PaperBLAST
PaperBLAST Hits for sp|Q9HU77|HUTF_PSEAE Formimidoylglutamate deiminase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=hutF PE=1 SV=1 (453 a.a., MSAIFAERAL...)
Show query sequence
>sp|Q9HU77|HUTF_PSEAE Formimidoylglutamate deiminase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=hutF PE=1 SV=1
MSAIFAERALLPEGWARNVRFEISADGVLAEIRPDANADGAERLGGAVLPGMPNLHSHAF
QRAMAGLAEVAGNPNDSFWTWRELMYRMVARLSPEQIEVIACQLYIEMLKAGYTAVAEFH
YVHHDLDGRSYADPAELSLRISRAASAAGIGLTLLPVLYSHAGFGGQPASEGQRRFINGS
EAYLELLQRLRAPLEAAGHSLGLCFHSLRAVTPQQIATVLAAGHDDLPVHIHIAEQQKEV
DDCQAWSGRRPLQWLYENVAVDQRWCLVHATHADPAEVAAMARSGAVAGLCLSTEANLGD
GIFPATDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDRKRNRLYRDDQPMIGRTL
YDAALAGGAQALGQPIGSLAVGRRADLLVLDGNDPYLASAEGDALLNRWLFAGGDRQVRD
VMVAGRWVVRDGRHAGEERSARAFVQVLGELLD
Running BLASTp...
Found 96 similar proteins in the literature:
HUTF_PSEAE / Q9HU77 Formimidoylglutamate deiminase; Formiminoglutamate deiminase; N-formimino-L-glutamate deiminase; N-formimino-L-glutamate iminohydrolase; EC 3.5.3.13 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 3 papers)
Q9HU77 formimidoylglutamate deiminase (EC 3.5.3.13); formimidoylglutamase (EC 3.5.3.8) from Pseudomonas aeruginosa (see paper)
NP_253793 N-formimino-L-glutamate deiminase from Pseudomonas aeruginosa PAO1
PA5106 atrazine chlorohydrolase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- function: Catalyzes the hydrolysis of N-formimino-L-glutamate to N- formyl-L-glutamate and ammonia.
catalytic activity: N-formimidoyl-L-glutamate + H2O = N-formyl-L-glutamate + NH4(+) (RHEA:22832)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit (PubMed:25559274). Can also use Cd(2+), Ni(2+) or Cu(2+) (PubMed:16475788, PubMed:17128965).)
subunit: Homodimer. - Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...3332 Q9HY86 4414 Q9I2X9 87 Q9HU21 1169 Q51465 2251 G3XCZ4 3333 Q9HY89 4415 Q9I2Y0 88 Q9HU77 1170 Q51466 2252 G3XCZ7 3334 Q9HY90 4416 Q9I2Y1 89 Q9HUF7 1171 Q51468 2253 G3XCZ9 3335 Q9HY91 4417 Q9I2Y3 90 Q9HUI9 1172 Q51480 2254 G3XD02 3336 Q9HY93 4418 Q9I2Y4 91 Q9HUK9...”
- Annotating enzymes of unknown function: N-formimino-L-glutamate deiminase is a member of the amidohydrolase superfamily.
Martí-Arbona, Biochemistry 2006 (PubMed)- GeneRIF: Pa5106 was shown to catalyze the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate.
- Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin-rifampicin combination against Pseudomonas aeruginosa
Mahamad, Journal of biomedical science 2022 - “...1.90 Leucine degradation 3-Methylbutanoyl-CoA 2.20 liuA 2.68 liuB 2.64 liuE 3.51 Histidine degradation Urocanate 1.77 PA5106 1.12 N -Formimino- l -glutamate 1.54 Tyrosine degradation l -Tyrosine 2.01 phhC 1.02 hpd 3.37 hmgA 2.75 maiA 2.93 fahA 2.82 No significantly changed metabolites and DEGs at this time...”
- Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel
Gunasekera, Applied and environmental microbiology 2017 - “...6.6 6.04 5.85 5.78 PA3284 PA5359 5.33 5.32 PA4575 PA5106 5.21 4.92 PA2562 4.75 PA0276 PA4290 PA3568 4.69 4.43 4.42 PA1333 4.06 Reference(s) 58-61 62 63-66 67,...”
- Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa
Fedorov, Biochemistry 2015 - “...purposes. N -Formimino- l -glutamate iminohydrolase (HutF), from Pseudomonas aeruginosa with a locus tag of Pa5106 (gi|15600299), is a member of the amidohydrolase superfamily. This enzyme catalyzes the deamination of N -formimino- l -glutamate to N -formyl- l -glutamate and ammonia in the histidine degradation pathway....”
- “...-helices, whereas the smaller domain is made up of eight -strands. The active site of Pa5106 contains a single zinc atom that is coordinated by His-56, His-58, His-232, and Asp-320. The nucleophilic solvent water molecule coordinates with the zinc atom at a distance of 2.0 and...”
- Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25
Zhang, Genetics 2007 - “...HutG (75) PP5029 (73) HutG (72) Not available PP5036 (82) PA5106 (76) (38) (97) (86) (80) PA5105 (84) PA5104 (54) HutU (91) PA5099 (79) PA5096 (77) PA5095 (90)...”
- “...(2006) characterized three proteins from P. aeruginosa (PA5106, PA5091, and PA3175) with predicted roles in the breakdown of formiminoglutamate. Chemical...”
- Annotating enzymes of unknown function: N-formimino-L-glutamate deiminase is a member of the amidohydrolase superfamily
Martí-Arbona, Biochemistry 2006 (PubMed)- “...transformations is a difficult problem. The protein Pa5106 from Pseudomonas aeruginosa has been identified as a member of the amidohydrolase superfamily...”
- “...authenticated members of this superfamily. The function of Pa5106 has been annotated as a probable chlorohydrolase or cytosine deaminase. A close examination of...”
- Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosa
McPhee, Journal of bacteriology 2006 - “...aprA (PA1249) PA2050-PA2051 PA4500 PA2505-PA2506 PA3868 PA4498-PA4499 PA5106 Sequencea 4002 MCPHEE ET AL. J. BACTERIOL. FIG. 3. Demonstration of binding of...”
- “...PA0053, PA4500, PA2505, PA2506, PA3868, PA4498, PA4499, and PA5106. These results suggest either that these genes are not regulated by Mg2 and PhoP/PmrA at...”
4rdvB / Q9HU77 The structure of n-formimino-l-glutamate iminohydrolase from pseudomonas aeruginosa complexed with n-formimino-l-aspartate
100% identity, 100% coverage
- Ligands: n-[(e)-iminomethyl]-l-aspartic acid; zinc ion (4rdvB)
PfGW456L13_330 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Pseudomonas fluorescens GW456-L13
80% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
hutF / Q4KJP1 formiminoglutamate deiminase subunit (EC 3.5.3.13) from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (see paper)
80% identity, 100% coverage
Pf1N1B4_1591 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Pseudomonas fluorescens FW300-N1B4
79% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
AO356_09645 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Pseudomonas fluorescens FW300-N2C3
79% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
AO353_12235 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Pseudomonas fluorescens FW300-N2E3
79% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Pf6N2E2_3808 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Pseudomonas fluorescens FW300-N2E2
79% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
PFLU0358 putative hydrolase from Pseudomonas fluorescens SBW25
76% identity, 100% coverage
PS417_01705 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Pseudomonas simiae WCS417
76% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
PP5036, PP_5036 chlorohydrolase family protein from Pseudomonas putida KT2440
78% identity, 100% coverage
- FinR Regulates Expression of nicC and nicX Operons, Involved in Nicotinic Acid Degradation in Pseudomonas putida KT2440
Xiao, Applied and environmental microbiology 2018 - “...PP_4735 PP_4736 PP_4737 PP_5029 PP_5030 PP_5031 PP_5032 PP_5033 PP_5036 PP_5073 PP_5269 PP_5270 PP_5338 PP_5549 Log2 fold change 2.207 2.856 3.701 3.623 2.447...”
- Genome features of Pseudomonas putida LS46, a novel polyhydroxyalkanoate producer and its comparison with other P. putida strains
Sharma, AMB Express 2014 - “...other P. putida strains (Additional file 1 : Table S6). Three chlorohyrolases i.e. atrazine chlorohydrolase (PP5036, PP2584) and hydroxydechloroatrazine ethylaminohydrolase (PP3209) detected in P. putida KT2440 were also identified in P. putida LS46 (PPUTLS46_10994, PPUTLS46_005456, and PPUTLS46_008014). However, chloride channel protein of P. putida KT2440 (PP3959)...”
- Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
Puchałka, PLoS computational biology 2008 - “...EC:2.6.1.11 Succinylornithine transaminase; EC 2.6.1.81 a PP5029 Formiminoglutamase; EC:3.5.3.8 N -Formylglutamate deformylase; EC 3.5.1.68 a PP5036 Atrazine chlorohydrolase N -Formylglutamate deformylase; EC 3.5.1.68 a PP5257 Oxidoreductase, FAD-binding l -Pipecolate oxidase; EC 1.5.3.7 [36] PP5258 Aldehyde dehydrogenase family protein; EC:1.2.1.3 l -Aminoadipate-semialdehyde dehydrogenase; EC 1.2.1.31 [36] a...”
- The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents
Duque, Journal of bacteriology 2007 - “...PP4870 PP5028 PP5029 PP5030 PP5031 PP5032 PP5033 PP5036 PP5390 PP5392 Conserved hypothetical protein Pyridine nucleotide transhydrogenase, beta subunit Efflux...”
- Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25
Zhang, Genetics 2007 - “...PP5030 HutG (75) PP5029 (73) HutG (72) Not available PP5036 (82) PA5106 (76) (38) (97) (86) (80) PA5105 (84) PA5104 (54) HutU (91) PA5099 (79) PA5096 (77)...”
PPUTLS46_005456 formimidoylglutamate deiminase from Pseudomonas putida LS46
78% identity, 100% coverage
EAMY_1258 Formiminoglutamate deiminase from Erwinia amylovora CFBP1430
60% identity, 96% coverage
SMc00673 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Sinorhizobium meliloti 1021
SMc00673 PUTATIVE HYDROLASE PROTEIN from Sinorhizobium meliloti 1021
56% identity, 97% coverage
Ac3H11_2549 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Acidovorax sp. GW101-3H11
53% identity, 93% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
BTH_I1825 formiminoglutamate deiminase from Burkholderia thailandensis E264
52% identity, 98% coverage
4f0lB / Q2YIL4 Crystal structure of amidohydrolase from brucella melitensis
52% identity, 99% coverage
- Ligand: fe (iii) ion (4f0lB)
PGA1_c36360 Formiminoglutamic iminohydrolase (EC 3.5.3.13) from Phaeobacter inhibens DSM 17395
48% identity, 99% coverage
- mutant phenotype: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
MXAN_1010 formiminoglutamate deiminase from Myxococcus xanthus DK 1622
42% identity, 93% coverage
PITG_00577 uncharacterized protein from Phytophthora infestans T30-4
33% identity, 51% coverage
ArtHe_13950 8-oxoguanine deaminase from Arthrobacter sp. Helios
29% identity, 86% coverage
- Transcriptional response of the xerotolerant Arthrobacter sp. Helios strain to PEG-induced drought stress
Hernández-Fernández, Frontiers in microbiology 2022 - “...E ArtHe_12865 ABC transporter permease 11 1.2996E09 E ArtHe_12870 ABC transporter permease 11 1.5486E25 F ArtHe_13950 8-oxoguanine deaminase 4 9.251E08 T ArtHe_16365 Universal stress protein 3 0.01644528 The 8-oxoguanine deaminase coding gene was found upregulated in Arthrobacter sp. Helios ( Table 3 ). The 8-oxoguanine deaminase...”
- “...ArtHe_04665 and ArtHe_04675 ), a universal stress protein ( ArtHe_11205 ), the 8-oxoguanine deaminase ( ArtHe_13950 ), the highly induced cluster involved in phenylethylamine metabolism, and a higher number of induced ABC transporters for amino acids, peptides and iron and, on the other hand, we have...”
GBAA1865 chlorohydrolase family protein from Bacillus anthracis str. 'Ames Ancestor'
26% identity, 87% coverage
PA0142 / Q9I6Z0 8-oxoguanine deaminase monomer (EC 3.5.4.32) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
OXODE_PSEAE / Q9I6Z0 8-oxoguanine deaminase; EC 3.5.4.32 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
Q9I6Z0 8-oxoguanine deaminase (EC 3.5.4.32) from Pseudomonas aeruginosa (see paper)
PA0142 hydroxydechloroatrazine ethylaminohydrolase from Pseudomonas aeruginosa PAO1
27% identity, 85% coverage
- function: Specifically deaminates 8-Oxoguanine (8-oxoG) to uric acid. 8-oxoG is formed via the oxidation of guanine within DNA by reactive oxygen species and leads, if uncorrected, to the incorporation of 8- oxoG:A mismatches and eventually to G:C to T:A transversions.
catalytic activity: 8-oxoguanine + H2O + H(+) = urate + NH4(+) (RHEA:32067)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
subunit: Homodimer. - Global transcriptome analysis of Pseudomonas aeruginosa NT06 response to potassium chloride, sodium lactate, sodium citrate, and microaerophilic conditions in a fish ecosystem
Tomaś, FEMS microbiology letters 2024 - “...), efflux pump systems ( mexPQ-opmE and nalD ), ammonia production (PA1214, ilvA2 , and PA0142), biogenic amines production ( pauA , PA1566, and PA4774), amino acid degradation ( arcB, arcC, hutU , and PA0747), carbohydrate metabolism ( pgl, glcD , and PA3516), and lipid degradation...”
- “...involved in nitrogen compound degradation, whose activity results in ammonia formation (PA1214, ilvA2 , and PA0142). In KCl/NaL/NaC-treated cells, there was significant repression of PA2530, PA5196, and plcN , which encode metalloprotease TldD/E, ATP-dependent zinc protease, and nonhemolytic phospholipase, respectively, with a role in protein degradation...”
- Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy
Guo, iScience 2023 - “...structure of VCZ was solved by molecular replacement method with the structure of 8-oxoguanine deaminase Pa0142 (PDB code: 3HPA ) as a search model according to the structure prediction results by PHYRE2. 20 , 22 There are two VCZ molecules in the asymmetric unit that formed...”
- “...further performed sequence alignment with the putative ICD (VCZ, URA3, URA4, KANOS), 18 8-oxo-G deaminase (Pa0142), 20 5-methylcytosine deaminase (5mCD), 26 and classical cytosine deaminase (CodA) 24 , 25 ( FigureS5 ). The sequence alignment results revealed that the residues for zinc ion chelating are conservative...”
- Nucleobase deaminases: a potential enzyme system for new therapies
Gaded, RSC advances 2018 - “...groups of deaminases. 52,53 Using the above approach, one of their findings was the enzyme Pa0142 from Pseudomonas aeruginosa , which belongs to the AHS superfamily. This enzyme was found to deaminate the mutagenic bases 8-oxoguanine and isocytosine. 52 Similarly, this method of classifying enzymes was...”
- Methylthioadenosine deaminase in an alternative quorum sensing pathway in Pseudomonas aeruginosa
Guan, Biochemistry 2012 - “...putative deaminases based on zinc binding motif. These included PA0134 (guanine deaminase), PA1521 (guanine deaminase), PA0142 (guanine deaminase), PA0148 (adenosine deaminase), PA2499 (unspecified deaminase), PA3480 (deoxycytidine triphosphate deaminase), PA0437 (cytosine deaminase), and PA3170 (guanine deaminase). We searched all of the corresponding protein sequences against the PDB...”
- The hunt for 8-oxoguanine deaminase
Hall, Journal of the American Chemical Society 2010 - “...the principles of fair use under the copyright law. An enzyme from Pseudomonas aeruginosa , Pa0142 (gi|9945972) has been identified for the first time that is able to catalyze the deamination of 8-oxoguanine (8-oxoG) to uric acid. 8-Oxoguanine is formed by the oxidation of guanine residues...”
- “...T:A transversions. The value of k cat /K m for the deamination of 8-oxoG by Pa0142 at pH 8.0 and 30 C is 2.0 10 4 M 1 s 1 . This enzyme can also catalyze the deamination of isocystosine and guanine at rates that are...”
- Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase
Hall, Biochemistry 2010 - “...Sgx9339a and Sgx9236b, were aligned with two of the newly discovered enzymes that deaminate 8-oxoguanine (Pa0142 from Pseudomonas aeruginosa and Sgx9236e) and guanine deaminases from Homo sapiens and E. coli . 2 The sequence alignment is shown in Figure 9 . The eight -strands from the...”
- “...and the threonine at the C-terminal end of -strand 2. For the two 8-oxoguanine deaminases (Pa0142 and Sgx9236e), these residues (in addition to a conserved tyrosine found at the C-terminal end of -strand 2) are highlighted in light blue and the proposed substrate binding residues specific...”
- Transcriptome analysis of Pseudomonas aeruginosa after interaction with human airway epithelial cells
Frisk, Infection and immunity 2004 - “...8.6 8.5 0.044 0.019 0.050 PA4770 PA5412 PA0805 PA1540 PA0674 PA0142 PA0163 PA2673 8.2 7.5 7.0 6.7 6.3 6.2 5.8 5.5 0.027 0.005 0.035 0.013 0.001 0.024 0.006...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...2083 Q9I5G4 3165 Q9HXC0 4247 Q9I272 1002 Q9I6Y5 2084 Q9I5G9 3166 Q9HXC1 4248 Q9I274 1003 Q9I6Z0 2085 Q9I5H2 3167 Q9HXC6 4249 Q9I275 1004 Q9I6Z2 2086 Q9I5J7 3168 Q9HXC8 4250 Q9I276 1005 Q9I6Z3 2087 Q9I5L3 3169 Q9HXC9 4251 Q9I277 1006 Q9I6Z9 2088 Q9I5L8 3170 Q9HXD0 4252 Q9I278...”
F1721_08470 amidohydrolase family protein from Saccharopolyspora hirsuta
30% identity, 85% coverage
BC1793 Chlorohydrolase/deaminase family protein from Bacillus cereus ATCC 14579
25% identity, 87% coverage
cyrG / B0LI30 CyrG from Cylindrospermopsis raciborskii AWT205 (see 2 papers)
31% identity, 44% coverage
SPD_1190 Atz/Trz family protein from Streptococcus pneumoniae D39
24% identity, 91% coverage
- Pivotal Roles for Ribonucleases in Streptococcus pneumoniae Pathogenesis
Sinha, mBio 2021 - “...1.74E24 SPD_SR44 c thiE1 , spd_0625 2.07 1.54E07 SPD_SR57 spd_0988 , spd_0987 1.83 2.62E05 SPD_SR54 spd_1190 , rplJ 1.95 7.51E07 SPD_SR70 b spd_1216 , spd_1217 2.00 0.00011 SPD_SR73 spd_1289 , spd_1288 2.39 4.19E10 SPD_SR74 b spd_1308 , spd_1307 1.94 7.70E06 SPD_SR77 asnS , rpsF 2.00 0.00019...”
- Redefining the Small Regulatory RNA Transcriptome in Streptococcus pneumoniae Serotype 2 Strain D39
Sinha, Journal of bacteriology 2019 - “...spd_1161, spd_1160 spd_1175, spd_1174 spd_1180, spd_1179 spd_1190, rplJ spd_1191, spd_1190 spd_1216, spd_1217 spd_1233, spd_1232 guaA, spd_1273 spd_1289,...”
- Biological and Chemical Adaptation to Endogenous Hydrogen Peroxide Production in Streptococcus pneumoniae D39
Lisher, mSphere 2017 - “...= 4 [ Fig.5C ]) were identified. These proteins are potential regulatory candidates and include SPD_1190, an uncharacterized aminohydrolase superfamily member with some similarity to adenosine deaminase, and PyrC (dihydrooratase [eR = 1]), which along with PyrG (CTP synthase [eR = 4.5]), are involved in de...”
- Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
Hendriksen, Infection and immunity 2008 - “...SPD_0900 SPD_0901 SPD_1004 SPD_1011 SPD_1156 SPD_1158 SPD_1190 SPD_1191 SPD_1192 SPD_1276 SPD_1464 SPD_1472 SPD_1500 SPD_1563 SPD_1564 SPD_1585 SPD_1596...”
SP_1356 chlorohydrolase from Streptococcus pneumoniae TIGR4
23% identity, 91% coverage
cyrH / B0LI34 CyrH from Cylindrospermopsis raciborskii AWT205 (see 2 papers)
28% identity, 44% coverage
XAC2378 conserved hypothetical protein from Xanthomonas axonopodis pv. citri str. 306
27% identity, 88% coverage
4dzhA / Q8P8H1 Crystal structure of an adenosine deaminase from xanthomonas campestris (target nysgrc-200456) with bound zn
27% identity, 89% coverage
- Ligands: magnesium ion; zinc ion (4dzhA)
PXO_00380 Amidohydrolase family protein from Xanthomonas oryzae pv. oryzae PXO99A
27% identity, 89% coverage
Bphyt_7136 amidohydrolase from Burkholderia phytofirmans PsJN
25% identity, 94% coverage
- Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase
Hall, Biochemistry 2010 - “...is Bxe_A2016 from Burkholderia xenovorans LB400 and the closest homologue of Sgx9236b (95% identical) is Bphyt_7136 from Burkholderia phytofirmans PsJN. Both of these proteins are currently annotated by NCBI as ATZ/TRZ-like amidohydrolases. The three-dimensional structure of Sgx9339a was determined at 2.7 resolution. Using a combination of...”
D5VT65 5'-deoxyadenosine deaminase from Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME)
23% identity, 87% coverage
- Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine
Miller, Journal of bacteriology 2014 - “...D3DYL9, Q8TYD4, Q2RJW1, B1BCH5, A4FW32, F2KTB3, Q8U0P7, D5VT65, Q9X034, Q58936, and C7P5A2. preferred substrates (Table 2). Surprisingly, the double mutant...”
PF1538 n-ethylammeline chlorohydrolase from Pyrococcus furiosus DSM 3638
Q8U0P7 5-methylthioadenosine/S-adenosylhomocysteine deaminase from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
22% identity, 93% coverage
- Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus
Reichelt, BMC genomics 2016 - “...downstream operon PF1535 alpha-glucan phosphorylase same promoter region downstream PF1536 hypothetical protein PF1537 hypothetical protein PF1538 N-ethylammeline chlorohydrolase singleton PF1539 dihydroorotate dehydrogenase 1B singleton PF2016 preprotein translocase subunit SecG - downstream singleton PF2047 l-asparaginase - upstream Genes containing a TrmBL1 binding site in their promoter region...”
- “...and activator. On the one hand it inhibits reverse transcription of the operon transcribed from PF1538 to PF1535. On the other hand it enhances forward transcription of the gene PF1539. A comparable transcriptional regulation mechanism was already shown for the archaeal sulphur response regulator SurR, which...”
- A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data
Lancaster, BMC bioinformatics 2011 - “...isomerase 1IX5 4 PF1675 Asp/Glu/hydantoin racemase 2ZSK 4 PF1731 Signal recognition particle 54 3DM5 5 PF1538 Amidohydrolase 1 1P1M Ni 7 PF0523 Protein of unknown function DUF509 1ZD0 Mg 7 PF1222 Protein of unknown function DUF217 8 PF1587 Protein of unknown function DUF89 2G8L 9 PF0212...”
- Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins
Weinberg, Journal of bacteriology 2005 - “...TABLE 1--Continued ORF Carbohydrate metabolism PF1535 PF1536 PF1537 PF1538 Descriptiona Mean fluorescence intensity ratio atc: TMDsb 1h 2h 0 0 5 0 1.2 0.1...”
- “...up-regulation of two 4-ORF operons, one (PF1535 to PF1538) encoding a TABLE 3. Activities and relative expression levels of key cold-responsive enzymes ORF...”
- Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
Schut, Journal of bacteriology 2003 - “...oxidoreductase I PF1327 PF1328 [Unknown] PF1536 PF1537 PF1538 PF1592 [Histidine biosynthesis] PF1657 PF1658 PF1659 PF1661 Mean intensity ratio (log SD)b...”
- Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine
Miller, Journal of bacteriology 2014 - “...Q9KC82, D3DYL9, Q8TYD4, Q2RJW1, B1BCH5, A4FW32, F2KTB3, Q8U0P7, D5VT65, Q9X034, Q58936, and C7P5A2. preferred substrates (Table 2). Surprisingly, the double...”
8is4A Structure of an isocytosine specific deaminase vcz in complexed with 5-fu (see paper)
26% identity, 86% coverage
- Ligands: 5-fluorouracil; zinc ion (8is4A)
3lnpA / D3KFX9 Crystal structure of amidohydrolase family protein olei01672_1_465 from oleispira antarctica (see paper)
25% identity, 90% coverage
- Ligand: calcium ion (3lnpA)
Bcep18194_A5267 Amidohydrolase from Burkholderia sp. 383
25% identity, 88% coverage
- The hunt for 8-oxoguanine deaminase
Hall, Journal of the American Chemical Society 2010 - “...and it is 98% identical to a protein of unknown function from Burkholderia sp. 383 (Bcep18194_A5267). The gene was codon-optimized for expression in E. coli , synthesized, and TOPO (Invitrogen, USA) cloned into a vector that yields a protein with a non-cleavable histidine tag. The sequence...”
XF2472 conserved hypothetical protein from Xylella fastidiosa 9a5c
30% identity, 44% coverage
- In vitro Determination of Extracellular Proteins from Xylella fastidiosa
Mendes, Frontiers in microbiology 2016 - “...0.097 Adenylosuccinate lyase (ASL) 50.6 XF1553 XF1289 P44797 No No 0.076 Amidohydrolase family protein 47.3 XF2472 XF2144 O66851 No No 0.069 Aminopeptidase (peptidase M28 family protein) 57.7 XF0820 XF0671 O54697 No No 0.529 Antitoxin (HTH-type transcriptional regulator) 15 XF2491 XF2163 Q46864 No No 0.149 Autolytic lysozyme...”
- “...calcium supplementation (control), 26 proteins were identified, including serine proteases (XF1851 and XF1026), an amidohydrolase (XF2472) and an enolase (XF1291). The decrease in extracellular proteins in the 9a5c strain was also apparent in the SDS-PAGE analysis of total extracellular proteins ( Figure 2A ). In both...”
dadD / Q58936 5'-deoxyadenosine deaminase monomer (EC 3.5.4.28; EC 3.5.4.4; EC 3.5.4.31; EC 3.5.4.41) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see paper)
DADD_METJA / Q58936 5'-deoxyadenosine deaminase; 5'-dA deaminase; 5'-methylthioadenosine deaminase; MTA deaminase; Adenosine deaminase; S-adenosylhomocysteine deaminase; SAH deaminase; EC 3.5.4.41; EC 3.5.4.31; EC 3.5.4.4; EC 3.5.4.28 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see 2 papers)
Q58936 S-adenosylhomocysteine deaminase (EC 3.5.4.28); S-methyl-5'-thioadenosine deaminase (EC 3.5.4.31); adenosine deaminase (EC 3.5.4.4); 5'-deoxyadenosine deaminase (EC 3.5.4.41) from Methanocaldococcus jannaschii (see paper)
MJ1541 N-ethylammeline chlorohydrolase (trzA) from Methanocaldococcus jannaschii DSM 2661
22% identity, 87% coverage
- function: Catalyzes the deamination of three SAM-derived enzymatic products, namely 5'-deoxyadenosine, S-adenosyl-L-homocysteine, and 5'- methylthioadenosine, to produce the inosine analogs. Can also deaminate adenosine. The preferred substrate for this enzyme is 5'- deoxyadenosine, but all these substrates are efficiently deaminated (PubMed:24375099). Likely functions in a S-adenosyl-L-methionine (SAM) recycling pathway from S-adenosyl-L-homocysteine (SAH) produced from SAM-dependent methylation reactions (PubMed:25917907). May also be involved in the recycling of 5'-deoxyadenosine, whereupon the 5'- deoxyribose moiety of 5'-deoxyinosine is further metabolized to deoxyhexoses used for the biosynthesis of aromatic amino acids in methanogens (PubMed:24375099).
catalytic activity: 5'-deoxyadenosine + H2O + H(+) = 5'-deoxyinosine + NH4(+) (RHEA:42892)
catalytic activity: S-adenosyl-L-homocysteine + H2O + H(+) = S-inosyl-L- homocysteine + NH4(+) (RHEA:20716)
catalytic activity: S-methyl-5'-thioadenosine + H2O + H(+) = S-methyl-5'- thioinosine + NH4(+) (RHEA:25025)
catalytic activity: adenosine + H2O + H(+) = inosine + NH4(+) (RHEA:24408)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
subunit: Homotetramer. - S-Inosyl-L-Homocysteine Hydrolase, a Novel Enzyme Involved in S-Adenosyl-L-Methionine Recycling
Miller, Journal of bacteriology 2015 - “...mM S-adenosyl-L-homocysteine with 18.2 ng of DadD (the MJ1541 gene product) overnight at 25C in 1 ml of 50 mM 1,3-bis[tris(hydroxymethylmethylamino]propane (BIS...”
- Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine
Miller, Journal of bacteriology 2014 - “...Robert H. White We characterize here the MJ1541 gene product from Methanocaldococcus jannaschii, an enzyme that was annotated as a...”
- “...5=-methylthioadenosine/S-adenosylhomocysteine deaminase (EC 3.5.4.31/3.5.4.28). The MJ1541 gene product catalyzes the conversion of 5=-deoxyadenosine to...”
- Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine
Miller, Journal of bacteriology 2014 - “...coli. The MJ1541 gene (Swiss-Prot accession number Q58936) was amplified by PCR from genomic DNA using oligonucleotide primers MJ1541-Fwd...”
- “...Q2RJW1, B1BCH5, A4FW32, F2KTB3, Q8U0P7, D5VT65, Q9X034, Q58936, and C7P5A2. preferred substrates (Table 2). Surprisingly, the double mutant Y136R/E150R failed...”
PG0559 chlorohydrolase family protein from Porphyromonas gingivalis W83
22% identity, 85% coverage
- Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays
Yu, BMC molecular biology 2011 - “...were performed. The antisense strand of five highly expressed ORFs was targeted: PG0279, PG0933, PG1069, PG0559, and PG0775 (marked A1-5, respectively). Strong antisense signals were detected in these regions from the cDNA-based profile while only near background levels of signals were found in the corresponding areas...”
- “...RT-PCR targeting P. gingivalis W83 genes . Antisense sequences targeted by RT-PCR: PG0279, PG0933, PG1069, PG0559, and PG0775 (marked A1-5, respectively). A3L and A5L were longer PCR products from PG1069 and PG0775. C1, PG1159 and C2, PG1144 were sense sequences targeted by RT-PCR. Columns from left...”
4f0rA / Q7NZ90 Crystal structure of an adenosine deaminase homolog from chromobacterium violaceum (target nysgrc-019589) bound zn and 5'- methylthioadenosine (unproductive complex)
24% identity, 85% coverage
- Ligands: zinc ion; 5'-deoxy-5'-methylthioadenosine (4f0rA)
BPSL2112 putative amino hydrolase from Burkholderia pseudomallei K96243
25% identity, 82% coverage
PP2584, PP_2584 chlorohydrolase family protein from Pseudomonas putida KT2440
25% identity, 84% coverage
AA671_03765 8-oxoguanine deaminase from Delftia tsuruhatensis
25% identity, 86% coverage
3hpaA Crystal structure of an amidohydrolase gi:44264246 from an evironmental sample of sargasso sea (see paper)
26% identity, 91% coverage
Amet_4572 N-ethylammeline chlorohydrolase from Alkaliphilus metalliredigenes QYMF
23% identity, 45% coverage
- Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome
Ravcheev, Frontiers in genetics 2019 - “...-encoded enzyme can be specific for six or five atoms ring. 3) The Amet_4583 and Amet_4572 genes encode amidohydrolases. 4) The Amet_4581 gene encodes a decarboxylase of aromatic compounds. 5) Finally, the Amet_4586 gene encodes a formimidoyltransferase. Figure 6 Predicted BMC for xanthine utilization, a locus...”
- “...required. The only protein with homologs harboring such activity is Amet_4587 (XauA). Thus, another aminohydrolase, Amet_4572 (XauE), was considered to be responsible for the fifth step of the pathway. The protein Amet_4581 (XauD) was the only decarboxylase among the analyzed proteins; thus, it was considered to...”
atzA / P72156 AtzA (EC 3.8.1.8) from Pseudomonas sp. (strain ADP) (see 3 papers)
ATZA_PSESD / P72156 Atrazine chlorohydrolase; EC 3.8.1.8 from Pseudomonas sp. (strain ADP) (see 5 papers)
P72156 atrazine chlorohydrolase (EC 3.8.1.8) from Pseudomonas sp. ADP (see paper)
4v1xE / P72156 The structure of the hexameric atrazine chlorohydrolase, atza (see paper)
23% identity, 90% coverage
- function: Hydrolytically dechlorinates atrazine to hydroxyatrazine. Also dechlorinates simazine and desethylatrazine, but is not active with terbutylazine or desethyldesisopropylatrazine (PubMed:8759853). Has no deaminase activity with melamine (PubMed:22768133, PubMed:8759853).
catalytic activity: atrazine + H2O = hydroxyatrazine + chloride + H(+) (RHEA:11312)
cofactor: Fe(2+) (Binds 1 Fe(2+) ion per subunit (PubMed:12450410, PubMed:25760618). In vitro can also use Co(2+) or Mn(2+) (PubMed:12450410).)
subunit: Homohexamer; trimer of dimers. - Ligand: fe (iii) ion (4v1xE)
- Food for Thought: Proteomics for Meat Safety
Tarbeeva, Life (Basel, Switzerland) 2023 - “...77 ] katG, kasA Q88GQ0, A0A379J0D7 * Isoniazid [ 73 ] triA, triB, triC, opmH P72156, A0A8F9V618 *, A0A8G1K8C1 *, A0A8G6KPN1 * Triclosan [ 73 , 78 ] *unreviewed proteins according to the UniProt database....”
- Biochemical and Genetic Analysis of 4-Hydroxypyridine Catabolism in Arthrobacter sp. Strain IN13
Vaitekūnas, Microorganisms 2020 - “...[ 32 ], as well as Fe 2+ -dependent atrazine chlorohydrolase from Pseudomonas sp. ADP (P72156) [ 33 ], are active with just one metal ion per subunit. Remarkably, the extradiol 2,5-dihydroxypyridine 5,6-dioxygenases NicX and HpdF, which participate in the catabolic conversion of nicotinic acid and...”
- SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana, Nucleic acids research 2019 - “...95% 3dsl 3.4.24.49 Bothropasin O93523 3.5.4.45 Melamine deaminase Q9EYU0 98% 4v1x 4v1y 3.8.1.8 Atrazine chlorohydrolase P72156 3.7.1.13 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase Q9AQM4 98% 1j1i 3.7.1.8 2,6-dioxo-6-phenylhexa-3-enoate hydrolase Q84II3 4.1.2.9 Phosphoketolase Q9AEM9 95% 3ahc 3ahd 3ahe 3ahf 3ahg 3ahh 3ahi 3ahj 4.1.2.22 Fructose-6-phosphate phosphoketolase D6PAH1 4.2.3.32 Levopimaradiene synthase H8ZM70...”
- Amine-synthesizing enzyme N-substituted formamide deformylase: screening, purification, characterization, and gene cloning
Fukatsu, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...is from Pseudomonas sp. ADP (SwissProt accession no. P72156), cytosine deaminase (CodA) is from E. coli (SwissProt accession no. P25524), dihydroorotase (PyrC)...”
Q8GG87 atrazine chlorohydrolase (EC 3.8.1.8) from Arthrobacter sp. (see paper)
23% identity, 90% coverage
MSMEG_1297 hydroxydechloroatrazine ethylaminohydrolase from Mycobacterium smegmatis str. MC2 155
26% identity, 82% coverage
pNG7259 N-ethylammeline chlorohydrolase from Haloarcula marismortui ATCC 43049
24% identity, 88% coverage
- Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
Haft, Biology direct 2008 - “...8 b2878 4 EF_2581 ygfL selenium metabolism protein SsnA TIGR03314 3 b2879 6 EF_2582 8 pNG7259 ygfM selenate reductase, FAD-binding subunit b2880 ygfN selenate reductase, Mo-binding subunit 14 b2881 (EF_2570) 3 pNG7246 3 ( CD2099 ) 5 (pNG7244) 4 CD2073 5 (CD2079) ygfO xanthine/uracil family permease...”
BAB1_0383 Amidohydrolase from Brucella melitensis biovar Abortus 2308
28% identity, 49% coverage
- Transcriptome analysis of the Brucella abortus BvrR/BvrS two-component regulatory system
Viadas, PloS one 2010 - “...ATPase 0.8 BAB2_0762 ompR , transcriptional regulatory protein 0.8 BAB2_0943 nirK , nitrite reductase 0.8 BAB1_0383 guanine deaminase 0.8 BAB1_0872 fabF , acyltransferase 0.7 BAB1_0115 omp25d, outer membrane protein 0.6 BAB1_0246 ucpA , oxidoreductase 0.6 BAB1_0237 lclR , transcriptional regulator 0.6 BAB2_0955 norC , nitric-oxide reductase...”
- “..., BAB2_0928) were up regulated. On the other hand, two deaminases (glutaminase, BAB2_0863; guanine deaminase, BAB1_0383) were also affected. Since Brucella is an intracellular facultative pathogen, the bacteria could use these denitrification reactions to grow under low-oxygen condition by respiration of nitrate. Brucella may also take...”
EF1223 chlorohydrolase family protein from Enterococcus faecalis V583
21% identity, 82% coverage
SPAC1F8.04c hydrolase (predicted) from Schizosaccharomyces pombe
22% identity, 87% coverage
- An essential role for the Ino80 chromatin remodeling complex in regulation of gene expression during cellular quiescence
Zahedi, Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2023 - “...Chr Start End Gene_name T1_T0_SMT0_logFC T1_T0_SMT0 P -value SPNCRNA.602 I 50851 51545 SPNCRNA.602 3,25973596 2,7274E-05 SPAC1F8.04c I 92387 93931 SPAC1F8.04c 3,53511935 3,0867E-06 SPNCRNA.607 I 99046 101140 fta5-antisense-1 2,7031025 0,00024108 SPAC11D3.19 I 106893 108361 SPAC11D3.19 3,01020676 4,5012E-05 SPAC11D3.03c I;I;I 110904;112098;112378 112046;112333;112499 SPAC11D3.03c 4,44873642 8,8882E-09 SPAC11D3.16c I 140381...”
- Dataset describing the genome wide effects on transcription resulting from alterations in the relative levels of the bZIP transcription factors Atf1 and Pcr1 in Schizosaccharomyces pombe
Basu, Data in brief 2022 - “...List of genes upregulated in atf1 cells. Table 3 Gene ID Gene Symbol Gene Function SPAC1F8.04c SPAC1F8.04c hydrolase, implicated in cellular detoxification SPRRNA.01 rnl large subunit (21S) rRNA, rnl SPRRNA.02 rns small subunit (15S) rRNA, rns SPMIT.06 SPMIT.06 mitochondrial DNA binding endonuclease (intron encoded) SPCC576.01c xan1...”
- Cellular economy in fission yeast cells continuously cultured with limited nitrogen resources
Chikashige, Scientific reports 2015 - “...logratio-exp1 logratio-exp2 logratio-exp3 logratio-exp4 isp4 induced OPT oligopeptide transporter family Isp4 2.91 3.28 3.65 3.09 SPAC1F8.04c induced hydrolase (predicted) 2.21 2.31 2.96 2.39 mmf2 induced homologous Pmf1 factor 1, implicated in isoleucine biosynthesis (predicted) 2.02 2.04 2.96 2.30 isp6 induced vacuolar serine protease Isp6 1.52 1.74...”
- The global transcriptional response of fission yeast to hydrogen sulfide
Jia, PloS one 2011 - “...4-epimerase ght4 5.46 up hexose transporter Ght4 (PMID 10735857) SPCC1739.08c 6.91 up short chain dehydrogenase SPAC1F8.04c 2.27 up hydrolase (predicted) isp7 2.07 up 2-OG-Fe(II) oxygenase superfamily protein SPBC4F6.17c 2.51 up mitochondrial matrix chaperone Hsp78 (predicted) SPBC1271.07c 6.52 up N-acetyltransferase (predicted) SPBC1683.06c 5.45 up uridine ribohydrolase (predicted)...”
- Mfc1 is a novel forespore membrane copper transporter in meiotic and sporulating cells
Beaudoin, The Journal of biological chemistry 2011 - “...SPBC1198.14c SPAC3C7.14c SPCC663.11 SPAC24C9.12c SPAC1F8.04c SPCC1739.05 SPBC530.07c SPAPB1A11.02 SPAC5H10.02c SPBC32F12.03c SPAC9E9.13 SPAC23C11.06c Fold...”
- Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation
Nugent, BMC genomics 2010 - “...SPBPB2B2.07c 1.93 9.41E-10 SPBC725.10 2.57 9.52E-05 SPAPB1A11.03 3.59 1.50E-13 nta1 1.94 3.20E-06 SPBC83.19c 2.58 3.49E-12 SPAC1F8.04c 3.59 5.41E-07 SPCC191.01 1.94 5.61E-06 SPCC1393.12 2.58 4.35E-11 SPAC11D3.01c 3.61 1.72E-07 SPCC70.04c 1.95 2.09E-06 SPBPB2B2.08 2.60 0.007868315 SPBPB8B6.03 3.64 2.07E-12 meu7 1.96 2.81E-05 SPCC777.04 2.63 3.77E-05 SPBP4G3.03 3.65 2.74E-13 SPAC9.10...”
- Multiple pathways differentially regulate global oxidative stress responses in fission yeast
Chen, Molecular biology of the cell 2008 - “...name ctt1 gly1 gpa2 meu8 SPAC11D3.05 SPAC11D3.13 SPAC1F8.04c SPAC2E1P3.01 hsr1 SPAC869.02c SPBC409.13 trr1 trx1 Annotation Catalase Predicted threonine aldolase...”
- A NASP (N1/N2)-related protein, Sim3, binds CENP-A and is required for its deposition at fission yeast centromeres
Dunleavy, Molecular cell 2007 - “...affected by sim3-143 and 113 genes were affected by sim3-205 . Surprisingly, only one gene (SPAC1F8.04c) was similarly affected by both sim3 alleles. Thus, we conclude that relatively few genes and distinct sets of genes were affected in the two sim3 mutant alleles. The annotation of...”
SMb21293 putative guanine deaminase protein from Sinorhizobium meliloti 1021
28% identity, 51% coverage
Mmwyl1_4101 amidohydrolase from Marinomonas sp. MWYL1
24% identity, 91% coverage
- Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase
Hall, Biochemistry 2010 - “...from Figure 1 ) which share a threonine-serine dyad at this position. These genes are: Mmwyl1_4101 (gi|152998097) from Marinomonas sp. MWYL1 ; HMPREF0023_2011 (gi|226953181) from Acinetobacter sp. ATCC 27244 ; PputW619_2587 (gi|170721762) from Pseudomonas putida W619 ; and PP_3209 (gi| 26989928) from Pseudomonas putida KT2440 ....”
DhpD / Q9VMY9 guanine deaminase (EC 3.5.4.3) from Drosophila melanogaster (see paper)
GUAD_DROME / Q9VMY9 Guanine deaminase; Dihydropterin deaminase; EC 3.5.4.3; EC 3.5.4.- from Drosophila melanogaster (Fruit fly) (see paper)
NP_649439 dihydropterin deaminase from Drosophila melanogaster
25% identity, 45% coverage
- function: Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia. Also has 7,8-dihydropterin deaminase activity, which plays a role in synthesis of the red eye pigment aurodrosopterin.
catalytic activity: guanine + H2O + H(+) = xanthine + NH4(+) (RHEA:14665)
cofactor: Zn(2+) - Guanine deaminase functions as dihydropterin deaminase in the biosynthesis of aurodrosopterin, a minor red eye pigment of Drosophila
Kim, The Journal of biological chemistry 2009 - GeneRIF: Dihydropterin deaminase encoded by CG18143 plays a role in the biosynthesis of aurodrosopterin.
- “...RefSeq accession number deaminate pteridine compounds as NP_649439) is highly homologous to guanine deaminases of human (NCBI RefSeq accession number...”
- Guanine deaminase functions as dihydropterin deaminase in the biosynthesis of aurodrosopterin, a minor red eye pigment of Drosophila.
Kim, The Journal of biological chemistry 2009 - GeneRIF: Dihydropterin deaminase encoded by CG18143 plays a role in the biosynthesis of aurodrosopterin.
- “...RefSeq accession number deaminate pteridine compounds as NP_649439) is highly homologous to guanine deaminases of human (NCBI RefSeq accession number...”
- Apocrine secretion in Drosophila salivary glands: subcellular origin, dynamics, and identification of secretory proteins
Farkaš, PloS one 2014 - “...C-terminal Src kinase Q9VGK8 87.2 protein modification cytoplasmic dIAP1 Q24306 48.0 apoptosis cytoplasmic Dihydropterin deaminase Q9VMY9 48.9 guanine/pigment metabolism cytoplasmic Dispatched Q9VNJ5 139.0 smo signaling membrane drICE O01382 37.4 apoptosis caspase cytoplasmic Egalitarian Q9W1K4 125.0 RNA transport nuclear Elongation factor 1-alpha 1(EF-1-alpha 1) P08736 50.3 protein...”
HMPREF0023_2011 amidohydrolase family protein from Acinetobacter sp. ATCC 27244
23% identity, 84% coverage
- Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase
Hall, Biochemistry 2010 - “...threonine-serine dyad at this position. These genes are: Mmwyl1_4101 (gi|152998097) from Marinomonas sp. MWYL1 ; HMPREF0023_2011 (gi|226953181) from Acinetobacter sp. ATCC 27244 ; PputW619_2587 (gi|170721762) from Pseudomonas putida W619 ; and PP_3209 (gi| 26989928) from Pseudomonas putida KT2440 . It appears that the Thr-Ser dyad may...”
PA14_23240 putative hydrolase from Pseudomonas aeruginosa UCBPP-PA14
26% identity, 50% coverage
Q9HZ64 S-methyl-5'-thioadenosine deaminase (EC 3.5.4.31) from Pseudomonas aeruginosa (see paper)
PA3170 N-ethylammeline chlorohydrolase from Pseudomonas aeruginosa PAO1
26% identity, 50% coverage
4dykA / Q9HZ64 Crystal structure of an adenosine deaminase from pseudomonas aeruginosa pao1 (target nysgrc-200449) with bound zn
26% identity, 50% coverage
- Ligands: zinc ion; magnesium ion (4dykA)
SMc02416 PUTATIVE HYDROLASE PROTEIN from Sinorhizobium meliloti 1021
25% identity, 46% coverage
- The Sinorhizobium meliloti fur gene regulates, with dependence on Mn(II), transcription of the sitABCD operon, encoding a metal-type transporter
Chao, Journal of bacteriology 2004 - “...enzymatic proteins (mdeA, glnD, sma2137, smc01821, and smc02416), and seven proteins which have been annotated as hypothetical proteins (smc01637, sma1413,...”
- “...smc02508 (sitB) smc02507 (sitC) smc02506 (sitD) smc02474 smc02416 smc02025 smc01821 smc01701 smc01666 (mdeA) smc01664 smc01637 smc01124 (glnD) smb21403 smb20532...”
OG1RF_11962 putative aminohydrolase SsnA from Enterococcus faecalis OG1RF
22% identity, 89% coverage
- Comparative Biofilm Assays Using Enterococcus faecalis OG1RF Identify New Determinants of Biofilm Formation
Willett, mBio 2021 - “...1121988 IGR between OG1RF_11078 and OG1RF_11079 OG1RF_11674 1746502 DUF1831 domain-containing protein Intergenic_2022 2075283 IGR between OG1RF_11962 and OG1RF_11963 Intergenic_2295 2348175 IGR between OG1RF_12228 and OG1RF_12229 OG1RF_12447 2581857 DUF3298 domain-containing protein OG1RF_12502 2644218 WxL domain-containing protein Intergenic_2613 2692363 IGR between OG1RF_r10012 and OG1RF_12535, encodes OG1RF_RS13855 OG1RF_12540 2699893...”
C7P5A2 5'-deoxyadenosine deaminase from Methanocaldococcus fervens (strain DSM 4213 / JCM 15782 / AG86)
21% identity, 87% coverage
Q9I3J2 Guanine deaminase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA1521 probable guanine deaminase from Pseudomonas aeruginosa PAO1
28% identity, 49% coverage
triA / Q9EYU0 melamine deaminase subunit (EC 3.5.4.45) from Paracidovorax citrulli (see 2 papers)
TRIA_PARCI / Q9EYU0 Melamine deaminase; EC 3.5.4.45 from Paracidovorax citrulli (Acidovorax citrulli) (see 3 papers)
Q9EYU0 melamine deaminase (EC 3.5.4.45) from Acidovorax citrulli (see 2 papers)
24% identity, 43% coverage
- function: Displaces two of the three amino groups from melamine, producing ammeline and ammelide as sequential products (PubMed:11274097). Can also catalyze deamination of other s-triazines such as CAAT (2-chloro-4,6-diamino-s-triazine) and aminoatrazine (PubMed:11274097, PubMed:12200330). Has no activity with ammelide, atrazine, halo-triazine substrates or with pyrimidines (PubMed:11274097).
catalytic activity: melamine + H2O = ammeline + NH4(+) (RHEA:26197)
catalytic activity: ammeline + H2O + H(+) = ammelide + NH4(+) (RHEA:26201)
cofactor: Fe(2+) (Binds 1 Fe(2+) ion per subunit.) - SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana, Nucleic acids research 2019 - “...1.8.1.4 Dihydrolipoyl dehydrogenase P31023 3.4.24.73 Jararhagin P30431 95% 3dsl 3.4.24.49 Bothropasin O93523 3.5.4.45 Melamine deaminase Q9EYU0 98% 4v1x 4v1y 3.8.1.8 Atrazine chlorohydrolase P72156 3.7.1.13 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase Q9AQM4 98% 1j1i 3.7.1.8 2,6-dioxo-6-phenylhexa-3-enoate hydrolase Q84II3 4.1.2.9 Phosphoketolase Q9AEM9 95% 3ahc 3ahd 3ahe 3ahf 3ahg 3ahh 3ahi 3ahj 4.1.2.22...”
DDA3937_RS12145 guanine deaminase from Dickeya dadantii 3937
28% identity, 40% coverage
- Tailocin-Mediated Interactions Among Soft Rot Pectobacteriaceae
Borowicz, Molecular ecology 2025 - “...(locus tag in D. dadantii 3937: DDA3937_RS1200) and guaD (locus tag in D. dadantii 3937: DDA3937_RS12145). Accession numbers of genomes from which the tailocin regions were extracted are listed in Table S1 and Dataset S4 . The extracted sequences were then subjected to synteny analysis and...”
PP_4281 guanine aminohydrolase from Pseudomonas putida KT2440
30% identity, 48% coverage
EF_2582 putative aminohydrolase SsnA from Enterococcus faecalis V583
EF2582 chlorohydrolase family protein from Enterococcus faecalis V583
22% identity, 89% coverage
- Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
Haft, Biology direct 2008 - “...Fe-S subunit 8 b2878 4 EF_2581 ygfL selenium metabolism protein SsnA TIGR03314 3 b2879 6 EF_2582 8 pNG7259 ygfM selenate reductase, FAD-binding subunit b2880 ygfN selenate reductase, Mo-binding subunit 14 b2881 (EF_2570) 3 pNG7246 3 ( CD2099 ) 5 (pNG7244) 4 CD2073 5 (CD2079) ygfO xanthine/uracil...”
- Genomewide Profiling of the Enterococcus faecalis Transcriptional Response to Teixobactin Reveals CroRS as an Essential Regulator of Antimicrobial Tolerance
Darnell, mSphere 2019 - “...and EF0413 [9.7-fold]), and 1 regulator (EF2966 [9.3-fold]) ( Table2 ). The remaining two genes, EF2582 (9.0-fold) and EF2223 (8.8-fold), encode a chlorohydrolase/aminohydrolase and an ABC transporter, respectively, both of which are of unknown function ( Table2 ). E. faecalis JH2-2 teixobactin MICs and MBCs were...”
- “...71 9.4 PTS mannose/fructose/sorbose/ N -acetylglucosamine subunit IIB EF2966 2467 9.3 MltR-like mannitol-operon transcriptional regulator EF2582 2168 9.0 Chlorohydrolase/aminohydrolase EF3138 139 9.0 PTS mannose transporter subunit IID EF2964 2465 ulaA 8.9 PTS ascorbate transporter subunit IIC EF2223 1927 8.8 ABC transporter family EF3212 70 8.7 PTS...”
- Tracing the Enterococci from Paleozoic Origins to the Hospital
Lebreton, Cell 2017 - “...distinct insertions), EF2562 (2 distinct insertions), EF2570 (2 distinct insertions), EF2578, EF2579 (two distinct insertions), EF2582, EF3046 and EF3277. The genomes of mutants EF2559 and , with centrally located insertions, were re-sequenced to confirm that transposon insertion was the only genetic difference with the WT strain...”
A1RCX5 hydroxydechloroatrazine ethylaminohydrolase (EC 3.5.4.43) from Paenarthrobacter aurescens (see paper)
AAur_pTC10218 hydroxyatrazine hydrolase from Arthrobacter aurescens TC1
26% identity, 81% coverage
- Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1.
Kundu, The ISME journal 2019 - “...LFC Adj. p -value A1RCJ9 AAur_pTC10087 TrzN, triazine hydrolase 0.94 0.087 0.36 0.422 0.57 0.404 A1RCX5 AAur_pTC10218 AtzB, hydroxyatrazine hydrolase 1.48 0.025 0.89 0.089 2.37 0.019 A1RCX2 Aur_pTC10212 AtzC, N -isopropylammelide isopropylaminohydrolase 0.61 0.294 0.81 0.126 1.42 0.084 2 A1RDQ3 AAur_pTC20216 Amino-acid permease 2.71 0.004 1.87...”
- Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1
Kundu, The ISME journal 2019 - “...Adj. p -value A1RCJ9 AAur_pTC10087 TrzN, triazine hydrolase 0.94 0.087 0.36 0.422 0.57 0.404 A1RCX5 AAur_pTC10218 AtzB, hydroxyatrazine hydrolase 1.48 0.025 0.89 0.089 2.37 0.019 A1RCX2 Aur_pTC10212 AtzC, N -isopropylammelide isopropylaminohydrolase 0.61 0.294 0.81 0.126 1.42 0.084 2 A1RDQ3 AAur_pTC20216 Amino-acid permease 2.71 0.004 1.87 0.020...”
- Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1
Mongodin, PLoS genetics 2006 - “...these previous findings. All three triazine hydrolase genes, trzN , atzB , and atzC (AAur_pTC10087, AAur_pTC10218, and AAur_pTC10212, respectively), were located on plasmid pTC1 and nowhere else in the A. aurescens TC1 genome. A complete cluster of genes involved in the biodegradation of isopropylamine (ipu) was...”
atzB / P95442 hydroxyatrazine ethylaminohydrolase monomer (EC 3.5.4.43) from Pseudomonas sp. (strain ADP) (see 2 papers)
ATZB_PSESD / P95442 Hydroxydechloroatrazine ethylaminohydrolase; Hydroxyatrazine hydrolase; EC 3.5.4.43 from Pseudomonas sp. (strain ADP) (see paper)
26% identity, 83% coverage
- function: Catalyzes the deamination reaction of hydroxyatrazine to N- isopropylammelide (dihydroxy-isopropyl-atrazine). The enzyme is also capable of catalyzing some dechlorinating reactions.
catalytic activity: hydroxyatrazine + H2O + H(+) = N-isopropylammelide + ethylamine (RHEA:23092)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
subunit: Homodimer. - TrzN from Arthrobacter aurescens TC1 Is a zinc amidohydrolase
Shapir, Journal of bacteriology 2006 - “...with AtzA (accession no. NP_862474), AtzB (accession no. P95442), AtzC (accession no. O52063), and E. coli cytosine deaminase (CodA) (accession no. P25524)...”
SPCC1672.03c guanine deaminase (predicted) from Schizosaccharomyces pombe
25% identity, 40% coverage
FGSG_05323 hypothetical protein from Fusarium graminearum PH-1
26% identity, 42% coverage
trzA / Q52725 s-triazine hydrolase subunit (EC 3.5.4.45) from Gordonia rubripertincta (see 2 papers)
trzA / AAA90931.1 N-ethylammeline chlorohydrolase from Gordonia rubripertincta (see paper)
25% identity, 38% coverage
A6V2Q5 5-methylthioadenosine/S-adenosylhomocysteine deaminase from Pseudomonas aeruginosa (strain PA7)
22% identity, 90% coverage
- Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine
Miller, Journal of bacteriology 2014 - “...B6YUF8, Q5JER0, O66851, A6UUG9, I9MDY4, O27549, Q4K8M5, A6V2Q5, G0PU20, M1Z1T6, Q9KC82, D3DYL9, Q8TYD4, Q2RJW1, B1BCH5, A4FW32, F2KTB3, Q8U0P7, D5VT65, Q9X034,...”
PFLU4595 guanine deaminase from Pseudomonas fluorescens SBW25
28% identity, 48% coverage
trzN / Q8VS01 triazine hydrolase subunit (EC 3.8.1.8) from Nocardioides sp. C190 (see paper)
23% identity, 77% coverage
Dgeo_0576 amidohydrolase from Deinococcus geothermalis DSM 11300
26% identity, 47% coverage
MMP0378 Atrazine chlorohydrolase related protein from Methanococcus maripaludis S2
18% identity, 86% coverage
mtaD / Q9X034 5-methylthioadenosine/S-adenosylhomocysteine deaminase (EC 3.5.4.31; EC 3.5.4.28) from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
MTAD_THEMA / Q9X034 5-methylthioadenosine/S-adenosylhomocysteine deaminase; MTA/SAH deaminase; EC 3.5.4.28; EC 3.5.4.31 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
Q9X034 S-methyl-5'-thioadenosine deaminase (EC 3.5.4.31) from Thermotoga maritima (see paper)
TM0936 conserved hypothetical protein from Thermotoga maritima MSB8
23% identity, 90% coverage
- function: Catalyzes the deamination of 5-methylthioadenosine and S- adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L- homocysteine, respectively. Is also able to deaminate adenosine. Adenosine-5-monophosphate (AMP) and S-adenosyl-L-methionine (SAM) are not enzyme substrates.
catalytic activity: S-adenosyl-L-homocysteine + H2O + H(+) = S-inosyl-L- homocysteine + NH4(+) (RHEA:20716)
catalytic activity: S-methyl-5'-thioadenosine + H2O + H(+) = S-methyl-5'- thioinosine + NH4(+) (RHEA:25025)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.) - Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine
Miller, Journal of bacteriology 2014 - “...Q8TYD4, Q2RJW1, B1BCH5, A4FW32, F2KTB3, Q8U0P7, D5VT65, Q9X034, Q58936, and C7P5A2. preferred substrates (Table 2). Surprisingly, the double mutant Y136R/E150R...”
- High-throughput computational and experimental techniques in structural genomics
Chance, Genome research 2004 - “...T5 T16 T18 P53889 P43215 Q11176 Q58484 P22262 O28301 Q9X034 P75899 7448840 P77407 P72500 O28020 Q51063 P17577 P24253 O31743 1pv1 1q2y 1q6w 1q98 1q9j 1r3d 1rc6...”
- “...protein OS: Streptococcus pneumoniae SIMILARITY-Nudix Hydrolase AC: Q9X034 Hypothetical protein TM0936 OS: Thermotoga maritima SIMILARITY - Atz/Trz Family AC:...”
- Transition-State Analogues of Phenylethanolamine N-Methyltransferase
Mahmoodi, Journal of the American Chemical Society 2020 - “...developed coupled-enzyme methyltransferase assay to measure inhibition constants of the hPNMT-catalyzed reaction. 37 The SAH-deaminase TM0936 from Thermotoga maritima catalyzes the deamination of SAH to form S -inosyl- l -homocysteine (SIH), Figure 9 . 38 TM0936 is a robust and effective catalyst that functions well across...”
- “...is stable through multiple freeze/thaw cycles. This coupled-enzyme assay benefits from a sole reliance on TM0936 to convert SAH to SIH. More importantly, the methyltransferase byproduct SAH is consumed, which relieves the PNMT assay from the observed product inhibition by SAH. Furthermore, the experiments can be...”
- A simplified characterization of S-adenosyl-l-methionine-consuming enzymes with 1-Step EZ-MTase: a universal and straightforward coupled-assay for in vitro and in vivo setting
Burgos, Chemical science 2017 - “...worksheet for the determination of glycine N -methyltransferase activity within biological samples. Samples of purified TM0936 will be distributed upon request. See DOI: 10.1039/c7sc02830j Burgos Emmanuel S. http://orcid.org/0000-0003-4555-7673 a Walters Ryan O. b c d Huffman Derek M. b c d Shechter David http://orcid.org/0000-0001-9388-6004 a a...”
- “...a histone-lysine N -methyltransferase (DIM-5) and a sarcosine/dimethylglycine N -methyltransferase (SDMT). Since the coupling deaminase TM0936 displays robust activity over a broad pH-range we determined the pH dependence of SDMT reaction rates. TM0936 reactions are monitored at 263 nm, so a drawback may arise when methyl...”
- Biochemical functional predictions for protein structures of unknown or uncertain function
Mills, Computational and structural biotechnology journal 2015 - “...study, performed by one of the Bridging Projects, aided in assigning function to Thermotoga maritima Tm0936, a member of the AH superfamily whose function was previously unknown. Tm0936 was predicted to have a novel function as an S -adenosylhomocysteine deaminase [91] . This study involved docking...”
- “...the SALSA method of annotating protein function. Fig.5 The metabolites above dock in silico into Tm0936 and are substrates of the enzyme Tm0936. The general structure of these three metabolites is the same with the exception of the moieties shown in the boxes....”
- Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa
Fedorov, Biochemistry 2015 - “...from the AHS. 3 A comparison of the coordinating environment of Pa5106 with that of Tm0936 from Thermotoga maritima is presented in Figure 2 B (PDB id: 2PLM). Residues involved in the binding of the divalent cation in the active site of Tm0936 are also conserved...”
- “...(B) Superimposition of the metal binding residues of Pa5106 (PDB id: 3MDW) with those of Tm0936 from Thermotoga maritima (PDB id: 2PLM). Protein-Inhibitor Interactions The electrostatic interactions between N -formimino- l -aspartate and the protein are depicted in Figure 3 A. N -Formimino- l -aspartate is...”
- Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome
Fleischman, Protein science : a publication of the Protein Society 2014 - “...coworkers33 docked a library of high-energy intermediates into Tm0936, an enzyme with a known structure but unknown function from T. maritima. The computational...”
- Structure-guided discovery of new deaminase enzymes
Hitchcock, Journal of the American Chemical Society 2013 - “...amidohydrolase superfamily using a structure-guided approach that integrates bioinformatics, computational biology and molecular enzymology. Previously, Tm0936 from Thermotoga maritima was shown to catalyze the deamination of S-adenosylhomocysteine (SAH) to Sinosylhomocysteine (SIH). Homologues of Tm0936 homologues were identified, and substrate profiles were proposed by docking metabolites to...”
- “...catalyzes the deamination of nucleic acid bases. 5 , 7 Previously, we successfully predicted that Tm0936, an enzyme from Thermotoga maritima , would catalyze the deamination of S -adenosylhomocysteine (SAH) to S -inosylhomocysteine (SIH). 5 Here we significantly expand the scope of these efforts by addressing...”
- Identification of a new class of adenosine deaminase from Helicobacter pylori with homologs among diverse taxa
Miller, Journal of bacteriology 2013 - “...of Hp0267 (45,540 Da). Bioinformatics methods. Hp0267 and Tm0936 orthologs used for sequence alignments were selected from BLAST hits exhibiting E values...”
- “...characterized S-adenosylhomocysteine (SAH) deaminase from Thermotoga maritima (Tm0936) (25). There is currently a group of enzymes in the NCBI database...”
- Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking
Fan, Journal of the American Chemical Society 2013 - “...enzyme structure 7 , 8 . This method was used to predict the substrates of Tm0936 from Thermotoga maritima 9 . High-energy intermediate forms of thousands of candidate metabolites were docked to the X-ray structure of Tm0936, and those highly ranked by docking energy score were...”
- More
1p1mA / Q9X034 Structure of thermotoga maritima amidohydrolase tm0936 bound to ni and methionine
23% identity, 90% coverage
- Ligand: methionine (1p1mA)
trzN / A1RCJ9 triazine hydrolase (EC 3.8.1.8) from Paenarthrobacter aurescens (strain TC1) (see 3 papers)
AAur_pTC10087 triazine hydrolase from Arthrobacter aurescens TC1
A1RCJ9 Triazine hydrolase from Paenarthrobacter aurescens (strain TC1)
23% identity, 77% coverage
- Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1
Kundu, The ISME journal 2019 - “...D0.018/CHEM RET/D0.018 LFC Adj. p -value LFC Adj. p -value LFC Adj. p -value A1RCJ9 AAur_pTC10087 TrzN, triazine hydrolase 0.94 0.087 0.36 0.422 0.57 0.404 A1RCX5 AAur_pTC10218 AtzB, hydroxyatrazine hydrolase 1.48 0.025 0.89 0.089 2.37 0.019 A1RCX2 Aur_pTC10212 AtzC, N -isopropylammelide isopropylaminohydrolase 0.61 0.294 0.81 0.126...”
- Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1
Mongodin, PLoS genetics 2006 - “...position: 115622110496) ( Figure 2 ). This repeat region includes the triazine hydrolase gene, trzN (AAur_pTC10087), and an exact gene duplication of a toprim domain protein (AAur_pTC10084 and AAur_pTC10091) ( Figure 2 ), a conserved region from DNA primase, corresponding to the topoisomeraseprimase domain common to...”
- “...with these previous findings. All three triazine hydrolase genes, trzN , atzB , and atzC (AAur_pTC10087, AAur_pTC10218, and AAur_pTC10212, respectively), were located on plasmid pTC1 and nowhere else in the A. aurescens TC1 genome. A complete cluster of genes involved in the biodegradation of isopropylamine (ipu)...”
- Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1.
Kundu, The ISME journal 2019 - “...RET/CHEM D0.018/CHEM RET/D0.018 LFC Adj. p -value LFC Adj. p -value LFC Adj. p -value A1RCJ9 AAur_pTC10087 TrzN, triazine hydrolase 0.94 0.087 0.36 0.422 0.57 0.404 A1RCX5 AAur_pTC10218 AtzB, hydroxyatrazine hydrolase 1.48 0.025 0.89 0.089 2.37 0.019 A1RCX2 Aur_pTC10212 AtzC, N -isopropylammelide isopropylaminohydrolase 0.61 0.294 0.81...”
O66851 5-methylthioadenosine/S-adenosylhomocysteine deaminase from Aquifex aeolicus (strain VF5)
22% identity, 49% coverage
- In vitro Determination of Extracellular Proteins from Xylella fastidiosa.
Mendes, Frontiers in microbiology 2016 - “...lyase (ASL) 50.6 XF1553 XF1289 P44797 No No 0.076 Amidohydrolase family protein 47.3 XF2472 XF2144 O66851 No No 0.069 Aminopeptidase (peptidase M28 family protein) 57.7 XF0820 XF0671 O54697 No No 0.529 Antitoxin (HTH-type transcriptional regulator) 15 XF2491 XF2163 Q46864 No No 0.149 Autolytic lysozyme 23.4 XF2392...”
2imrA / Q9RW45 Crystal structure of amidohydrolase dr_0824 from deinococcus radiodurans
25% identity, 46% coverage
RL3577 putative guanine deaminase from Rhizobium leguminosarum bv. viciae 3841
28% identity, 47% coverage
Q4K8M5 5-methylthioadenosine/S-adenosylhomocysteine deaminase from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
23% identity, 85% coverage
- Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine
Miller, Journal of bacteriology 2014 - “...follows: B6YUF8, Q5JER0, O66851, A6UUG9, I9MDY4, O27549, Q4K8M5, A6V2Q5, G0PU20, M1Z1T6, Q9KC82, D3DYL9, Q8TYD4, Q2RJW1, B1BCH5, A4FW32, F2KTB3, Q8U0P7, D5VT65,...”
T1Z209 atrazine chlorohydrolase (EC 3.8.1.8) from Arthrobacter sp. DNS10 (see paper)
22% identity, 75% coverage
IXPDE_UNKP / P0CI72 Isoxanthopterin deaminase; EC 3.5.4.11 from Unknown prokaryotic organism (see paper)
P0CI72 pterin deaminase (EC 3.5.4.11) from unidentified prokaryotic organism (see paper)
23% identity, 80% coverage
- catalytic activity: a 2-amino-4-hydroxypteridine + H2O + H(+) = a 2,4- dihydroxypteridine + NH4(+) (RHEA:36055)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
WP_031508998 amidohydrolase family protein from Streptomyces megasporus
27% identity, 42% coverage
PA0134 probable guanine deaminase from Pseudomonas aeruginosa PAO1
Q9I6Z8 Guanine deaminase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
31% identity, 49% coverage
- Methylthioadenosine deaminase in an alternative quorum sensing pathway in Pseudomonas aeruginosa
Guan, Biochemistry 2012 - “...database contains several genes annotated as putative deaminases based on zinc binding motif. These included PA0134 (guanine deaminase), PA1521 (guanine deaminase), PA0142 (guanine deaminase), PA0148 (adenosine deaminase), PA2499 (unspecified deaminase), PA3480 (deoxycytidine triphosphate deaminase), PA0437 (cytosine deaminase), and PA3170 (guanine deaminase). We searched all of the...”
- The hunt for 8-oxoguanine deaminase
Hall, Journal of the American Chemical Society 2010 - “...can utilize 8-oxoG as a substrate. Two putative guanine deaminases were cloned, purified, and characterized: Pa0134 from P. aeruginosa (gi|15595332) and b2883 from Escherichia coli K12 (gi|16130785). These enzymes efficiently catalyze the deamination of guanine but not any other compounds. For Pa0134 the values of k...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...9 G3XD97 1091 O31038 2173 Q9I6Y9 3255 Q9HXT0 4337 Q9I2K2 10 G3XDA8 1092 O52658 2174 Q9I6Z8 3256 Q9HXT1 4338 Q9I2K3 11 O05927 1093 O52759 2175 Q9I701 3257 Q9HXT2 4339 Q9I2K5 12 O30508 1094 O52761 2176 Q9I713 3258 Q9HXT3 4340 Q9I2K6 13 O33407 1095 O68281 2177 Q9I714...”
MQNX_DEIRA / Q9RW45 Aminodeoxyfutalosine deaminase; AFL deaminase; Aminofutalosine deaminase; EC 3.5.4.40 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (see paper)
Q9RW45 aminodeoxyfutalosine deaminase (EC 3.5.4.40) from Deinococcus radiodurans (see paper)
DR0824 hydrolase, putative from Deinococcus radiodurans R1
25% identity, 46% coverage
- function: Catalyzes the deamination of aminodeoxyfutalosine (AFL) into futalosine (FL). To a lesser extent, can also deaminate 5'- deoxyadenosine, 5'-methylthioadenosine, 2'-deoxyadenosine, adenosine, 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide (NECA), and S-adenosylhomocysteine.
catalytic activity: 6-amino-6-deoxyfutalosine + H2O + H(+) = futalosine + NH4(+) (RHEA:40075)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.) - Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori
Feng, Biochemistry 2021 - “...been reported in Sav2595 from Steptomyces avermitilis as well as its distantly related orthologs (Acel0264, Dr0824, and Nis0429) from three thermophilic bacteria. 39 The characterized catalytic efficiencies for AFL deamination range from 4.8 10 6 to 7.9 10 5 M 1 s 1 , which are...”
- “...k cat / K m values for MTA and 5Ado than other AFL deaminases except Dr0824 from Deinococcus radiodurans . It is worth noting that the kinetic characterization of these four enzymes was carried out at 30 C instead of 25 C, which was used to...”
- Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes
Goble, Biochemistry 2013 - “...from Steptomyces avermitilis MA-4680, Acel0264 from Acidothermus cellulolyticus 11B, Nis0429 from Nitratiruptor sp. SB155-2 and Dr0824 from Deinococcus radiodurans R1 were cloned, purified, and their substrate profiles determined. These enzymes were previously incorrectly annotated as adenosine deaminases or chlorohydrolases. It was shown here that these enzymes...”
- “...In this model Ser-145 interacts with the carboxylate moiety of the substrate. The structure of Dr0824 was also determined, but a collapsed active site pocket prevented docking of substrates. A computational model of Sav2595 was built based on the crystal structure of adenosine deaminase and substrates...”
Bxe_A2016 amidohydrolase from Burkholderia xenovorans LB400
24% identity, 84% coverage
- Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase
Hall, Biochemistry 2010 - “...Sea under the Global Ocean Sampling Project. The closest homologue to Sgx9339a (88% identical) is Bxe_A2016 from Burkholderia xenovorans LB400 and the closest homologue of Sgx9236b (95% identical) is Bphyt_7136 from Burkholderia phytofirmans PsJN. Both of these proteins are currently annotated by NCBI as ATZ/TRZ-like amidohydrolases....”
MSMEG_1298 guanine deaminase from Mycobacterium smegmatis str. MC2 155
29% identity, 36% coverage
- Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture
Petridis, BMC genomics 2015 - “...3.89 2.39E-17 OHCU decarboxylase msmeg_1296 3.78 2.28E-07 uricase msmeg_2748 3.69 1.44E-05 soluble pyridine nucleotide transhydrogenase msmeg_1298 3.67 6.88E-12 guanine deaminase msmeg_3996 3.53 3.56E-13 phenylhydantoinase msmeg_1295 3.52 2.55E-12 transthyretin msmeg_3553 d 2.95 1.98E-04 phenylhydantoinase msmeg_6116 2.64 1.09E-08 OHCU decarboxylase msmeg_3473 2.55 6.53E-03 uracil phosphoribosyltransferase msmeg_5727 2.21 4.92E-06...”
CV_0578 probable guanine deaminase from Chromobacterium violaceum ATCC 12472
28% identity, 38% coverage
KPN_01791 guanine deaminase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
27% identity, 38% coverage
Hqrw_2212 amidohydrolase family protein from Haloquadratum walsbyi C23
22% identity, 50% coverage
- Haloquadratum walsbyi: limited diversity in a global pond
Dyall-Smith, PloS one 2011 - “...Comparison with C23 T shows this is a deletion because the corresponding C23 T ORF, Hqrw_2212, remains intact. The ends of the undeleted region in C23 T have a direct repeat, ACATCATTCT , while in HBSQ001 there is only one copy directly at the deletion border....”
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The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
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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