietic cells with roles in cell growth, survival, differentiation, cytokine production, chemotaxis, vesicle trafficking and phagocytosis....”
NIT2_YEAST / P47016 Deaminated glutathione amidase; dGSH amidase; Nitrilase homolog 1; EC 3.5.1.128 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
P47016 deaminated glutathione amidase (EC 3.5.1.128) from Saccharomyces cerevisiae (see paper)
YJL126W Nit protein, one of two proteins in S. cerevisiae with similarity to the Nit domain of NitFhit from fly and worm and to the mouse and human Nit protein which interacts with the Fhit tumor suppressor; nitrilase superfamily member from Saccharomyces cerevisiae
NP_012409 putative hydrolase from Saccharomyces cerevisiae S288C
29% identity, 56% coverage
MSMEG_0566 aliphatic amidase from Mycobacterium smegmatis str. MC2 155
28% identity, 81% coverage
4hg3A / P47016 Structural insights into yeast nit2: wild-type yeast nit2 in complex with alpha-ketoglutarate (see paper)
29% identity, 56% coverage
- Ligand: 2-oxoglutaric acid (4hg3A)
Bd0943 putative amidohydrolase from Bdellovibrio bacteriovorus HD100
31% identity, 61% coverage
Rv0480c POSSIBLE AMIDOHYDROLASE from Mycobacterium tuberculosis H37Rv
P9WJ01 Hydrolase Rv0480c from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
30% identity, 84% coverage
- The unfoldase ClpC1 of Mycobacterium tuberculosis regulates the expression of a distinct subset of proteins having intrinsically disordered termini
Lunge, The Journal of biological chemistry 2020 (secret) - Dissecting the antibacterial activity of oxadiazolone-core derivatives against Mycobacterium abscessus
Madani, PloS one 2020 - “...MAB_2477c 55.217 Rv1393c - Probable monoxygenase IM/R MAB_2478c 15.382 - uncharacterized protein - MAB_2545c 35.436 Rv0480c M/WCL Possible amidohydrolase IM/R MAB_2943c 31.546 Rv1543 M/WCL Possible fatty acyl-CoA reductase LM MAB_3336c 54.339 Rv2045c - Carboxylesterase LipT IM/R MAB_3398 17.635 Rv3178 - uncharacterized protein - MAB_3661 57.093 Rv3308...”
- Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories
Ioerger, Journal of bacteriology 2010 - “...H37RvHA H37RvLP A3C A3C Mutations shared by cluster 3 Rv0480c Rv0538 Rv0573c Rv2940c/mase Rv3785 R9H P402S L275L GC 17 bp R9H P402S L275L GC 17 bp Mutations...”
- “...mas and a synonymous mutation in Rv0573c): R9H in Rv0480c, P402S in Rv0538, and a 17-bp deletion in Rv3785. Rv0480c encodes a putative nitrilase, but the...”
- Proteomic definition of the cell wall of Mycobacterium tuberculosis
Wolfe, Journal of proteome research 2010 - “...Rv0431 Rv0431 x Rv0432 sodC x x yes ( 45 , 46 , 19 ) Rv0480c Rv0480c x ( 24 ) Rv0507 mmpL2 x ( 24 ) Rv0512 hemB x Rv0559c Rv0559c x yes ( 42 , 16 ) Rv0583c lpqN x yes yes ( 16...”
- Genetic requirements for the survival of tubercle bacilli in primates
Dutta, The Journal of infectious diseases 2010 - “...( gpsA ), triacylglycerol ( tgs 1) and GMP ( guaB3 ), intermediary metabolism (Rv0458, Rv0480c, Rv0696, fucA , mapA , Rv0895, zwf 1, amiB1, amiB2 , glgP , Rv1393c, epiA , Rv1526c, Rv1869c, amiA2 , Rv3049c, Rv3085, Rv3175, Rv3224), isoniazid resistance ( iniA ), heat...”
- Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments
Cubillos-Ruiz, BMC research notes 2008 - “...in Haarlem Strain) 474110 125 Rv0401 (Probable conserved transmembrane protein) 565404 113 Intergenic region between Rv0480c (Probable amidohydrolase) and Rv0481c (Hypothetical protein) 956083 54 Intergenic region between ercc3 (Probable DNA helicase) and Rv0862c (Hypothetical protein) 1984522 109 C-terminal end wag22 (PE-PGRS) 2354142 214 PE-PGRS36 2456125 115...”
BAS3851 hydrolase, carbon-nitrogen family from Bacillus anthracis str. Sterne
GBAA_4149 formamidase from Bacillus anthracis str. 'Ames Ancestor'
24% identity, 69% coverage
HSUHS1_0888, HSUHS5_0231 aliphatic amidase from Helicobacter suis HS1
29% identity, 56% coverage
- Genome sequence of Helicobacter suis supports its role in gastric pathology
Vermoote, Veterinary research 2011 - “...H. pylori 98 (64) HSUHS1_0230 HSUHS5_1130 Arginase ( rocF ) of H. pylori 99 (75) HSUHS1_0888 HSUHS5_0231 Acylamide amidohydrolase ( amiE ) of H. pylori 100 (93) HSUHS1_0680 HSUHS5_0265 Formamidase ( amiF ) of H. pylori 100 (98) HSUHS1_0161 HSUHS5_1077 -Carbonic anhydrase of H. pylori 92...”
- “...pylori 98 (64) HSUHS1_0230 HSUHS5_1130 Arginase ( rocF ) of H. pylori 99 (75) HSUHS1_0888 HSUHS5_0231 Acylamide amidohydrolase ( amiE ) of H. pylori 100 (93) HSUHS1_0680 HSUHS5_0265 Formamidase ( amiF ) of H. pylori 100 (98) HSUHS1_0161 HSUHS5_1077 -Carbonic anhydrase of H. pylori 92 (69)...”
B0V8W9 NAD+ synthase (glutamine-hydrolysing) (EC 6.3.5.1) from Acinetobacter baumannii (see paper)
ABAYE2955 putative glutamine-dependent NAD(+) synthetase (NAD(+) synthase [glutamine-hydrolyzing]) (NadE) from Acinetobacter baumannii AYE
ABBFA_002755 Probable glutamine-dependent NAD(+) synthetase from Acinetobacter baumannii AB307-0294
HMPREF0010_01353 NAD+ synthase from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
26% identity, 44% coverage
5khaA / V5VHL3 Structure of glutamine-dependent NAD+ synthetase from acinetobacter baumannii in complex with adenosine diphosphate (adp)
25% identity, 45% coverage
- Ligand: adenosine-5'-diphosphate (5khaA)
XHV734_1262 NAD+ synthase from Xanthomonas hortorum pv. vitians
30% identity, 40% coverage
alr2001 nitrilase homolog from Nostoc sp. PCC 7120
29% identity, 83% coverage
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...Glr1682, Glr2043 n.d Gll2207, Gll1504, Glr3848, Gll2805 Nostoc sp. PCC 7120 All3401, All4887 Alr2310 n.d Alr2001 n.d Alr2826, Alr3771, All3556, All5022 Nostoc punctiforme PCC 73102 Npun02000556, Npun02000612 Npun02002114 n.d Npun02002053 n.d Npun02003427, Npun02002895, Npun02002692, Npun02003702 Anabaena variabilis ATCC 29413 Ava_2157, Ava_3423 Ava_0127 n.d Ava_5061 n.d Ava_1107,...”
TERTU_3828 hydrolase, carbon-nitrogen family from Teredinibacter turnerae T7901
31% identity, 53% coverage
XC_1067 NH3-dependent NAD synthetase from Xanthomonas campestris pv. campestris str. 8004
31% identity, 36% coverage
- Structural insights into Xanthomonas campestris pv. campestris NAD<sup>+</sup> biosynthesis via the NAM salvage pathway
Xu, Communications biology 2024 - “...the meanSD of triplicate measurements. WT, wild-type strain; Nampt , XC_0719 deletion mutant; Nads , XC_1067 deletion mutant; Nampt Nads , XC_0719 and XC_1067 double deletion mutant. To test whether the de novo, Preiss-Handler and the NAM salvage pathways are functional in Xcc , we investigated...”
- “...(NADS) homologue XC_1067 and the NAMPT homologue XC_0719, in NAD synthesis and bacterial growth. Specifically, XC_1067 is responsible for the last step of NAD + production in both the de novo and Preiss-Handler pathways, while XC_0719 catalyzes the rate-limiting step of the NAM salvage pathway. To...”
P59701 formamidase (EC 3.5.1.49) from Bacillus cereus (see paper)
24% identity, 69% coverage
Ava_5061 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase from Anabaena variabilis ATCC 29413
29% identity, 83% coverage
- Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Schriek, BMC genomics 2007 - “...n.d Npun02002053 n.d Npun02003427, Npun02002895, Npun02002692, Npun02003702 Anabaena variabilis ATCC 29413 Ava_2157, Ava_3423 Ava_0127 n.d Ava_5061 n.d Ava_1107, Ava_1554, Ava_3534, Ava_2258 N.d. = not detected. Table 6 Database entries of genes from 24 cyanobacterial genomes encoding putative arginases (B1), L-ornithine transaminases (C2), and 1 pyrroline-5-carboxylate dehydrogenases...”
SS1G_14415 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
29% identity, 83% coverage
AMIE_RHOER / Q01360 Aliphatic amidase; Acylamide amidohydrolase; Wide spectrum amidase; EC 3.5.1.4 from Rhodococcus erythropolis (Arthrobacter picolinophilus)
27% identity, 62% coverage
- function: Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia. Hydrolyzes propionamide, acetamide and acrylamide. Enables the organism to use such amides as both carbon and nitrogen source.
function: Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine or hydrazine to form hydroxamates and acid hydrazides respectively. The highest level of acyl transfer activity is observed with acetamide.
catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
subunit: Homotetramer
D2SGH7 nitrilase (EC 3.5.5.1) from Geodermatophilus obscurus (see paper)
30% identity, 96% coverage
AMIE_BACSP / Q9L543 Aliphatic amidase; Acylamide amidohydrolase; EC 3.5.1.4 from Bacillus sp. (see paper)
29% identity, 57% coverage
- function: Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia.
function: Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates.
catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
y0194 putative carbon-nitrogen hydrolase from Yersinia pestis KIM
37% identity, 42% coverage
NIT1_YEREN / P0DP68 Deaminated glutathione amidase; dGSH amidase; Nitrilase homolog 1; yeNit1; EC 3.5.1.128 from Yersinia enterocolitica (see paper)
P0DP68 deaminated glutathione amidase (EC 3.5.1.128) from Yersinia enterocolitica (see paper)
36% identity, 42% coverage
- function: Hydrolyzes deaminated glutathione (dGSH, 2-oxoglutaramate) to alpha-ketoglutarate (alpha-KG) and cysteinylglycine (specific activity 6.50 umol/min/mg), has less activity against alpha-ketoglutaramate (a- KGM, specific activity 0.20 umol/min/mg), very little activity on glutathione and none on L-glutamine. May function as a metabolite repair enzyme.
catalytic activity: N-(4-oxoglutaryl)-L-cysteinylglycine + H2O = L- cysteinylglycine + 2-oxoglutarate (RHEA:54532)
4gylA / Q9L543 The e142l mutant of the amidase from geobacillus pallidus showing the result of michael addition of acrylamide at the active site cysteine (see paper)
29% identity, 58% coverage
- Ligands: propionamide; chloride ion (4gylA)
XP_002289996 aliphatic amidase from Thalassiosira pseudonana CCMP1335
27% identity, 60% coverage
NCU05757 nitrilase from Neurospora crassa OR74A
33% identity, 62% coverage
- Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa
Wang, mSystems 2022 - “...assigned, 7 of which are functionally annotated, coding for peptidase M4 mpr-20 (NCU05756), nitrilase-5 nse-5 (NCU05757), pheromone receptor pre-2 (NCU05758), oligopeptide transporter-5 opt-5 (NCU17269), zinc-finger transcription factor-10 znf-10 (NCU05767), mating-response protein poi-2 (NCU05768), and a putative septal pore-associated protein (NCU05769). Excluding three cluster-flanking genes (NCU05755, -05756,...”
NRL4_ARATH / P46011 Bifunctional nitrilase/nitrile hydratase NIT4; Cyanoalanine nitrilase; Nitrilase 4; EC 3.5.5.1; EC 3.5.5.4; EC 4.2.1.65 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT5G22300 NIT4 (NITRILASE 4); 3-cyanoalanine hydratase/ cyanoalanine nitrilase/ indole-3-acetonitrile nitrilase/ nitrilase/ nitrile hydratase from Arabidopsis thaliana
NP_197622 nitrilase 4 from Arabidopsis thaliana
27% identity, 74% coverage
- function: Highly specific for beta-cyano-L-alanine (Ala(CN)). Low activity with 3-phenylpropionitrile (PPN) or allylcyanide and no activity with indole-3-acetonitrile. Not associated with auxin production but may be involved in cyanide detoxification.
catalytic activity: a nitrile + 2 H2O = a carboxylate + NH4(+) (RHEA:21724)
catalytic activity: 3-cyano-L-alanine + 2 H2O = L-aspartate + NH4(+) (RHEA:11188)
catalytic activity: L-asparagine = 3-cyano-L-alanine + H2O (RHEA:15385)
subunit: Forms a homopentamer composed of five dimers. - Fine-Tuning of Arabidopsis thaliana Response to Endophytic Colonization by Gluconacetobacter diazotrophicus PAL5 Revealed by Transcriptomic Analysis
Soares, Plants (Basel, Switzerland) 2024 - “...only genes involved in the degradation of glucosinolates were observed (at1g54020; MBP1, at1g52040; and NIT4, at5g22300). Five DEGs related to the biosynthetic pathway of phenylpropanoids were detected. In shoots, three DEGs were induced (UGT72E1, at3g50740; UGT72E2, at5g66690; and OMTF3, at3g61990), and one was repressed (PRR1, at1g32100)....”
- Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant
Abdullah-Zawawi, Scientific reports 2022 - “...clade 1, At NIT2 ( At3g44300 ), At NIT1 ( At3g44310 ), At NIT4 ( At5g22300 ) and Os NRT2 ( LOC_Os02g42330 ) were present together (Fig. 2 ). Figure 2 Phylogenetic analysis of collated sulfur-encoding biosynthetic genes in Arabidopsis thaliana and rice ( Oryza sativa...”
- Effects of the Developmental Regulator BOLITA on the Plant Metabolome
Lazcano-Ramírez, Genes 2021 - “...AT2G25450 GLUCOSINOLATE HYDROXYLASE (GSL-OH) 2.6089 AT3G09710 IQ-DOMAIN 1 (IQD1) 0.5063 AT3G44300 NITRILASE 2 (NIT2) 3.4643 AT5G22300 NITRILASE 4 (NIT4) 12.8733 ( B ) C16516 Indolylmethylthiohydroximate 1.7184 C17222 2-(5-Methylthio)pentylmalate 0.4602 C17245 5-Methylthiopentanaldoxime 1.6259 C17251 8-Methylthiooctanaldoxime 0.0365...”
- Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis
Grigoreva, Genes 2021 - “...(Linonate) 0.493 0.003 nd AT5G04040 (SDP1) 0.9 0.055 C00049 (L-Aspartate) 0.621 0.009 nd AT2G30970 (ASP1); AT5G22300 (NIT4) 0.386; 0.533 0.097; 0.006 C00065 (L-Serine) 0.393 0.008 0.001 AT1G55920 (ATSERAT2;1) 1.448 5.492 10 5 genes-12-00952-t005_Table 5 Table 5 Description of differentially expressed guar transcripts involved in the phosphatidylinositol...”
- Genetic Architecture and Genome-Wide Adaptive Signatures Underlying Stem Lenticel Traits in Populus tomentosa
Li, International journal of molecular sciences 2021 - “...example, we identified an association of Ptom.016G.00430 , a homolog gene encoding a NIT4 enzyme (AT5G22300), with LA ( Table S6 ). Previous studies have demonstrated that NIT4 plays a key role in cyanide detoxification during ethylene biosynthesis in Arabidopsis [ 37 ]. Additional evidence has...”
- GSNOR Contributes to Demethylation and Expression of Transposable Elements and Stress-Responsive Genes
Rudolf, Antioxidants (Basel, Switzerland) 2021 - “...Start bp CH 3 Feature Gene Id log2FC padj. Description Chr5 7376314 54 3kb up AT5G22300 1.82 1.3 10 39 Bifunctional nitrilase/nitrile hydratase NIT4 (UV stress, biotic stress) Chr3 9173846 95 3kb up AT3G25190 1.30 2.7 10 4 Vacuolar iron transporter homolog 2.1 (biotic stress) Chr5...”
- Expression and Role of Biosynthetic, Transporter, Receptor, and Responsive Genes for Auxin Signaling during Clubroot Disease Development
Robin, International journal of molecular sciences 2020 - “...AGAGAACGTCTTTCGTGTGT At3g12830 BrSAUR2 Bra039345 402 GAATCTTTCCTCCGGTCTTC 187 TTTGCTCGTAACCATACTCC At3g44300 BrNIT1 Bra028932 1032 GAATCAGAGGGTCTCATCAC 151 TCGAAACGAATGTAACTGGT At5g22300 BrNIT2 Bra020184 1074 GCAAGTATCTTGCTTCTGCT 157 TGACCATGTGAGTCAAAGAA At5g01990 BrPILS1 Bra014265 1296 GAAGCAAATCATCCAACCTG 167 GTGCCAGTAATATACAGGGG At1g59500 BrGH3.3 Bra041046 1764 TAAGCTTCCTCCAGAACAAC 157 GAGCAAACCTCTACCAAGAA At4g14550 BrIAA1 Bra039855 702 CTCTACCAAAGAAGGATCCG 163 TTCGCTACACTTCTGATGAG At4g03400 BrGH3.4 Bra034205...”
- Overexpression of a soybean YABBY gene, GmFILa, causes leaf curling in Arabidopsis thaliana
Yang, BMC plant biology 2019 - “...DEGs were up-regulated in transgenic Arabidopsis including At2g29470 / GSTU3 (glutathione transferase) [ 58 ], At5g22300 / NIT4 (nitrilase) [ 59 ] and At5g27420 / CNI (ubiquitin ligase) [ 60 ]. Many genes related to biotic/abiotic stresses were also found to be up-regulated in transgenic Arabidopsis...”
- More
- Discovery and characterization of a highly efficient enantioselective mandelonitrile hydrolase from Burkholderia cenocepacia J2315 by phylogeny-based enzymatic substrate specificity prediction
Wang, BMC biotechnology 2013 - “...35 This study Bradyrhizobium japonicum USDA 110 NP_770037 nitrilase 35 [ 30 ] Arabidopsis thaliana NP_197622 nitrilase 35 [ 31 ] Methylibium petroleiphilum PM1 YP_001022666 nitrilase 34 This study Synechocystis sp. PCC 6803 NP_442646 nitrilase 34 [ 24 ] Burkholderia phymatum STM815 YP_001861308 unnamed protein product...”
- Polysaccharide Fraction Extracted from Endophytic Fungus Trichoderma atroviride D16 Has an Influence on the Proteomics Profile of the Salvia miltiorrhiza Hairy Roots
Peng, Biomolecules 2019 - “...oxidase subunit 5C-1 1.72 O80575 6,7-dimethyl-8-ribityllumazine synthase, chloroplastic 0.64 Synthesis and metabolism of amino acids P46011 Bifunctional nitrilase/nitrile hydratase NIT4 1.57 Q56WN1 Glutamine synthetase cytosolic isozyme 1-1 0.52 1.67 Q9C8S5 Chlorophyll A-B-binding protein 2, 5 partial; 1-750 (Fragment) 1.64 Q9M9F1 Glutathione S-transferase U23 1.63 Q8LF21 Dynamin-related...”
- Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline-alkali stress
Jia, Horticulture research 2019 - “...aminotransferase 3 P46644 2.471 1.305 ASN1 Asparagine synthetase P49078 3.228 1.690 NIT4 Bifunctional nitrilase/nitrile hydratase P46011 0.452 1.147 GLN11 Glutamine synthetase cytosolic isozyme 11 Q56WN1 0.470 1.088 Metabolites Metabolite Adducts VIP Fold change P -value d -Phenylalanine M+H 3.853 5.873 0.00060 Phenylacetylglycine 2MH 2.574 0.198 0.00004...”
NP_001172021 deaminated glutathione amidase isoform 2 from Homo sapiens
32% identity, 53% coverage
- Bi-allelic NIT1 variants cause a brain small vessel disease characterized by movement disorders, massively dilated perivascular spaces, and intracerebral hemorrhage.
Rutten, Genetics in medicine : official journal of the American College of Medical Genetics 2024 (PubMed)- GeneRIF: Bi-allelic NIT1 variants cause a brain small vessel disease characterized by movement disorders, massively dilated perivascular spaces, and intracerebral hemorrhage.
- The Rosetta Stone Hypothesis-Based Interaction of the Tumor Suppressor Proteins Nit1 and Fhit.
Mittag, Cells 2023 - GeneRIF: The Rosetta Stone Hypothesis-Based Interaction of the Tumor Suppressor Proteins Nit1 and Fhit.
- NIT1 suppresses tumour proliferation by activating the TGFβ1-Smad2/3 signalling pathway in colorectal cancer.
Lin, Cell death & disease 2018 - GeneRIF: NIT1 suppresses colorectal cancer cell proliferation through a positive feedback loop between NIT1 and activation of the TGFbeta-Smad2/3 signalling pathway.
- Nitrilase 1 modulates lung tumor progression in vitro and in vivo.
Wang, Oncotarget 2016 - GeneRIF: Data show that cisplatin response was enhanced in human lung cancer cells when Nit1 was knocked down and mice Nit1-/-:KrasG12D/+ tumors showed increased sensitivity to cisplatin in vivo.
- Human nitrilase-like protein does not catalyze the hydrolysis of vildagliptin.
Asakura, Drug metabolism and pharmacokinetics 2014 (PubMed)- GeneRIF: Human NIT1/2 are not involved in the metabolism of vildagliptin.
- Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Hendrickson, PloS one 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Biological functions of mammalian Nit1, the counterpart of the invertebrate NitFhit Rosetta stone protein, a possible tumor suppressor.
Semba, The Journal of biological chemistry 2006 (PubMed)- GeneRIF: Nit1 and Fhit share tumor suppressor signaling pathways, while localization of the NIT1 gene at a stable chromosome site explains the paucity of gene alterations and in frequent loss of expression of the NIT1 gene in human malignancies.
Q5KR04 N-carbamoylputrescine amidase (EC 3.5.1.53) from Selenomonas ruminantium (see paper)
24% identity, 80% coverage
FQ085_05485 carbon-nitrogen hydrolase family protein from Planococcus sp. ANT_H30
26% identity, 81% coverage
NMB0441 nitrilase from Neisseria meningitidis MC58
26% identity, 86% coverage
idhX / AAC43641.1 idhX from Sphingobium yanoikuyae (see paper)
31% identity, 35% coverage
NIT4A / Q5QGZ8 β-cyano-L-alanine nitrilase (EC 3.5.5.4; EC 4.2.1.65) from Lupinus angustifolius (see paper)
NRL4A_LUPAN / Q5QGZ8 Bifunctional nitrilase/nitrile hydratase NIT4A; LaNIT4A; 3-cyanoalanine hydratase; Cyanoalanine nitrilase A; EC 3.5.5.4; EC 4.2.1.65 from Lupinus angustifolius (Narrow-leaved blue lupine) (see paper)
Q5QGZ8 cyanoalanine nitrilase (EC 3.5.5.4); 3-Cyanoalanine hydratase (EC 4.2.1.65) from Lupinus angustifolius (see paper)
28% identity, 74% coverage
- function: Involved in the cyanide detoxification pathway. Has nitrilase and nitrile-hydratase activity in the ratio 4.0:1, producing both asparagine and aspartic acid from beta-cyano-L-alanine (Ala(CN)). Can also use 3-phenylpropionitrile as substrate, but not indole-3- acetonitrile.
catalytic activity: L-asparagine = 3-cyano-L-alanine + H2O (RHEA:15385)
catalytic activity: 3-cyano-L-alanine + 2 H2O = L-aspartate + NH4(+) (RHEA:11188)
B7G8X8 Aliphatic amidase from Phaeodactylum tricornutum (strain CCAP 1055/1)
28% identity, 53% coverage
TERTU_0619 hydrolase, carbon-nitrogen family from Teredinibacter turnerae T7901
31% identity, 76% coverage
BCIN_14g01750 Bcnit3 from Botrytis cinerea B05.10
27% identity, 83% coverage
NIT4B / Q3LRV4 β-cyano-L-alanine nitrilase (EC 3.5.5.4; EC 4.2.1.65) from Lupinus angustifolius (see paper)
NRL4B_LUPAN / Q3LRV4 Bifunctional nitrilase/nitrile hydratase NIT4B; LaNIT4B; 3-cyanoalanine hydratase; Cyanoalanine nitrilase B; EC 3.5.5.4; EC 4.2.1.65 from Lupinus angustifolius (Narrow-leaved blue lupine) (see paper)
Q3LRV4 cyanoalanine nitrilase (EC 3.5.5.4) from Lupinus angustifolius (see paper)
26% identity, 71% coverage
- function: Involved in the cyanide detoxification pathway. Has nitrilase and nitrile-hydratase activity in the ratio 3.3:1, producing both asparagine and aspartic acid from beta-cyano-L-alanine (Ala(CN)). Can also use 3-phenylpropionitrile as substrate, but not indole-3- acetonitrile.
catalytic activity: L-asparagine = 3-cyano-L-alanine + H2O (RHEA:15385)
catalytic activity: 3-cyano-L-alanine + 2 H2O = L-aspartate + NH4(+) (RHEA:11188)
A9762_26525 carbon-nitrogen hydrolase family protein from Pandoraea sp. ISTKB
29% identity, 83% coverage
AMIF_HELPY / O25836 Formamidase; Formamide amidohydrolase; EC 3.5.1.49 from Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) (see 2 papers)
HP1238 aliphatic amidase (aimE) from Helicobacter pylori 26695
24% identity, 69% coverage
- function: Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide. Probably involved in the nitrogen metabolism of H.pylori.
catalytic activity: formamide + H2O = formate + NH4(+) (RHEA:21948)
subunit: Homotetramer. - AI-2 Induces Urease Expression Through Downregulation of Orphan Response Regulator HP1021 in Helicobacter pylori
Yang, Frontiers in medicine 2022 - “...ABC transporter permease 1.2716 HP0605 Membrane protein 1.2728 HP1400 Iron(III) dicitrate transport protein FecA 1.2869 HP1238 Formamidase 1.2907 HP0186 Hypothetical protein 1.2945 HP0753 Flagellar biosynthesis protein FliS 1.3035 HP0455 Pseudogene 1.3066 HP0607 Multidrug resistance protein 1.3128 HP0808 Holo-[acyl-carrier-protein] synthase 1.3146 HP0939 Amino acid ABC transporter permease...”
- Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System
Loh, Infection and immunity 2021 (secret) - The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
Xu, Frontiers in microbiology 2021 - “...HP1165 tetA 1.2466 HP1167 Predicted gene 4.0239 HP1215 Predicted gene 1.2189 HP1233 Predicted gene 2.281 HP1238 amiF 1.387 HP1258 Predicted gene 1.0603 HP1321 ATP-binding protein 1.45 HP1390 Predicted gene 3.3507 HP1391 Predicted gene 1.915 HP1440 Predicted gene 3.7316 HP1505 Predicted gene 1.123 HP1519 Predicted gene 2.1358...”
- Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Marcus, Helicobacter 2018 - “...1.91 0.10 0.04 1.25 0.16 0.28 1.02 0.16 0.47 aliphatic amidase ( amiE ) HPG27_RS06200 HP1238 1.92 0.03 0.00 1.76 0.04 0.01 1.46 0.03 0.01 formamidase ( amiF ) F O F 1 -ATPase HPG27_RS04065 HP0828 1.99 0.06 0.00 1.80 0.04 0.00 2.39 0.26 0.03 ATP-synthase...”
- Survival of Helicobacter pylori in gastric acidic territory
Ansari, Helicobacter 2017 - “...the expression of other several genes, including those that encode urease, amidase (HP0294) and formamidase (HP1238) for acid resistance in H. pylori [ 120 ]. All these enzymes are involved in ammonia generation, are likely to play an important role in acid resistance [ 35 ,...”
- Structural and functional aspects of the Helicobacter pylori secretome
Zanotti, World journal of gastroenterology 2014 - “...aliphatic amidases have been identified, hp0294 and hp1238. The corresponding proteins are called AmiE and AmiF, respectively[134,135]. Aliphatic amidases are...”
- Molecular aspects of bacterial pH sensing and homeostasis
Krulwich, Nature reviews. Microbiology 2011 - “...HP1186 2.680.98 2.15 4.64 carbonic anhydrase HP0294 5.311.78 1.72 2.28 aliphatic amidase ( amiE ) HP1238 1.970.25 1.09 1.32 formamidase ( amiF ) HP0649 2.420.60 1.37 2.56 Aspartase ( aspA ) HP1399 15.942.90 1.81 7.11 arginase ( rocF ) Relative fold changes as compared to levels...”
- Trans-translation in Helicobacter pylori: essentiality of ribosome rescue and requirement of protein tagging for stress resistance and competence
Thibonnier, PloS one 2008 - “...In a last step, using a Kpn I restriction site, we added the amiF ( hp1238 ) transcriptional terminator downstream from the fusion genes using a Kpn I restriction site and obtained pILL2332 (fusion with stop and terminator) and pILL2333 (fusion without stop and with terminator),...”
- More
- Carbamate C-N Hydrolase Gene ameH Responsible for the Detoxification Step of Methomyl Degradation in Aminobacter aminovorans Strain MDW-2
Jiang, Applied and environmental microbiology 2020 (secret) - Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function
Liao, Scientific reports 2016 - “...on acetamide, propionamide, butyramide, and acrylamide 73 74 . The Cluster I enzyme, UniprotKB ID O25836 from Helicobacter pylori , was reported to only catalyze the conversion of formamide 75 . While limited, the experimental data (particularly for Cluster II) indicate that functional specialization (substrate preference...”
- Biochemical and mutational studies of the Bacillus cereus CECT 5050T formamidase support the existence of a C-E-E-K tetrad in several members of the nitrilase superfamily
Soriano-Maldonado, Applied and environmental microbiology 2011 - “...of Helicobacter pylori (HpyAmiF; GenBank accession no. O25836) (77% similarity). Sequence alignment of formamidases from several organisms classified under EC...”
- “...toward formamide, i.e., HpyAmiF (GenBank accession no. O25836), BceAmiF (this work), the Methylophilus methylotrophus enzyme (GenBank accession no. DAA01135),...”
PD0839 NH3-dependent NAD synthetase from Xylella fastidiosa Temecula1
31% identity, 40% coverage
blr0973 amidase from Bradyrhizobium japonicum USDA 110
27% identity, 62% coverage
A0A0E3D8K7 nitrilase (EC 3.5.5.1); Aliphatic nitrilase (EC 3.5.5.7) from Fusarium proliferatum (see paper)
28% identity, 80% coverage
NIT2_SCHPO / O94660 Probable hydrolase nit2; EC 3.5.-.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPBC651.02 nitrilase (predicted) from Schizosaccharomyces pombe
29% identity, 65% coverage
- Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants
Sánchez, G3 (Bethesda, Md.) 2015 - “...csn71 Others cbf11, dcd1, vps60, SPBC1711.15C, SPBC1289.14, mpp6, SPAC1635.01, SPAC1071.09C, SPBP16F5.05C, naa30, nup60, SPBP16F5.08C, rga8, SPBC651.02, urm1,SPCC1442.02, ppk3, sde2, SPBC27.05, pmp3, SPBC1711.09C, hmt1, atg22, fep1 GO, Gene Ontology; E-MAP, epistatic miniarray profile. Comparison of Brc1 and Rtt107 E-MAPs Fission yeast Brc1 and budding yeast Rtt107 are...”
I1GUE5 CN hydrolase domain-containing protein from Brachypodium distachyon
25% identity, 56% coverage
- Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon
Barros, The Plant cell 2022 - “...I1HTL6; aldo-keto reductase, I1HIH2; 3-methylcrotonyl-CoA carboxylase, I1I750); BdC4H1i (magnesium chelatase, I1GRM4; FAD diphosphatase, I1ISL9; beta-ureidopropionase, I1GUE5; asparaginase, I1J2P3; glutathione transferase, I1I5M2; glutathione transferase, I1H6R5; glutathione transferase, I1GZH6; glutathione transferase, I1HNH0; chitinase, I1HTL6; GPI-anchor transamidase, I1ILR8; gamma-glutamylcyclotransferase, I1IY91); BdC3 H1i (magnesium chelatase, I1GRM4; uncharacterized protein, I1HCQ4; beta-ureidopropionase,...”
Afu6g12100 nitrilase family protein from Aspergillus fumigatus Af293
29% identity, 64% coverage
- TrpE feedback mutants reveal roadblocks and conduits toward increasing secondary metabolism in Aspergillus fumigatus
Wang, Fungal genetics and biology : FG & B 2016 - “...A. fumigatus with nearby putative anthranilate synthase gene Afu6g12110 ( icsA).* Abbreviation: 12090, Afu6g12090; 12100, Afu6g12100; 12110, Afu6g12110. (B) Biosynthetic route of fumiquinazolines in A. fumigatus . Abbreviations: Ant, anthranilate; l -Trp, l -tryptophan; l -Ala, l -alanine; FqF, fumiquinazoline F; FqA, fumiquinazoline A; FqC, fumiquinazoline...”
W6QY63 Formamidase from Pseudomonas pseudoalcaligenes (strain CECT 5344)
24% identity, 64% coverage
BUP1_DICDI / Q964D8 Beta-ureidopropionase; Beta-alanine synthase; N-carbamoyl-beta-alanine amidohydrolase; EC 3.5.1.6 from Dictyostelium discoideum (Social amoeba) (see paper)
24% identity, 59% coverage
- function: Catalyzes a late step in pyrimidine degradation. Converts N- carbamoyl-beta-alanine (3-ureidopropanoate) into beta-alanine, ammonia and carbon dioxide (PubMed:11454750). Likewise, converts N-carbamoyl- beta-aminoisobutyrate (3-ureidoisobutyrate) into beta-aminoisobutyrate, ammonia and carbon dioxide (By similarity).
catalytic activity: 3-(carbamoylamino)propanoate + H2O + 2 H(+) = beta-alanine + NH4(+) + CO2 (RHEA:11184)
catalytic activity: 3-(carbamoylamino)-2-methylpropanoate + H2O + 2 H(+) = (R)-3- amino-2-methylpropanoate + NH4(+) + CO2 (RHEA:37339)
subunit: Homodimer and higher homooligomers.
HPG27_RS06200 formamidase from Helicobacter pylori G27
23% identity, 69% coverage
RLO149_c028370 aliphatic amidase from Roseobacter litoralis Och 149
27% identity, 58% coverage
- Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis
Kalhoefer, BMC genomics 2011 - “...metabolism were identified in islands 1, 6 and 9 including different amidases (RLO149_c009550, RLO149_c040080, RLO149_c040170, RLO149_c028370), a second uncommon urease gene cluster (RLO149_c028310 - RLO149_c028360) and assimilatory nitrite and nitrate reductases (RLO149_c039830 - RLO149_c039850). Island 4 contains a carbon monoxide dehydrogenase encoding gene (CODH, RLO149_c017450 -...”
AMIE_GEOSE / Q9RQ17 Aliphatic amidase; Acylamide amidohydrolase; Wide spectrum amidase; EC 3.5.1.4 from Geobacillus stearothermophilus (Bacillus stearothermophilus) (see paper)
26% identity, 57% coverage
- function: Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia. Efficiently hydrolyzes propionamide, acetamide and acrylamide, but shows a very weak activity with aromatic and longer chain aliphatic amides.
function: Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates.
catalytic activity: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) (RHEA:12020)
NP_001105196 nitrilase 2 from Zea mays
B4FQE2 cyanoalanine nitrilase from Zea mays
27% identity, 71% coverage
SS1G_10281 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
26% identity, 78% 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