PaperBLAST
PaperBLAST Hits for tr|A0A1X9Z8E1|A0A1X9Z8E1_9SPHI Acetylornithine deacetylase OS=Sphingobacteriaceae bacterium GW460-11-11-14-LB5 OX=1986952 GN=CA265_18500 PE=4 SV=1 (355 a.a., MSLENIQKES...)
Show query sequence
>tr|A0A1X9Z8E1|A0A1X9Z8E1_9SPHI Acetylornithine deacetylase OS=Sphingobacteriaceae bacterium GW460-11-11-14-LB5 OX=1986952 GN=CA265_18500 PE=4 SV=1
MSLENIQKESLDLLRQLIRIQSFSKEEDRTANLIAQFLEERGIKTQRKMNNVWAYNKHFD
ATKPTLLLNSHHDTVKPNSGYTRDPYDAAIEGDKLFGLGSNDAGGCLVSLIGTFLYYYEQ
EGLKYNICLAATAEEEISGNNGLELVLPDLGELEFGIVGEPTEMNLAIAERGLLVLDCVS
HGKAGHAAREEGENAIYKALKDIEWFRNYQFPKVSEVFGPLKMTVTIINAGSQHNVVPAN
CTFTVDVRVTDAYTNEEVLEIIRANVDCDVTPRSIRLKPSSIDKNHPVVQAGVALGKTTY
GSPTTSDQALLDIPSVKCGPGFSGRSHMADEFLYVREVAEGVEGYVNMLRPVVIG
Running BLASTp...
Found 168 similar proteins in the literature:
CA265_RS18500 N-succinylcitrulline desuccinylase (EC 3.5.1.-) from Pedobacter sp. GW460-11-11-14-LB5
100% identity, 100% coverage
- mutant phenotype: Important for fitness in most defined media, except when arginine is provided. Distantly related to succinyl-diaminopimelate desuccinylases, so this probably provides the missing N-succinylcitrulline desuccinylase activity. See PMC7311316.
Echvi_3851 N-succinylcitrulline desuccinylase (EC 3.5.1.-) from Echinicola vietnamensis KMM 6221, DSM 17526
53% identity, 96% coverage
- mutant phenotype: Important for fitness in most defined media, except when arginine is provided. Distantly related to succinyl-diaminopimelate desuccinylases, so this probably provides the missing N-succinylcitrulline desuccinylase activity. See PMC7311316.
BT3549 N-succinylcitrulline desuccinylase (EC 3.5.1.-) from Bacteroides thetaiotaomicron VPI-5482
BT3549 acetylornithine deacetylase from Bacteroides thetaiotaomicron VPI-5482
51% identity, 98% coverage
- mutant phenotype: Important for fitness in most defined media, except when arginine is provided. Distantly related to succinyl-diaminopimelate desuccinylases, so this probably provides the missing N-succinylcitrulline desuccinylase activity. See PMC7311316.
- GapMind: Automated Annotation of Amino Acid Biosynthesis
Price, mSystems 2020 - “...desuccinylating enzyme, most likely an N -succinylcitrulline desuccinylase ( Fig.3B ). The genetic data identified BT3549 as a candidate for this step ( Fig.3C ); BT3549 is distantly related (under 30% identity) to succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis ( 25 ), which is a similar chemical...”
SMGWSS_116 putative acetylornithine deacetylase (argE)/succinyl-diaminopimelate desuccinylase (dapE) from Candidatus Sulcia muelleri GWSS
47% identity, 98% coverage
- One bacterial cell, one complete genome
Woyke, PloS one 2010 - “...subunit 92.73 DMIN_02450 SMGWSS_249 putative delta-1-pyrroline-5-carboxylate dehydrogenase 92.74 DMIN_00970 SMGWSS_101 chaperone protein DnaJ 94.13 DMIN_01120 SMGWSS_116 putative acetylornithine deacetylase (ArgE)/succinyl-diaminopimelate desuccinylase (DapE) 94.52 DMIN_00050 SMGWSS_006 phenylalanyl-tRNA synthetase beta subunit 95.04 DMIN_01320 SMGWSS_136 50S ribosomal subunit protein L19 95.29 DMIN_01570 SMGWSS_160 tryptophanyl-tRNA synthetase 95.3 DMIN_01250 SMGWSS_129 ATP-dependent...”
DMIN_01120 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase-related deacylase from Candidatus Sulcia muelleri DMIN
45% identity, 96% coverage
- One bacterial cell, one complete genome
Woyke, PloS one 2010 - “...delta subunit 92.73 DMIN_02450 SMGWSS_249 putative delta-1-pyrroline-5-carboxylate dehydrogenase 92.74 DMIN_00970 SMGWSS_101 chaperone protein DnaJ 94.13 DMIN_01120 SMGWSS_116 putative acetylornithine deacetylase (ArgE)/succinyl-diaminopimelate desuccinylase (DapE) 94.52 DMIN_00050 SMGWSS_006 phenylalanyl-tRNA synthetase beta subunit 95.04 DMIN_01320 SMGWSS_136 50S ribosomal subunit protein L19 95.29 DMIN_01570 SMGWSS_160 tryptophanyl-tRNA synthetase 95.3 DMIN_01250 SMGWSS_129...”
Igni_0315 acetylornithine deacetylase from Ignicoccus hospitalis KIN4/I
25% identity, 89% coverage
- Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association
Rawle, Biochimica et biophysica acta. General subjects 2017 - “...Succinyl-CoA synthetase (ADP-forming) alpha subunit t Igni_0086 Succinyl-CoA synthetase (ADP-forming) beta subunit t Succinate m Igni_0315 Acetylornithine deacetylase p L-Ornithine m Igni_0363 Hypothetical protein t Igni_1361 Glucokinase p Igni_0415 Glucose-6-phosphate isomerase t Igni_0678 Fumarase Fumarate m Igni_1079 Deoxyribose-phosphate aldolase t,p Igni_0257 Acyl-coenzyme A synthetase/AMP-(fatty) acid ligase-like...”
IYO_RS24010 M20 family metallopeptidase from Pseudomonas syringae pv. actinidiae ICMP 18884
26% identity, 91% coverage
lpg1164 acetylornithine deacetylase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
24% identity, 89% coverage
AWC34_RS13195 M20 family metallopeptidase from Staphylococcus equorum
25% identity, 76% coverage
CLJU_c29950 YgeY family selenium metabolism-linked hydrolase from Clostridium ljungdahlii DSM 13528
26% identity, 90% coverage
- Pleiotropic Regulator GssR Positively Regulates Autotrophic Growth of Gas-Fermenting Clostridium ljungdahlii
Zhang, Microorganisms 2023 - “...and reduction 22 CLJU_c29940 xanthine dehydrogenase related protein, molybdopterin bindin 5.36 Oxidation and reduction 23 CLJU_c29950 putative deacetylase 5.39 Post-translational modification 24 CLJU_c29960 N-acyl-D-amino-acid deacylase 4.61 Post-translational modification 25 CLJU_c29970 predicted ABC-type transporter, permease component 3.70 Transporter 26 CLJU_c29980 predicted ABC-type transporter, permease component 3.96 Transporter...”
SPCC757.05c acetylornithine deacetylase (predicted) from Schizosaccharomyces pombe
29% identity, 85% coverage
- Response to sulfur in Schizosaccharomyces pombe
Ohtsuka, FEMS yeast research 2021 - “...decomposition mechanism for GSH. S. pombe has dug1 + as a homolog of DUG1 and SPCC757.05c as a homolog of DUG2 . In addition, it has been confirmed that Ggt1 and Ggt2 have glutathione hydrolase activity as homologs of Ecm38 (Park etal . 2004 ). In...”
J9YVI9 Acetylornithine deacetylase ArgE from alpha proteobacterium HIMB5
24% identity, 86% coverage
EF_3178 ArgE/DapE family deacylase from Enterococcus faecalis V583
EF3178 peptidase, M20/M25/M40 family from Enterococcus faecalis V583
25% identity, 90% coverage
PA5390 acetylornithine deacetylase from Pseudomonas aeruginosa PAO1
Q9HTH4 Probable peptidic bond hydrolase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
26% identity, 86% coverage
C0NAB3 Probable carboxypeptidase HCBG_00059 from Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)
27% identity, 80% coverage
dapE / P44514 N-succinyl-L,L-diaminopimelate desuccinylase subunit (EC 3.5.1.18) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see paper)
DAPE_HAEIN / P44514 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see 7 papers)
P44514 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Haemophilus influenzae (see 3 papers)
WP_005693818 succinyl-diaminopimelate desuccinylase from Haemophilus influenzae RdAW
HI0102 succinyl-diaminopimelate desuccinylase (dapE) from Haemophilus influenzae Rd KW20
24% identity, 91% coverage
- function: Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminopimelate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso- diaminopimelic acid, an essential component of bacterial cell walls. It can only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and is inactive toward D,L-, L,D-, and D,D-SDAP.
catalytic activity: N-succinyl-(2S,6S)-2,6-diaminopimelate + H2O = (2S,6S)-2,6- diaminopimelate + succinate (RHEA:22608)
cofactor: Zn(2+) (Binds 2 Zn(2+) ion per subunit.)
subunit: Homodimer. - Perspectives of aminoacylases in biocatalytic synthesis of N-acyl-amino acids surfactants
Haeger, Applied microbiology and biotechnology 2024 - “...deacetylase from E. coli (UniProt : P23908); HiDapE, succinyl-diaminopimelate desuccinylase from Haemophilus influenzae (accession number: WP_005693818); L-ACY-1, aminoacylase 1 from Heliothis virescens (GenBank: AET43034); pAcy1, porcine aminoacylase-1 (accession number: NP_999061); hAcy1, human aminoacylase-1 (accession number: NP_000657); PM20D1, human N-fatty-acyl-amino acid hydrolase (UniProt: Q6GTS8); MsAA, aminoacylase from...”
- Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor
López-López, mSystems 2022 - “...) Phosphatidate cytidylyltransferase Peptidoglycan biosynthesis 2.7.2.4, 1.1.1.3 HI0089 ( thrA ) Bifunctional aspartokinase/homoserine dehydrogenase 3.5.1.18 HI0102 ( dapE ) Succinyl-diaminopimelate desuccinylase 4.3.3.7 HI0255 ( dapA ) 4-Hydroxy-tetrahydrodipicolinate synthase 1.3.1.98 HI0268 ( murB ) UDP-N-acetylenolpyruvoylglucosamine reductase 2.4.1.129, 3.4.16.4 HI0440 ( ponA ) Penicillin-binding protein 1A 2.7.7.23, 2.3.1.157...”
5vo3A / P44514 Crystal structure of dape in complex with the products (succinic acid and diaminopimelic acid) (see paper)
24% identity, 91% coverage
- Ligands: succinic acid; 2,6-diaminopimelic acid; zinc ion (5vo3A)
CLOSPO_02130 hypothetical protein from Clostridium sporogenes ATCC 15579
24% identity, 85% coverage
- A widely distributed gene cluster compensates for uricase loss in hominids
Liu, Cell 2023 - “...CAGAAAACAGCCAACCTAACCGAAAAGCGAAAGCT GATACGGGAACAGAGCACGGTTGGAAAGCGATGAG TTACCTAAAGACAATCGGGTACGACTGAGTCGCAAT GTTAATCAGATATAAGGTATAAGTTGTGTTTACTGAA CGCAAGTTTCTAATTTCGGTTGCTATCCGATAGAGG AAAGTGTCTGAAACCTCTAGTACAAAGAAAGGTAAG TTACAATGTACGACTTATCTGTTATCACCACATTTGT ACAATCTGTAGGAGAACCTATGG Integrated DNA technologies N/A ygeY (CLOSPO_02130, 358s) gBlock: ATAAAGTTGTGTAATTTTTAAGCTTTATAATTATCCTT AGGCGGCATGGCCGTGCGCCCAGATAGGGTGTTAA GTCAAGTAGTTTAAGGTACTACTCTGTAAGATAACA CAGAAAACAGCCAACCTAACCGAAAAGCGAAAGCT GATACGGGAACAGAGCACGGTTGGAAAGCGATGAG TTACCTAAAGACAATCGGGTACGACTGAGTCGCAAT GTTAATCAGATATAAGGTATAAGTTGTGTTTACTGAA CGCAAGTTTCTAATTTCGATTCCGCCTCGATAGAGG AAAGTGTCTGAAACCTCTAGTACAAAGAAAGGTAAG TTAGAGGCCATGACTTATCTGTTATCACCACATTTGT ACAATCTGTAGGAGAACCTATGG Integrated DNA technologies N/A xdhAC (CLOSPO_02131, 1084s) gBlock: ATAAAGTTGTGTAATTTTTAAGCTTTATAATTATCCTT AGATGGCGATGGAGTGCGCCCAGATAGGGTGTTAA GTCAAGTAGTTTAAGGTACTACTCTGTAAGATAACA CAGAAAACAGCCAACCTAACCGAAAAGCGAAAGCT GATACGGGAACAGAGCACGGTTGGAAAGCGATGAG...”
- “...DNA technologies N/A ssnA (CLOSPO_02129) sequencing Csp.ssnA-F: AAGGAAAACTTATAATGCCAG Csp.ssnA-R: CATTTCAGGAATTTCGGTC Integrated DNA technologies N/A ygeY (CLOSPO_02130) sequencing Csp.ygeY-F: TTTTAAAAGAAGGTGCTCT Csp.ygeY-R: TTCATACACATTTATTACCCC Integrated DNA technologies N/A xdhAC (CLOSPO_02131) sequencing Csp.xdhAC-F: ATTATTACAGCACAAGATGTCC Csp.xdhAC-R: CGCATGATGTTGTACACTCA Integrated DNA technologies N/A ygeW (b2870) -red recombination knockout F: TTTGCCTGTCATTCCACTACCGGGACTTTATGATGG TGTAGGCTGGAGCTGCTTC R: ATCGGCCCGAGGGGTTATTTCACGCGTTCTTGCGC...”
CD3183 peptidase from Clostridium difficile 630
25% identity, 88% coverage
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...dehydrogenase; gcvTPA (CD1657), bi-functional glycine dehydrogenase/aminomethyl transferase protein; gcvPB (CD1658), Glycine decarboxylase; CD1228, putative protease; CD3183, putative peptidase; CD2485, putative Xaa-Pro aminopeptidase; CD2347, putative Xaa-Pro dipeptidase; gcp (CD0152), putative O-sialoglycoprotein endopeptidase; CD2129, putative membrane-associated peptidase; pepI (CD3041), proline iminopeptidase. Thus, CcpA seems to play a key...”
- “...(CD0152) encoding an O -sialoglycoprotein endopeptidase and three other peptidases encoding genes (CD1228, CD2129 and CD3183) was induced by glucose in a CcpA-dependent manner. Similarly, the same type of regulation was found for the proline iminopeptidase gene pepI (CD3041) and peptidases encoding genes (CD2347 and CD2485)...”
HVO_A0634 M20 peptidase family protein from Haloferax volcanii DS2
27% identity, 64% coverage
Q1V055 Acetylornithine deacetylase from Pelagibacter ubique (strain HTCC1002)
24% identity, 86% coverage
BP3588 putative peptidase from Bordetella pertussis Tohama I
26% identity, 86% coverage
SXYL_00377 ArgE/DapE family deacylase from Staphylococcus xylosus
25% identity, 84% coverage
Q92Y75 acetylornithine deacetylase (EC 3.5.1.16) from Sinorhizobium meliloti (see paper)
SMa1836 putative ArgE acetylornithine deacetylase from Sinorhizobium meliloti 1021
25% identity, 73% coverage
- Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria
Yuan, Nucleic acids research 2006 - “...277.4 24.3 160 0.41 SMa1456 726.2 14.2 763 41.2 804.2 56 858.5 34.6 30 0.45 SMa1836 139.1 13.6 162.9 9.4 122.1 10.8 146.4 23.8 285 0.39 SMa2012 101.1 6 100.1 1.4 112.2 14 102.8 23.3 381 0.39 SMa2025 132 0.7 206.5 21.6 121.8 2.8 207.8 13.6...”
- Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid
Barnett, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...SMA1726 -1731; iron uptake, SMA1740 -1747; argE, SMA1836; gabD5, SMA1848; sulfur metabolism, SMA2067-2103; glyA2, SMA2135; tRNA-met, SMa2168; opine metabolism,...”
- “...We also identified a putative argE (acetylornithine deacetylase, SMa1836; Fig. 1) that is required for arginine biosynthesis in Myxococcus and enteric bacteria;...”
An02g12680 uncharacterized protein from Aspergillus niger
25% identity, 69% coverage
- Bioinformatic mapping of a more precise Aspergillus niger degradome
Dong, Scientific reports 2021 - “...M18 Aminopeptidase I Aspartyl aminopeptidase An02g11940 (S/G/A)HXDXV+P/GXXD+XEE+D/E+H An09g06250 M20A Glutamate carboxypeptidase Gly-Xaa carboxypeptidase An02g13740* / An02g12680 / An18g06210* M20D Carboxypeptidase Ss1 Met-Xaa dipeptidase An01g11610 EE An02g00990 An08g07280 An11g07760 An11g08890 An12g02360 An15g01800 M20F Carnosine dipeptidase II Cytosol nonspecific dipeptidase An04g10270 (S/G/A)HXDXV+P/GXXD+XEE+D/E+H An11g03000 / An11g11180 M28A Aminopeptidase S...”
Q4FL07 Acetylornithine deacetylase from Pelagibacter ubique (strain HTCC1062)
25% identity, 86% coverage
PAAG_00768 peptidase family protein from Paracoccidioides lutzii Pb01
26% identity, 78% coverage
- Transcriptional and proteomic responses to carbon starvation in Paracoccidioides
Lima, PLoS neglected tropical diseases 2014 - “...aminopeptidase # protein/peptide degradation PAAG_03464 bleomycin hydrolase # proteolysis PAAG_05583 cysteine protease PalB # proteolysis PAAG_00768 peptidase family protein # proteolysis PAAG_05417 mitochondrial-processing peptidase subunit beta # proteolysis PAAG_00739 peptidyl-prolyl cis-trans isomerase B # protein folding PAAG_02155 peroxisomal targeting signal 2 receptor (PTS2) # protein fate...”
wVul_1454 succinyl-diaminopimelate desuccinylase from Wolbachia endosymbiont of Armadillidium vulgare str. wVulC
25% identity, 60% coverage
- Investigating the Molecular Genetic Basis of Cytoplasmic Sex Determination Caused by Wolbachia Endosymbionts in Terrestrial Isopods
Badawi, Genes 2018 - “...73 , 74 ]; Peptidases/proteases that hydrolysepeptidic bounds [ 75 , 76 ] in wVul_1408, wVul_1454 and wVul_1775; Membranes: Mitofilin in wVul_0085 that is an inner membrane protein domain of mitochondria that controls cristae morphology [ 77 , 78 ]; IncA in wVul_1360 that is associated...”
- “...VulC candidate genes with no hit in the f element were wVul_0609, wVul_0626, wVul_1360, wVul_1408, wVul_1454, wVul_1646, wVul_1660 and wVul_1696. Among the 27 genes present in both w VulC and the f element, 20 presented identical copies at the amino acid level ( Table S5 )....”
lmo0265 similar to succinyldiaminopimelate desuccinylase from Listeria monocytogenes EGD-e
24% identity, 89% coverage
- Executioner caspases degrade essential mediators of pathogen-host interactions to inhibit growth of intracellular Listeria monocytogenes
Lavergne, Cell death & disease 2025 - “...A0A0H3GDD6 [210-217] [G].EDLEKFER.[L] Peptidoglycan-N-acetylglucosamine deacetylase PgdA A0A0H3GDH9 lmo0415 A0A0H3GDH9 [125-135] [K].AVQSEYVKEGR.[T] Probable succinyl-diaminopimelate desuccinylase A0A0H3GDI0 lmo0265 A0A0H3GDI0 [158-168] [D].GLIIGEPSGHR.[I] LytR_cpsA_psr domain-containing protein A0A0H3GDK2 lmo0443 A0A0H3GDK2 [191-199] [D].GKTLLQYAR.[F] 10 kDa chaperonin A0A0H3GDS3 lmo2069 A0A0H3GDS3 [29-46] [D].SAKEKPQSGKIVAVGSGR.[V] Manganese-binding lipoprotein mntA A0A0H3GDS9 lmo1847 A0A0H3GDS9 [282-298] [D].STAKKGEVGDTYLEMMR.[Y] 4-hydroxy-tetrahydrodipicolinate reductase A0A0H3GDZ1...”
- Transcriptomic analysis of Listeria monocytogenes biofilm formation at different times
Gou, Canadian journal of veterinary research = Revue canadienne de recherche veterinaire 2023 (secret) - Transcriptomic and Phenotypic Analyses of the Sigma B-Dependent Characteristics and the Synergism between Sigma B and Sigma L in Listeria monocytogenes EGD-e
Mattila, Microorganisms 2020 - “...PTS system component 3.3 2.8 lmo0784 PTS system component 3.7 3.2 Hypothetical and unclassified proteins lmo0265 peptidase, M20/M25/M40 family 2.2 2.4 lmo0602 protease synthase and sporulation negative regulatory protein pai 1, putative 1.3 2.8 lmo0937 hypothetical protein 3.2 2.8 lmo1241 conserved hypothetical protein 2.5 3.9 lmo2067...”
- “...PTS system component 2.1 2.9 lmo0784 PTS system component 2.1 3.8 Hypothetical and unclassified proteins lmo0265 peptidase, M20/M25/M40 family lmo0355 succinate dehydrogenase/fumarate reductase, flavoprotein 2.2 2.4 lmo0602 subunit 1.9 1.9 lmo2067 protease synthase and sporulation negative regulatory protein pai 1, putative 2.1 3 lmo2158 choloylglycine hydrolase...”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...ASCH domain-containing protein 2.02 0.02 LMRG_02427 lmo2856 rpmH 50S ribosomal protein L34 2.06 0.00 LMRG_02611 lmo0265 dapE Succinyl-diaminopimelate desuccinylase 2.87 0.00 LMRG_02646 lmo0263 inlC2 , inlH Internalin C2 2.22 0.04 LMRG_02700 lmo2568 LMRG_02700-LMRG_02701 Hypothetical protein 9.41 0.00 LMRG_02768 lmo1694 CDP-abequose synthase, Putative sugar nucleotide epimerase 3.68...”
- Blue Light Sensing in Listeria monocytogenes Is Temperature-Dependent and the Transcriptional Response to It Is Predominantly SigB-Dependent
Dorey, Frontiers in microbiology 2019 - “...proteins and lipoproteins Putative transporter kdpA 1.28 Transport/binding proteins and lipoproteins Potassium-transporting ATPase A chain lmo0265 1.47 Metabolism of amino acids and related molecules Acetylornithine deacetylase rli127 1.87 sRNA Unknown sbrE (rli47) 2.71 sRNA Unknown The Light Sensor RsbL Contributes to Light-Dependent Changes in Gene Expression...”
- Refinement of the Listeria monocytogenes σB regulon through quantitative proteomic analysis
Mujahid, Microbiology (Reading, England) 2013 - “...studies as sB-dependent (Fraser et al., 2003; Sue et al., 2003). lmo0265, which had a significant Pc value and a FC of 8.0 reported in the Oliver et al. (2010)...”
- “...al., 2008), which used an EGD-e array that had an lmo0265 probe with low (71 %) homology to the 10403S lmo0265 gene, likely leading to a false-negative result...”
- Characterisation of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditions reveal global stress-adaptation mechanisms
Durack, PloS one 2013 - “...Gene homolog ATCC19115 ScottA 70-1700 Predicted or known function NaCl 4C NaCl 4C NaCl 4C lmo0265 -3.11 ** -2.03 ** -2.28 *** -3.49 ** -1.91 *** -3.34 *** putative succinyl-diaminopimelate desuccinylase lmo0445 -2.67 ** -1.22 * -1.29 *** -1.10 ** -1.44 *** -1.09 *** similar to...”
- “...or indirectly activated by B showed strong down-regulation in stress-adapted cells, such as dapD ( lmo0265 ), in addition genes directly or indirectly repressed by B showed significant up-regulation in stress-adapted strains. Some of the highly activated genes repressed by B included rpmI ( lmo1784 ),...”
- Protein level identification of the Listeria monocytogenes sigma H, sigma L, and sigma C regulons
Mujahid, BMC microbiology 2013 - “...these proteins include Lmo2748, Lmo2213, Lmo2158, Lmo2047, Lmo1830, Lmo0913, Lmo0796, Lmo0794, Lmo0722, Lmo0654, Lmo0539, and Lmo0265. The 17 proteins that show higher levels in the parent strain as compared to the BCHL strain, but were not identified as positively regulated by any of the alternative factors...”
- More
AWH67_RS01345 succinyl-diaminopimelate desuccinylase from Bartonella bacilliformis
25% identity, 64% coverage
WP_002303488 ArgE/DapE family deacylase from Enterococcus faecium
24% identity, 89% coverage
7uoiA / A0A1S8KJG1 Crystallographic structure of dape from enterococcus faecium (see paper)
24% identity, 89% coverage
CD2084 peptidase from Clostridium difficile 630
25% identity, 88% coverage
- Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
Haft, Biology direct 2008 - “...10 b2871 7 EF_2579 7 CD2085 ygeY hydrolase, peptidase M20 family 4 b2872 3 EF_2578 (CD2084) ygeZ phenyl-hydantoinase 19 b2873 (EF_2580) 6 pNG7258 yqeA carbamate kinase 18 b2874 15 EF_2575 yqeB SDMH accessory protein TIGR03309 1 b2875 2 EF_2563 1 pNG7241 1 CD3478 yqeC SDMH accessory...”
A3K8M6 Acetylornithine deacetylase from Sagittula stellata (strain ATCC 700073 / DSM 11524 / E-37)
26% identity, 73% coverage
KPN_01464 putative peptidic bond hydrolase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
24% identity, 88% coverage
- A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
Hawkey, Genome research 2022 - “...deacetylase, and NACODA, N-acetylornithine deacetylaseboth of which may also be encoded by the product of KPN_01464 (homologs of this gene were identified in only those genomes that were not associated with loss-of-growth phenotype). Comparison of the K. pneumoniae strain CG43 (ST86) chromosome lacking KPN_01464 to K....”
- “...harboring KPN_01464 showed that CG43 contained a 10 kbp deletion resulting in the loss of KPN_01464. This deletion was replicated in the K. africana 200023T genome and the remaining 12 K. pneumoniae genomes that lacked KPN_01464 (33.24% identity for the best bidirectional BLASTP hit, no alternate...”
ABD05_RS31940 acetylornithine deacetylase from Burkholderia pyrrocinia
24% identity, 85% coverage
A6TC94 Succinyl-diaminopimelate desuccinylase from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
24% identity, 66% coverage
NP_384531 PROBABLE SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE PROTEIN from Sinorhizobium meliloti 1021
27% identity, 54% coverage
LMOf6854_0278 peptidase, M20/M25/M40 family from Listeria monocytogenes str. 1/2a F6854
26% identity, 66% coverage
LSA0220_c Succinyl-diaminopimelate desuccinylase from Lactobacillus sakei subsp. sakei 23K
25% identity, 76% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...LSA1689 lsa1689 Putative peptidase M20 family 1.0 1.1 Metabolism of amino acids and related molecules LSA0220_c dapE Succinyl-diaminopimelate desuccinylase -1.4 -1.5 LSA0316 sdhB L-serine dehydratase, beta subunit (L-serine deaminase) -0.7 LSA0370* arcA Arginine deiminase (arginine dihydrolase) 1.9 LSA0372* arcC Carbamate kinase 0.5 LSA0463 lsa0463 Putative 2-hydroxyacid...”
AO090010000540 uncharacterized protein from Aspergillus oryzae RIB40
29% identity, 67% coverage
LMRG_02611 hypothetical protein from Listeria monocytogenes 10403S
26% identity, 66% coverage
blr5449 blr5449 from Bradyrhizobium japonicum USDA 110
25% identity, 83% coverage
MsgB / b2472 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
dapE / P0AED7 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Escherichia coli (strain K12) (see paper)
DAPE_ECOLI / P0AED7 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Escherichia coli (strain K12) (see paper)
dapE / RF|NP_416967 succinyl-diaminopimelate desuccinylase; EC 3.5.1.18 from Escherichia coli K12 (see 7 papers)
b2472 succinyl-diaminopimelate desuccinylase from Escherichia coli str. K-12 substr. MG1655
S2665 N-succinyl-diaminopimelate deacylase from Shigella flexneri 2a str. 2457T
24% identity, 68% coverage
- function: Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminopimelate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso- diaminopimelic acid, an essential component of bacterial cell walls.
catalytic activity: N-succinyl-(2S,6S)-2,6-diaminopimelate + H2O = (2S,6S)-2,6- diaminopimelate + succinate (RHEA:22608)
cofactor: Zn(2+) Co(2+) (Binds 2 Zn(2+) or Co(2+) ions per subunit.)
subunit: Homodimer. - Escherichia coli Strains Producing Selected Bacteriocins Inhibit Porcine Enterotoxigenic Escherichia coli (ETEC) under both In Vitro and In Vivo Conditions
Hrala, Applied and environmental microbiology 2021 (secret) - Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...HVO_1099 dapD yes 32% b0166 P0A9D8 [ 141 ] 6365916 2a HVO_1096 dapE yes 29% b2472 P0AED7 [ 142 ] 3276674 function supported by gene clustering 2a HVO_1097 dapF yes 35% b3809 P0A6K1 [ 143 ] 6378903 2a HVO_1098 lysA yes 38% b2838 P00861 [ 144...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...b0179 b0031 b0131, b0133, b0134 b0073 b0087 b0181 b0166 b0142, b0154, b0159 b0074 b0088 b0182 b2472 b0173, b0174, b0369 b3770 b0090 b0524 b2478 b0414, b0415, b0417 b3771 b0091 b0914 b2838 b0420, b0421, b0423 b3774 b0954 b0915 b3359 b0475, b0750, b0907 b1093 b0918 b3433 b1096, b1208, b1210...”
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...dapD yes 32% b0166 P0A9D8 [ 141 ] 6365916 2a HVO_1096 dapE yes 29% b2472 P0AED7 [ 142 ] 3276674 function supported by gene clustering 2a HVO_1097 dapF yes 35% b3809 P0A6K1 [ 143 ] 6378903 2a HVO_1098 lysA yes 38% b2838 P00861 [ 144 ]...”
- Fermented beetroot modulates gut microbial carbohydrate metabolism in prediabetes and prevents high-fat diet induced hyperglycemia in a prediabetic model
Daliri, Current research in food science 2025 (no snippet) - Antibacterial and antibiofilm activities and mechanisms of <i>Toona sinensis</i> extracts against <i>Bacillus cereus</i> and its application in milk
Wei, Current research in food science 2025 (no snippet) - Investigating the interaction between tangeretin metabolism and amelioration of gut microbiota disorders using dextran sulfate sodium-induced colitis and antibiotic-associated diarrhea models
Xu, Current research in food science 2025 (no snippet) - A novel bacteriocin against multiple foodborne pathogens from Lacticaseibacillus rhamnosus isolated from juice ferments: ATF perfusion-based preparation of viable cells, characterization, antibacterial and antibiofilm activity
Chen, Current research in food science 2023 (secret)
7lgpB / P0AED8 Dape enzyme from shigella flexneri
24% identity, 68% coverage
Z3730 N-succinyl-diaminopimelate deacylase from Escherichia coli O157:H7 EDL933
24% identity, 68% coverage
HVO_1096 Peptidase M20-M25-M40 superfamily from Haloferax volcanii DS2
30% identity, 65% coverage
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...140 ] 7893644 2a HVO_1099 dapD yes 32% b0166 P0A9D8 [ 141 ] 6365916 2a HVO_1096 dapE yes 29% b2472 P0AED7 [ 142 ] 3276674 function supported by gene clustering 2a HVO_1097 dapF yes 35% b3809 P0A6K1 [ 143 ] 6378903 2a HVO_1098 lysA yes 38%...”
- “...14343156 2a HVO_A0634 - unknown 25% b2472 P0AED7 [ 142 ] 3276674 function assigned to HVO_1096 in dap cluster 2b HVO_0790 fba2 special 67% OE_1472F B0R334 [ 145 ] 25216252 EC 2.2.1.10 activity of OE_1472F not yet confirmed in vitro 2b HVO_0790 (cont.) special 45% MJ0400...”
BMEII0268 SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE from Brucella melitensis 16M
27% identity, 64% coverage
Q3YZ81 Succinyl-diaminopimelate desuccinylase from Shigella sonnei (strain Ss046)
24% identity, 68% coverage
- Proteome based mapping and molecular docking revealed DnaA as a potential drug target against Shigella sonnei
Shahid, Saudi journal of biological sciences 2022 - “...biosynthesis Biosynthesis of secondary metabolites Microbial metabolism in diverse environments Biosynthesis of antibiotics Succinyl-diaminopimelate desuccinylase (Q3YZ81) ssn01230 ssn00300 ssn01100 ssn01120 Biosynthesis of amino acids Lysine biosynthesis Metabolic pathways Microbial metabolism in diverse environments Transketolase (Q3YZ88) ssn01200 ssn01230 ssn01100 ssn01110 ssn01120 ssn01130 ssn00030 Carbon metabolism Biosynthesis of...”
PMI1556 N-succinyl-diaminopimelate deacylase from Proteus mirabilis HI4320
25% identity, 66% coverage
- Proteus mirabilis and Urinary Tract Infections
Schaffer, Microbiology spectrum 2015 - “...- ( 87 ) pepQ PMI3551 proline peptidase + cr - ( 87 ) dapE PMI1556 N-succinyl-diaminopimelate deacylase + cr - ( 87 ) cmfA/cpsF PMI3190 colony migration factor (capsular polysaccharide) + cr + ( 57 , 63 ) ppaA PMI3600 P-type ATPase zinc transporter +...”
B0Y766 Probable carboxypeptidase AFUB_072730 from Aspergillus fumigatus (strain CBS 144.89 / FGSC A1163 / CEA10)
AFUA_6G06800 peptidase, putative from Aspergillus fumigatus Af293
25% identity, 79% coverage
- Assembly and disassembly of Aspergillus fumigatus conidial rodlets
Valsecchi, Cell surface (Amsterdam, Netherlands) 2019 - “...AFUB_064740 AFUA_4G07650 B0Y5V8 Peptidyl-prolyl cis-trans isomerase No 0.92 45.00 209 22.961 4038867 6.0 AFUB_072730 AFUA_6G06800 B0Y766 Probable carboxypeptidase Yes 0.58 25.90 440 46.377 3466967 5.7 AFUB_083440 AFUA_8G04120 B0YA52 Carboxypeptidase No 0.56 28.90 551 61.278 2966367 8.7 AFUB_059210 AFUA_5G11640 B0Y110 Secretory pathway protein Ssp120, putative Yes 0.64...”
- “...AFUB_087640 AFUA_7G01060 B0YBS2 Cysteine-rich secreted protein No 0.81 22.40 343 36.860 2169400 3.7 AFUB_072730 AFUA_6G06800 B0Y766 Probable carboxypeptidase Yes 0.58 25.90 440 46.377 1894433 3.7 AFUB_071360 AFUA_4G14205 B0Y546 Uncharacterized protein No 0.88 8.00 138 14.405 1737567 1.0 AFUB_046170 AFUA_3G02200 B0Y0H1 Uncharacterized protein No 0.89 17.20 192...”
- Assembly and disassembly of Aspergillus fumigatus conidial rodlets
Valsecchi, Cell surface (Amsterdam, Netherlands) 2019 - “...14.3 AFUB_064740 AFUA_4G07650 B0Y5V8 Peptidyl-prolyl cis-trans isomerase No 0.92 45.00 209 22.961 4038867 6.0 AFUB_072730 AFUA_6G06800 B0Y766 Probable carboxypeptidase Yes 0.58 25.90 440 46.377 3466967 5.7 AFUB_083440 AFUA_8G04120 B0YA52 Carboxypeptidase No 0.56 28.90 551 61.278 2966367 8.7 AFUB_059210 AFUA_5G11640 B0Y110 Secretory pathway protein Ssp120, putative Yes...”
- “...12.3 AFUB_087640 AFUA_7G01060 B0YBS2 Cysteine-rich secreted protein No 0.81 22.40 343 36.860 2169400 3.7 AFUB_072730 AFUA_6G06800 B0Y766 Probable carboxypeptidase Yes 0.58 25.90 440 46.377 1894433 3.7 AFUB_071360 AFUA_4G14205 B0Y546 Uncharacterized protein No 0.88 8.00 138 14.405 1737567 1.0 AFUB_046170 AFUA_3G02200 B0Y0H1 Uncharacterized protein No 0.89 17.20...”
GSTUM_00002523001 uncharacterized protein from Tuber melanosporum
D5G797 (Perigord truffle) hypothetical protein from Tuber melanosporum (strain Mel28)
24% identity, 79% coverage
- Proteins from Tuber magnatum Pico fruiting bodies naturally grown in different areas of Italy
Vita, Proteome science 2013 - “...Whole genome shotgun sequence assembly, scaffold_131, strain Mel28 104 4 78 46,2 6,2 5,82 2 GSTUM_00002523001 Aminoacylase ACY1 Peptidase M20 A 2 D5GJY5 T. melanosporum (Perigord truffle) Whole genome shotgun sequence assembly, scaffold_55, strain Mel28 378 11 162 86,3 5,4 5,16 7 GSTUM_00009270001 Ultrahigh sulfur keratin-associated...”
- Proteins from Tuber magnatum Pico fruiting bodies naturally grown in different areas of Italy
Vita, Proteome science 2013 - “...Tuber Gene annotation (h) KOG Definition (i) PFAM Definition (l) Protein Blast relation (m) 1 D5G797 T. melanosporum (Perigord truffle) Whole genome shotgun sequence assembly, scaffold_131, strain Mel28 104 4 78 46,2 6,2 5,82 2 GSTUM_00002523001 Aminoacylase ACY1 Peptidase M20 A 2 D5GJY5 T. melanosporum (Perigord...”
TM0129 carboxypeptidase G2, putative from Thermotoga maritima MSB8
26% identity, 90% coverage
BAB2_0993 ArgE/dapE/ACY1/CPG2/yscS:Peptidase M20/M25/M40:Proteobacterial succinyl-diaminopimelate desuccinylase from Brucella melitensis biovar Abortus 2308
26% identity, 64% coverage
MXAN_1012 acetylornithine deacetylase from Myxococcus xanthus DK 1622
25% identity, 78% coverage
F9UPP5 Probable succinyl-diaminopimelate desuccinylase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
25% identity, 82% coverage
DAPE_SALTY / Q8ZN75 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; Aspartyl peptidase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
STM2483 N-succinyl-diaminopimelate deacylase from Salmonella typhimurium LT2
25% identity, 68% coverage
- function: Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminopimelate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso- diaminopimelic acid, an essential component of bacterial cell walls. Can also hydrolyze all N-terminal Asp dipeptides except Asp-Pro. Asp- Ser is the best substrate, followed by Asp-Gly, Asp-Leu, and Asp-Cys.
catalytic activity: N-succinyl-(2S,6S)-2,6-diaminopimelate + H2O = (2S,6S)-2,6- diaminopimelate + succinate (RHEA:22608)
cofactor: Zn(2+) Co(2+) Mn(2+) (Binds 2 divalent cations per subunit, one with high affinity and the other with lower affinity. Zn(2+) and/or Co(2+) ions are used for desuccinylase activity. The form of DapE active as a peptidase contains Zn(2+) in the high-affinity site and Mn(2+) in the low-affinity site.)
subunit: Homodimer. - Identifying essential genes in bacterial metabolic networks with machine learning methods
Plaimas, BMC systems biology 2010 - “...3-ketoacyl-(acyl-carrier-protein) reductase ** STM1200 tmk 2.7.4.9 Thymidylate kinase STM1700 fabI 1.3.1.10 Enoyl-(acyl carrier protein) reductase STM2483 dapE 3.5.1.18 Succinyl-diaminopimelate desuccinylase STM2652 pssA 2.7.8.8 Phosphatidylserine synthase * STM3090 metK 2.5.1.6 STM3415 rpoA 2.7.7.6 DNA-directed RNA polymerase subunit alpha STM3724 kdtA 3-deoxy-D-manno-octulosonic-acid transferase * STM3730 dfp 4.1.1.36 Pantothenate...”
P37111 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 3.5.1.14) from Sus scrofa (see 6 papers)
NP_999061 aminoacylase-1 from Sus scrofa
27% identity, 59% coverage
- Perspectives of aminoacylases in biocatalytic synthesis of N-acyl-amino acids surfactants
Haeger, Applied microbiology and biotechnology 2024 - “...number: WP_005693818); L-ACY-1, aminoacylase 1 from Heliothis virescens (GenBank: AET43034); pAcy1, porcine aminoacylase-1 (accession number: NP_999061); hAcy1, human aminoacylase-1 (accession number: NP_000657); PM20D1, human N-fatty-acyl-amino acid hydrolase (UniProt: Q6GTS8); MsAA, aminoacylase from Mycolicibacterium smegmatis MKD8 (GenBank: AWT55079); SmAA, aminoacylase from Streptomyces mobaraensis (GenBank: BAI44523); SamAA, aminoacylase...”
- Probing the acyl-binding pocket of aminoacylase-1.
Lindner, Biochemistry 2008 (PubMed)- GeneRIF: T347S variant of human Acy1 exhibited markedly increased catalytic efficiency against N-benzoylamino acids
- Probing the catalytic center of porcine aminoacylase 1 by site-directed mutagenesis, homology modeling and substrate docking.
Liu, Journal of biochemistry 2006 (PubMed)- GeneRIF: Based on site-directed mutagenesis, homology modeling and substrate docking studies, a revised catalytic mechanism for porcine metalloenzyme aminoacylase 1 has been proposed.
- Aspartate-induced aminoacylase folding and forming of molten globule.
Xie, The international journal of biochemistry & cell biology 2003 (PubMed)- GeneRIF: Apo-aminoacylase followed similar rules as Holo-enzyme, which suggested the zinc ion may play more important roles on activity other than structure
- Label-Free Quantitative Analysis of Pig Liver Proteome after Hepatitis E Virus Infection
Martino, Viruses 2024 - “...isoform X1 13 50.36 0.0008 2.24 A0A286ZZN9 GLMS glutamine-fructose-6-phosphate aminotransferase 1 13 58.72 0.0000 2.19 P37111 ACY1 aminoacylase-1 12 86.53 0.0009 2.34 Q6Q2C2 EPHX2 bifunctional epoxide hydrolase 2 12 54.89 0.0174 1.66 A0A286ZRS0 GSS glutathione synthetase 11 44.56 0.0071 1.91 P28839 LAP3 xaa-Pro dipeptidase 11 48.18...”
- iTRAQ-based quantitative proteomic analysis of longissimus muscle from growing pigs with dietary supplementation of non-starch polysaccharide enzymes.
Zhang, Journal of Zhejiang University. Science. B 2015
MW1943 ORFID:MW1943~hypothetical protein, similar to succinyl-diaminopimelate desuccinylase from Staphylococcus aureus subsp. aureus MW2
25% identity, 70% coverage
LLNZ_02765 M20 family metallopeptidase from Lactococcus cremoris subsp. cremoris NZ9000
24% identity, 92% coverage
SAV2006 hypothetical protein from Staphylococcus aureus subsp. aureus Mu50
25% identity, 71% coverage
SA1814 hypothetical protein from Staphylococcus aureus subsp. aureus N315
25% identity, 70% coverage
- Proteomic and Membrane Lipid Correlates of Reduced Host Defense Peptide
Kohler, Antibiotics (Basel, Switzerland) 2019 - “...in parent AdhE (SA0143) Acetaldehyde DH 1.46 (SA2367) Theoretical protein 1.044 Decreased in mutant DapE (SA1814) Lysine metabolism 1.021 (SA2366) Theoretical protein 1.051 AgrA (SA1844) Virulence regulator 1.287 Increased in mutant IlvA1 (SA1271) Threonine/serine dehydrase 4.17 Ald1 (SA1272) -amino acid dehydrogenase 1.667 Ddh (SA2312) D-lactate dehydrogenase...”
- Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus
Peng, mSphere 2017 - “...NWMN_1710 bsaE 9.5 ABC transporter protein: lantibiotic NWMN_1711 bsaF 8.6 ABC transporter protein: lantibiotic NWMN_1929 SA1814 dapE 9.5 Succinyl-diaminopimelate desuccinylase (dinuclear) NWMN_1949 SA1847 scrR 3.1 4.0 Sucrose operon repressor NWMN_2026 SA1924 11.3 Aldehyde dehydrogenase family NWMN_2043 SA1941 25.8 Dps; nonheme Fe-containing ferritin Yes (3.0) NWMN_2044 SA1942...”
- Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
Scherr, Infection and immunity 2013 - “...SA1401 SA1820 SA1596 SA1182 SA1435 SA1364 SA2553 SA1814 SA2303 SA1693 SA0655 SA1109 SA2635 SA1844 SA0308 SA2195 SA0921 SA1876 SA1309 Rhodanese-like domain...”
- Microarray analysis of toxicogenomic effects of ortho-phenylphenol in Staphylococcus aureus
Jang, BMC genomics 2008 - “...precursor (Peptidyl-prolyl cis-trans isomerase plp) (Rotamase plp) prs A Posttranslational modification, protein turnover, chaperones sa_c10591s11046_s_at SA1814 1.99E-05 -3.3 1.99E-05 -2.9 succinyl-diaminopimelate desuccinylase (dapE) Amino acid transport and metabolism sa_c5023s4322_at SA2082 6.38E-07 -3.5 6.38E-07 -5.5 urease gamma chain (urea amidohydrolase) ure A Amino acid transport and metabolism...”
- “...lys C)-SA1226 ( asd )-SA1227 ( dap A)-SA1228 ( dap B)-SA1229 ( dap D), and SA1814 ( dap E) fall within a predicted operon and are all involved in diaminopimelate (DAP) biosynthesis (table 1 ). The disruption of biosynthetic pathways involved in building up bacterial cell...”
- Global gene expression in Staphylococcus aureus biofilms
Beenken, Journal of bacteriology 2004 - “...to SA2490 Glycosyl transferase, group 1 100% ID to SA1814 97.9% protein ID to structure of cassette chromosome (SCC)-like element, stra 61.3% protein ID to...”
SAR2109 putative peptidase from Staphylococcus aureus subsp. aureus MRSA252
25% identity, 70% coverage
- Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung
Chaffin, PloS one 2012 - “...Another gene that was lower at 30 in vivo compared to in vitro conditions was SAR2109 ( dapE ), however, this gene maybe miss-annotated since it is more similar to a protease than an aspartate biosynthetic gene. The only anabolic AA synthesis gene expressed at high...”
- The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
Kenny, PloS one 2009 - “...3.17 6.97E-04 SAR1430 murG putative N-acetylglucosamine transferase 5.26 1.86E-03 SAR1761 lysP lysine-specific permease 2.07 3.01E-02 SAR2109 dapE putative succinyl-diaminopimelate desuccinylase 4.89 3.00E-03 SAR2188 murA1 putative carboxyvinyltransferase 2.94 6.54E-03 SAR2269 putative alanine racemase 2.64 1.78E-03 SAR2346 fmhB putative pentaglycine interpeptide biosynthesis protein 2.49 4.22E-03 SAR2394 putative protein...”
- “...was observed, which would function to maintain the level of constituents for the PG-pentapeptide precursor. SAR2109 ( dapE ), which catalyses the formation of a substrate for lysine biosynthesis and the lysine-specific permease SAR1761 ( lysP ) were up-regulated, and this would increase the pool of...”
lin0289 similar to succinyldiaminopimelate desuccinylase from Listeria innocua Clip11262
25% identity, 68% coverage
Dgeo_0366 peptidase M20 from Deinococcus geothermalis DSM 11300
25% identity, 73% coverage
- Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti
de, PLoS genetics 2009 - “...Dgeo_1389 (49) Deinococcus -specific Deide_19480 (133) upstream DR_2342 (99289) Dgeo_2141 (137) fur Deide_19965 (63) upstream Dgeo_0366 (63) Deinococcus -specific Deide_20690 (83) upstream DR_0433 (84) upstream Dgeo_0316 (82105) Deinococcus -specific Deide_1p01660 (346) Dgeo_2813 (920nt); not in Genbank; frameshift? mannonate dehydratase Deide_2p00970 (81) downstream Dgeo_1505 (78) Deinococcus-specific Deide_2p00990...”
SAUSA300_1976 probable succinyl-diaminopimelate desuccinylase from Staphylococcus aureus subsp. aureus USA300_FPR3757
25% identity, 70% coverage
NWMN_1929 succinyl-diaminopimelate desuccinylase from Staphylococcus aureus subsp. aureus str. Newman
25% identity, 66% coverage
SAOUHSC_02244 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
Q2FWN8 Probable succinyl-diaminopimelate desuccinylase from Staphylococcus aureus (strain NCTC 8325 / PS 47)
25% identity, 70% coverage
XP_804169 glutamamyl carboxypeptidase, putative from Trypanosoma cruzi
25% identity, 83% coverage
- Subcellular proteomics of Trypanosoma cruzi reservosomes
Sant'Anna, Proteomics 2009 - “...5 XP_811082 Metallophosphoesterase Y (2) 14 Ubiquitin hydrolase XP_821344 Protein deubiquitination N 15 Glutamamyl carboxypeptidase XP_804169 Metallopeptidase activity, proteolysis N 16 Peptidase M20/M25/M40 XP_813635 Metallopeptidase activity N 17 Chagasin 2FO8 Cysteine Protease Inhibitor N (2) Endosomal/lysosomal membrane proteins 18 Golgi/lysosome glycoprotein XP_817916 Golgi/lysosome membrane protein Y...”
APL_1873 succinyl-diaminopimelate desuccinylase from Actinobacillus pleuropneumoniae L20
24% identity, 90% coverage
- Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis
Bello-Ortí, Veterinary research 2014 - “...APL_0222 Putative lipoprotein/NMB1162 precursor HS372_01892 APL_0133 Cys regulon transcriptional activator HS372_00988 APL_1295 Arginine repressor HS372_02252 APL_1873 Succinyl-diaminopimelate desuccinylase HS372_02064 APL_0036 hypothetical protein HS372_01893 APL_0134 hypothetical protein HS372_01521 APL_1320 Thiamine import ATP-binding protein ThiQ HS372_02387 APL_1059 Integrase core domain protein HS372_00061 APL_1207 prevent-host-death family protein HS372_00916 APL_0423...”
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...dehydratase large subunit 2 1.605 APL_1230 serB Phosphoserine phosphatase 1.438 APL_0620 aroG Phospho-2-dehydro-3-deoxyheptonate aldolase 1.428 APL_1873 dapE Succinyl-diaminopimelate desuccinylase 1.380 Biosynthesis of cofactors, prosthetic groups, and carriers APL_0207 Dxs 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) 1.555 APL_1461 menA 1,4-dihydroxy-2-naphthoateoctaprenyltransferase 1.631 APL_0382 ribD Riboflavin biosynthesis protein 1.726 APL_1408 gshA Glutathione...”
A7ML83 Acetylornithine deacetylase from Cronobacter sakazakii (strain ATCC BAA-894)
26% identity, 72% coverage
KPN_04246 acetylornithine deacetylase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
24% identity, 85% coverage
- A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
Hawkey, Genome research 2022 - “...lacking this region, with occasional reacquisition in some lineages. Unlike the KPN_03428 deletion, deletion of KPN_04246 resulted in predicted loss-of-growth phenotypes for all 145 substrates for the single K. africana strain plus 13 of 20 K. pneumoniae strains (comprising multiple distantly related lineages including representatives of...”
- “...145 substrates for between one and 14 strains each. In two cases (genes KPN_03428 and KPN_04246), the impacted strains were missing redundant genes that were present in the MGH78578 reference modelthat is, those encoding proteins with the same functional annotation as the deleted gene. Comparisons of...”
Pnuc_1459 succinyl-diaminopimelate desuccinylase from Polynucleobacter sp. QLW-P1DMWA-1
24% identity, 68% coverage
BB2360 putative peptidase from Bordetella bronchiseptica RB50
26% identity, 59% coverage
EB835_02985 acetylornithine deacetylase from Brevibacterium sp. S22
25% identity, 80% coverage
- Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment
Anast, Scientific reports 2019 - “...[92], EB835_13560 HinG EC 3.5.1.8 amidase (AWA45228) 43 [98], EB834_09805 42 [98], EB836_03650 40 [97], EB835_02985 HinH amidase (AWA45227) 48 [100], EB834_10875 50 [100], EB836_11500 48 [100], EB835_13575 HinI aspartate ammonia-lyase EC 4.3.1.1 (AWA45233) 56 [98], EB834_10895 56 [96], EB836_11520 54 [97], EB835_13555 HinL enamine deaminase...”
BPP1295 putative peptidase from Bordetella parapertussis 12822
26% identity, 59% coverage
SGGMMB4_05195 acetylornithine deacetylase from Sodalis glossinidius str. 'morsitans'
27% identity, 70% coverage
CPZ21_10715 ArgE/DapE family deacylase from Staphylococcus epidermidis
22% identity, 81% coverage
F1613_RS03870 ArgE/DapE family deacylase from Staphylococcus epidermidis
23% identity, 81% coverage
- Genome-wide transcription response of Staphylococcus epidermidis to heat shock and medically relevant glucose levels
Benjamin, Frontiers in microbiology 2024 - “...(PTS lactose/cellobiose transporter subunit IIA), F1613_RS11905 (lactose-specific PTS transporter subunit EIIC), lacG ), vraX , F1613_RS03870 (ArgE/DapE family deacylase), cytochrome ubiquinol oxidase subunits I and II (F1613_RS06745 and F1613_RS06750), F1613_RS01555 (MarR family transcription regulator), F1613_RS12445 (hypothetical protein), F1613_RS01550 (NAD(P)/FAD-dependent oxidoreductase), and F1613_RS03780 (MFS transporter) ( Supplementary...”
EB834_09805 acetylornithine deacetylase from Brevibacterium aurantiacum
25% identity, 80% coverage
- Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment
Anast, Scientific reports 2019 - “...[92], EB834_10890 60 [94], EB836_11515 61 [92], EB835_13560 HinG EC 3.5.1.8 amidase (AWA45228) 43 [98], EB834_09805 42 [98], EB836_03650 40 [97], EB835_02985 HinH amidase (AWA45227) 48 [100], EB834_10875 50 [100], EB836_11500 48 [100], EB835_13575 HinI aspartate ammonia-lyase EC 4.3.1.1 (AWA45233) 56 [98], EB834_10895 56 [96], EB836_11520...”
SERP2364 peptidase, M20/M25/M40 family from Staphylococcus epidermidis RP62A
22% identity, 81% coverage
F9URV7 Succinyl-diaminopimelate desuccinylase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
21% identity, 80% coverage
Bbr_1738 succinyl-diaminopimelate desuccinylase from Bifidobacterium breve UCC2003
27% identity, 59% coverage
PMI_RS16000 acetylornithine deacetylase from Proteus mirabilis HI4320
PMI3236 acetylornithine deacetylase from Proteus mirabilis HI4320
24% identity, 83% coverage
BLJ_1831 succinyl-diaminopimelate desuccinylase from Bifidobacterium longum subsp. longum JDM301
27% identity, 59% coverage
- Adaptational changes in physiological and transcriptional responses of Bifidobacterium longum involved in acid stress resistance after successive batch cultures
Wei, Microbial cell factories 2019 - “...after acid challenge. The l -lysine biosynthesis via DAP pathway (BLJ_0147, BLJ_0149, BLJ_0489, BLJ_1832, BLJ_1564, BLJ_1831, BLJ_1383 and BLJ_1843) was activated in JDM301AR (Additional file 2 ). During the process, the homologs of diaminopimelate decarboxylase (BLJ_1843, Log 2 FC=1.6) were shown to specifically catalyze the decarboxylation...”
- “...DAP pathway in parental strain, only 7 genes (BLJ_0147, BLJ_0149, BLJ_0489, BLJ_0490, BLJ_1299, BLJ_1383 and BLJ_1831) were upregulated after exposure to acid stress and the expression of BLJ_1843 was not changed (Additional file 2 ). The number of upregulated genes associated with amino acid metabolism in...”
A4I4L8 Putative glutamamyl carboxypeptidase from Leishmania infantum
27% identity, 72% coverage
Sant_3958 acetylornithine deacetylase from Sodalis praecaptivus
27% identity, 70% coverage
ABZR86_RS08710 N-acetylcitrulline deacetylase (EC 3.5.1.-) from Dyella japonica UNC79MFTsu3.2
24% identity, 72% coverage
- mutant phenotype: Important for fitness in most defined media, except when arginine is provided. 70% identical to argE�� from Xanthomona campestris (Q8P8J5), which is active on both N-acetylornithine and N-acetylcitrulline. But only the N-acetylcitrulline activity is expected to be relevant (see N-acetylornithine carbamoyltransferase N515DRAFT_3763)
O34984 Uncharacterized metallohydrolase YodQ from Bacillus subtilis (strain 168)
24% identity, 63% coverage
EB836_03650 acetylornithine deacetylase from Brevibacterium sp. S111
25% identity, 80% coverage
- Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment
Anast, Scientific reports 2019 - “...[94], EB836_11515 61 [92], EB835_13560 HinG EC 3.5.1.8 amidase (AWA45228) 43 [98], EB834_09805 42 [98], EB836_03650 40 [97], EB835_02985 HinH amidase (AWA45227) 48 [100], EB834_10875 50 [100], EB836_11500 48 [100], EB835_13575 HinI aspartate ammonia-lyase EC 4.3.1.1 (AWA45233) 56 [98], EB834_10895 56 [96], EB836_11520 54 [97], EB835_13555...”
ECO26_3961 putative peptidase from Escherichia coli O26:H11 str. 11368
25% identity, 81% coverage
YgeY / b2872 putative peptidase YgeY from Escherichia coli K-12 substr. MG1655 (see 3 papers)
NP_417348 putative peptidase YgeY from Escherichia coli str. K-12 substr. MG1655
P65807 Uncharacterized protein YgeY from Escherichia coli (strain K12)
b2872 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
25% identity, 81% coverage
- Response and adaptation of Escherichia coli to suppression of the amber stop codon
Wang, Chembiochem : a European journal of chemical biology 2014 - “...NP_415449 OmpF 0.27 NP_417573 YqjG 2.01 NP_417950 PitA 0.27 NP_417079 YfiQ 2.03 NP_418593 Hfq 0.32 NP_417348 YgeY 2.05 NP_418476 DnaB 0.32 NP_417432 AnsB 2.08 NP_417887 GlgA[ c ] 0.34 NP_414978 QueC 2.09 NP_415335 OmpX 0.34 NP_416476 HchA 2.11 NP_417875 MalQ[ c ] 0.34 NP_418222 IlvC 2.14...”
- Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange
Paerl, mBio 2023 - “...X X P94575 X Escherichia coli K-12 (taxid:83333) P30137 (3.8E-20) P30136 P76423 (2.4E-16) X X P65807 (4.5E-19) P31550 X X X X P75712 (4.82E-116) X R. pomeroyi DSS-3 (taxid:246200) Q5LWJ0 (4.5E-24) X X Q5LWK6 (5.6E-19) Q5LWK6 (1.0E-17) Q5LWK6 (4.6E-20) Q5LWK6 (2.6E-10) Q5LPN6 (6.9E-15) X Q5LWK7 (1.39E-39)...”
- A widely distributed gene cluster compensates for uricase loss in hominids
Liu, Cell 2023 - “...(b2871) -red recombination knockout F: CCCTCTATTTCCAGAGGCCAAAAGGATAGGATATGG TGTAGGCTGGAGCTGCTTC R: TTCCAATAGGGTGATTAAGGTGCTACAGCGTGTTTC CATATGAATATCCTCCTTAGT Integrated DNA technologies N/A ygeY (b2872) -red recombination knockout F: AAAACGGGGAGTAAAAAATCTGGAGAAAAATAATGG TGTAGGCTGGAGCTGCTTC R: GCCCATGATAGATACGCCGTTAGTTGAGAAGGTCC CCATATGAATATCCTCCTTAGT Integrated DNA technologies N/A hyuA (b2873) -red recombination knockout F: TCCGGTTCGCCGGAGGGTTTTTGGAGTTTGCTATG GTGTAGGCTGGAGCTGCTTC R: ATCCCTGGCAGTGGTTAGAGCACGGGAGGGACAAA CCATATGAATATCCTCCTTAGT Integrated DNA technologies N/A ygfK (b2878)...”
- “...DNA technologies N/A ygeX (b2871) sequencing Ec.ygeX-CHF: GAGCGTACTGAATTGCTGCG Ec.ygeX-CHR: CGTACGGATCGAAGTCCCAG Integrated DNA technologies N/A ygeY (b2872) sequencing Ec.ygeY-CHF: TGAAGCACTACCGCGAAGTT Ec.ygeY-CHR: TCGTAACTGCGTTCGTCCAA Integrated DNA technologies N/A hyuA (b2873) sequencing Ec.hyuA-CHF: CTGAAGCGCATGCACCTAAC Ec.hyuA-CHR: TCAGTTTTTGCGGCAGCTTC Integrated DNA technologies N/A ygfK (b2878) sequencing Ec.ygfK-CHF: AGGCAATCCAACGACCCAAT Ec.ygfK-CHR: ATCGCGCTGATTGAGTAGGG Integrated DNA technologies...”
- The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
Frick-Cheng, mBio 2020 - “...allantoin transporter 6.7 b0511 ygeW Putative carbamoyltransferase YgeW 6.9 b2870 ygeY Putative peptidase YgeY 6.1 b2872 ygfK Putative oxidoreductase, Fe-S subunit 5.8 b2878 yhjX Putative pyruvate transporter 5.4 b3547 ylbE DUF1116 domain-containing protein YlbE 5.6 b4572 10.1128/mBio.01412-20.5 TABLES2 Genes differentially downregulated in human patients and mice....”
- Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
Haft, Biology direct 2008 - “...ygeX diaminopropionate ammonia-lyase 10 b2871 7 EF_2579 7 CD2085 ygeY hydrolase, peptidase M20 family 4 b2872 3 EF_2578 (CD2084) ygeZ phenyl-hydantoinase 19 b2873 (EF_2580) 6 pNG7258 yqeA carbamate kinase 18 b2874 15 EF_2575 yqeB SDMH accessory protein TIGR03309 1 b2875 2 EF_2563 1 pNG7241 1 CD3478...”
- Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage
Xi, Journal of bacteriology 2000 - “...search Possible function b2866 b2867 b2868 b2869 b2870 b2871 b2872 b2873 b2874 b2875 b2876 b2877 b2878 b2879 b2880 b2881 b2882 b2883 b2884 b2885 b2886 b2887...”
lysK / Q4JAP7 [amino group carrier protein]-lysine/ornithine hydrolase (EC 3.5.1.130; EC 3.5.1.132) from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (see paper)
Q4JAP7 [LysW]-lysine/[LysW]-ornithine hydrolase from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
Saci_0756 peptidase from Sulfolobus acidocaldarius DSM 639
24% identity, 95% coverage
P9WHS9 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Mycobacterium tuberculosis (see 2 papers)
Rv1202 succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis H37Rv
YP_177796 succinyl-diaminopimelate desuccinylase DapE from Mycobacterium tuberculosis H37Rv
25% identity, 95% coverage
- Comprehensive identification of β-lactam antibiotic polypharmacology inMycobacterium tuberculosis
Devlin, 2025 - Metabolomics reveals that the cAMP receptor protein regulates nitrogen and peptidoglycan synthesis in Mycobacterium tuberculosis
Liu, RSC advances 2020 - “...lysine and peptidoglycan, the tetrahydrodipicolinate N -succinyltransferase DapD (Rv1201c) and the probable succinyl-diaminopimelate desuccinylase dapE (Rv1202), the two enzymes responsible for upstream synthesis of DAP, showed mild upregulations (log 2 FC = 0.67 and 0.62, respectively) in M. tuberculosis crp , while the other enzymes in...”
- Data Intensive Genome Level Analysis for Identifying Novel, Non-Toxic Drug Targets for Multi Drug Resistant Mycobacterium tuberculosis
Kaur, Scientific reports 2017 - “...the rest did not have compatible template structure for modeling. Of these 12 targets, 9 (Rv1202, Rv1436, Rv3053c, Rv1017c, Rv0632c, Rv3600c, Rv3052c, Rv1385, Rv0868c) were highly druggable (DS Index=0.700.97), 2 were druggable (Rv1082, Rv1711; DS=0.650.68) and 1 was poorly druggable (Rv0763c; DS Index=0.21). There were no...”
- “...mutations all along the polypeptide chain in the 1623 clinical isolates. Genes viz., Rv1305, Rv2361c, Rv1202, Rv2193 , and Rv1436 have shown least number of mutations in the 1623 clinical isolates and some are also experimentally essential, which could emerge out to be highly potential drug...”
- Reconstruction of diaminopimelic acid biosynthesis allows characterisation of Mycobacterium tuberculosis N-succinyl-L,L-diaminopimelic acid desuccinylase
Usha, Scientific reports 2016 - “...L -DAP by DapE (E.C. 3.5.1.18) which in M. tuberculosis (MtDapE) is encoded by dapE (Rv1202). L , L -DAP is epimerized to meso -DAP by DAP epimerase (DapF). In the dehydrogenase pathway, L -THDP is directly reduced to meso -DAP by NADP + -linked meso...”
- “...Coventry, U.K. Construction of Mt dapE and Ec argD in pET28b The Mt dapE gene (Rv1202) and E. coli argD 33 , (an orthologue of dapC in E. coli which functions as a N -Succinyl- L , L -DAP aminotransferase) were amplified from M. tuberculosis H37Rv...”
- The cell envelope glycoconjugates of Mycobacterium tuberculosis
Angala, Critical reviews in biochemistry and molecular biology 2014 - “...the enzymes Ask (Rv3709c), Asd (Rv3708c), DapA (Rv2753c), DapB (Rv2773c), DapC (Rv0858c), DapD (Rv1201c), DapE (Rv1202) and DapF (Rv2726c). As in other bacteria, the fully assembled sugar-peptide moiety of the Parks nucleotide is then transferred to a lipid carrier by the phospho- N -acetylmuramyl pentapeptide translocase...”
- Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis
Reinhard, Acta crystallographica. Section F, Structural biology and crystallization communications 2012 - “...analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis Succinyl-diaminopimelate desuccinylase from Mycobacterium...”
- “...strain H37Rv DapE is encoded by open reading frame Rv1202 (Cole et al., 1998a,b). The enzyme DapE from Mtb (Mtb-DapE) consists of 354 amino acids, resulting in...”
- Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis.
Reinhard, Acta crystallographica. Section F, Structural biology and crystallization communications 2012 - GeneRIF: crystals of dapE belonged to the monoclinic space group P2(1), with unit-cell parameters a = 79.7, b = 76.0, c = 82.9 A, beta = 119 degrees
G2YT91 Similar to peptidase (Secreted protein) from Botryotinia fuckeliana (strain T4)
24% identity, 87% coverage
YP2675 succinyl-diaminopimelate desuccinylase from Yersinia pestis biovar Medievalis str. 91001
Q7CJI9 Succinyl-diaminopimelate desuccinylase from Yersinia pestis
23% identity, 69% coverage
CSP5_0815 M20 family metallo-hydrolase from Cuniculiplasma divulgatum
26% identity, 67% coverage
- Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum
Bargiela, Microorganisms 2020 - “...cleavage system T protein/aminomethyltransferase, CSP5_2011, 1.35-fold), glycine synthesis (glycine hydroxymethyltransferase, CSP5_0506, 1.24-fold) and lysine metabolism (CSP5_0815, succinyl-diaminopimelate desuccinylase, 1.16-fold) were detected to be overexpressed as well ( Table S1 , Figure 3 ). Additionally, glutamine (CSP5_0284, 1.38-fold) and glutamate (CSP5_0381, 1.14-fold) synthetases, 4-aminobutyrate aminotransferase (CSP5_0018, 1.31-fold),...”
EHI_114340, XP_649738 acetylornithine deacetylase, putative from Entamoeba histolytica HM-1:IMSS
24% identity, 75% coverage
STM14_4955 acetylornithine deacetylase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM4120 acetylornithine deacetylase from Salmonella typhimurium LT2
24% identity, 88% coverage
ArgE / b3957 acetylornithine deacetylase (EC 3.5.1.16) from Escherichia coli K-12 substr. MG1655 (see 6 papers)
argE / P23908 acetylornithine deacetylase (EC 3.5.1.16) from Escherichia coli (strain K12) (see 5 papers)
ARGE_ECOLI / P23908 Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 from Escherichia coli (strain K12) (see 2 papers)
b3957 acetylornithine deacetylase from Escherichia coli str. K-12 substr. MG1655
NP_418392 acetylornithine deacetylase from Escherichia coli str. K-12 substr. MG1655
25% identity, 71% coverage
- function: Catalyzes the hydrolysis of the amide bond of N(2)-acetylated L-amino acids. Cleaves the acetyl group from N-acetyl-L-ornithine to form L-ornithine, an intermediate in L-arginine biosynthesis pathway, and a branchpoint in the synthesis of polyamines.
catalytic activity: N(2)-acetyl-L-ornithine + H2O = L-ornithine + acetate (RHEA:15941)
cofactor: Zn(2+) Co(2+) (Binds 2 Zn(2+) or Co(2+) ions per subunit.)
cofactor: glutathione
subunit: Homodimer. - Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris
Pechter, Journal of bacteriology 2015 - “...RPA3834 RPA4270 RPA4309 hisG ilvC idh thrB serC b3735 b2818 b3957 b2019 b3774 b1136 b0003 b0907 atpH argA argE hisG ilvC icd thrB serC ATP synthase F0F1 subunit...”
- A system-level model for the microbial regulatory genome
Brooks, Molecular systems biology 2014 - “...PurR MetR 512157 b3829 b3959 0.934393 MetR ArgR 512157;554056 b2913 b3941 0.932025 PurR MetR 512157 b3957 b3941 0.931565 ArgR MetR 512157;554056 b3172 b3829 0.930382 ArgR MetR 512157;554056 b2913 b3774 0.927776 PurR IlvY 512157;512477 b3941 b3774 0.927251 MetR IlvY 512157 b3960 b3941 0.921375 ArgR MetR 512157;554056 b3941...”
- Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
Cortés-Tolalpa, Microbial cell factories 2014 - “...N-acetylglutamylphosphate reductase Amino acid metabolism 53.4932 argD b3359 N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase Amino acid metabolism 21.9053 argE b3957 Acetylornithine deacetylase Amino acid metabolism 18.7485 argG b3172 Argininosuccinate synthase Amino acid metabolism 65.2192 argH b3960 Argininosuccinate lyase Amino acid metabolism 23.7859 argI b4254 Ornithine carbamoyltransferase chain I Amino acid...”
- Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains
Lennen, Applied and environmental microbiology 2014 - “...2.37 2.24 2.23 2.19 2.19 2.14 2.13 2.09 BL21(DE3) b3957 b2735 b4113 b2678 b4112 b3336 b3934 b0607 b3581 b2601 b4000 b2096 b2330 b2029 b4293 b2094 b2679 b0462...”
- Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models
Hamilton, Biophysical journal 2013 - “...glmS Lethal Lethal Nonlethal Lethal Nonlethal Nonlethal b3957 argE Lethal Lethal Nonlethal Lethal Nonlethal Lethal b3958 argC Lethal Lethal Nonlethal Lethal...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...b0945, b1062 b2942 b2818 b3018 b1094 b1131, b1281 b3939 b3172 b4041 b2316 b2312, b2476 b4013 b3957 b4160 b2323 b2499, b2507 s0001 b3958 b3255 b2557, b2780 b3959 b3256 b3642, b4005 b3960 b4006, b4177 s0001 b4244, b4245 SS NSP CAC GSM TTPM TIM genes b0639 b0720 b0907 b0908,...”
- Experimental and computational assessment of conditionally essential genes in Escherichia coli
Joyce, Journal of bacteriology 2006 - “...Amino acid metabolism ....................................... argA (b2818) argE (b3957) argH (b3960) aroA (b0908) aroB (b3389) aroC (b2329) aroD (b1693) aroE...”
- Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays
Winterberg, Applied and environmental microbiology 2005 - “...b0073 b2599 b3772 b3774 b4388 b0842 b3008 b3520 b3957 81170 2735838 3953883 3956841 4622451 883043 3150839 3669108 4151699 b Bottom strandc Distance (bp)d...”
- More
- Response and adaptation of Escherichia coli to suppression of the amber stop codon
Wang, Chembiochem : a European journal of chemical biology 2014 - “...NP_417479 ExbB 0.15 NP_415278 GalK 0.46 NP_416719 OmpC 0.19 NP_415280 GalE 0.47 NP_415772 OmpW 0.20 NP_418392 ArgE 0.47 NP_418232 WzzE[ c ] 0.21 NP_418392 ArgE 0.48 NP_415895 OmpN 0.27 NP_417616 YraM 0.49 NP_415085 NmpC 0.27 NP_418258 UvrD 2.00 NP_415449 OmpF 0.27 NP_417573 YqjG 2.01 NP_417950 PitA...”
- Structural characterization of Zn(II)-, Co(II)-, and Mn(II)-loaded forms of the argE-encoded N-acetyl-L-ornithine deacetylase from Escherichia coli.
Tao, Journal of inorganic biochemistry 2012 - GeneRIF: Data suggest the Zn(II), Co(II), and Mn(II) bind to N-acetyl-l-ornithine deacetylase (ArgE) in a cooperative manner.
- [Studies on the expression, purification and renaturation of recombinant N-acety-L-ornithine deacetylase].
Li, Sheng wu gong cheng xue bao = Chinese journal of biotechnology 2007 (PubMed)- GeneRIF: Data show that most N-acety-L-ornithine deacetylase(NAOase) was expressed as inclusion bodies.
- The Role of Propionate-Induced Rearrangement of Membrane Proteins in the Formation of the Virulent Phenotype of Crohn's Disease-Associated Adherent-Invasive Escherichia coli
Pobeguts, International journal of molecular sciences 2024 - “...194 10.14 1.32 Protein kinase P0ACY3 serine/threonine protein kinase YeaG 3.26 0.42 Diacylation of substrates P23908 acetylornithine deacetylase ArgE 105 1.90 0.26 Catabolism of short chain fatty acids P36683 Aconitate hydratase B AcnB 265 12.40 1.61 Reversible interconversion of acetyl-CoA and acetyl phosphate P0A9M8 phosphate acetyltransferase...”
- Perspectives of aminoacylases in biocatalytic synthesis of N-acyl-amino acids surfactants
Haeger, Applied microbiology and biotechnology 2024 - “...carboxypeptidase G2 from Pseudomonas sp. RS-16 (UniProt_P06621); ArgE, acetylornithine deacetylase from E. coli (UniProt : P23908); HiDapE, succinyl-diaminopimelate desuccinylase from Haemophilus influenzae (accession number: WP_005693818); L-ACY-1, aminoacylase 1 from Heliothis virescens (GenBank: AET43034); pAcy1, porcine aminoacylase-1 (accession number: NP_999061); hAcy1, human aminoacylase-1 (accession number: NP_000657); PM20D1,...”
- Label-free quantification of host cell protein impurity in recombinant hemoglobin materials
Henrion, Analytical and bioanalytical chemistry 2024 - “...co-purified, if using IMAC for cleanup. Particularly, YfbG (P77398), YodA (P76344), GlmS (P17169), and ArgE (P23908) correspond to proteins previously reported in this context [ 13 ]. They make up a fraction of 6070% (orange in Fig. 3 B) in the studied materials, but represent only...”
ACY1 / Q03154 aminoacylase 1 monomer (EC 3.5.1.14) from Homo sapiens (see 7 papers)
ACY1_HUMAN / Q03154 Aminoacylase-1; ACY-1; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14 from Homo sapiens (Human) (see 5 papers)
Q03154 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 3.5.1.14) from Homo sapiens (see 4 papers)
NP_000657 aminoacylase-1 isoform a from Homo sapiens
25% identity, 60% coverage
- function: Catalyzes the hydrolysis of N-acetylated amino acids to acetate and free amino acids.
catalytic activity: an N-acyl-L-amino acid + H2O = an L-alpha-amino acid + a carboxylate (RHEA:15565)
catalytic activity: N(alpha)-acetyl-L-methionine + H2O = L-methionine + acetate (RHEA:67440)
catalytic activity: N-acetyl-L-glutamine + H2O = L-glutamine + acetate (RHEA:67368)
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
subunit: Homodimer. Interacts with SPHK1 (By similarity). - Perspectives of aminoacylases in biocatalytic synthesis of N-acyl-amino acids surfactants
Haeger, Applied microbiology and biotechnology 2024 - “...Heliothis virescens (GenBank: AET43034); pAcy1, porcine aminoacylase-1 (accession number: NP_999061); hAcy1, human aminoacylase-1 (accession number: NP_000657); PM20D1, human N-fatty-acyl-amino acid hydrolase (UniProt: Q6GTS8); MsAA, aminoacylase from Mycolicibacterium smegmatis MKD8 (GenBank: AWT55079); SmAA, aminoacylase from Streptomyces mobaraensis (GenBank: BAI44523); SamAA, aminoacylase from Streptomyces ambofaciens ATCC 23877 (GenBank:...”
- LncRNA MAGI2-AS3 inhibits tumor progression and angiogenesis by regulating ACY1 via interacting with transcription factor HEY1 in clear cell renal cell carcinoma.
Wang, Cancer gene therapy 2022 (PubMed)- GeneRIF: LncRNA MAGI2-AS3 inhibits tumor progression and angiogenesis by regulating ACY1 via interacting with transcription factor HEY1 in clear cell renal cell carcinoma.
- Aminoacylase 1 (ACY-1) Mediates the Proliferation and Migration of Neuroblastoma Cells in Humans Through the ERK/Transforming Growth Factor β (TGF-β) Signaling Pathways.
Chen, Medical science monitor : international medical journal of experimental and clinical research 2021 - GeneRIF: Aminoacylase 1 (ACY-1) Mediates the Proliferation and Migration of Neuroblastoma Cells in Humans Through the ERK/Transforming Growth Factor beta (TGF-beta) Signaling Pathways.
- Identification and clinical significance of an elevated level of serum aminoacylase-1 autoantibody in patients with hepatitis B virus-related liver cirrhosis.
He, Molecular medicine reports 2016 (PubMed)- GeneRIF: with the elevated level in the disease progression of Chronic hepatitis B (CHB), ACY1 autoantibody may be a valuable serum biomarker for discriminating HBVrelated liver cirrhosis from CHB.
- Aminoacylase I deficiency due to ACY1 mRNA exon skipping.
Ferri, Clinical genetics 2014 (PubMed)- GeneRIF: Biochemical analysis showed absence of ACY1 enzyme activity in the patient's fibroblasts.
- Proteomics-based identification of the tumor suppressor role of aminoacylase 1 in hepatocellular carcinoma.
Wei, Cancer letters 2014 (PubMed)- GeneRIF: ACY1 acts as a tumor suppressor in hepatocellular carcinoma.
- Overexpression of aminoacylase 1 is associated with colorectal cancer progression.
Shi, Human pathology 2013 (PubMed)- GeneRIF: We concluded that ACY1 expression in colorectal cancer varies with stage and appears to play a role in cell proliferation and apoptosis
- Serum aminoacylase-1 is a novel biomarker with potential prognostic utility for long-term outcome in patients with delayed graft function following renal transplantation.
Welberry, Kidney international 2013 - GeneRIF: Report serum aminoacylase-1 as a novel biomarker with potential prognostic utility for long-term outcome in renal transplant recipients with delayed graft function.
- More
- Future of non-invasive graft evaluation: A systematic review of proteomics in kidney transplantation.
Avramidou, World journal of transplantation 2025 - “...Secreted Urine Elevated CCL2 MMP7 P09237 Secreted, extracellular space, extracellular matrix Urine Elevated MMP7 Aminoacylase-1 Q03154 Cytoplasm Serum Elevated ACY1 Chitinase-3-like protein 1 P36222 Cytoplasm, endoplasmic reticulum, secreted Urine Elevated CHI3 L1 Protein AMBP P02760 Extracellular region, secreted Plasma Elevated AMBP Alpha-1-acid glycoprotein 2 P19652 Extracellular...”
- Serum protein risk stratification score for diagnostic evaluation of metabolic dysfunction-associated steatohepatitis.
Lai, Hepatology communications 2024 - “...SL006713 Collectin-11 Collectin Kidney 1 COLEC11 Q9BWP8 2.24E05 0.0033 2.81 2.35 SL005574 Aminoacylase-1 Aminoacylase-1 ACY1 Q03154 1.44E06 0.0008 2.26 2.30 SL000528 NADPH--cytochrome P450 reductase NADPH-P450 Oxidoreductase POR P16435 2.18E04 0.0107 1.74 1.94 SL003179 Integrin alpha-I: beta-1 complex Integrin a1b1 ITGA1 ITGB1 P56199, P05556 2.69E05 0.0034 1.98...”
- Proteome-Wide Genetic Investigation of Large Artery Stiffness.
Dib, JACC. Basic to translational science 2024 - “...regulation Q9BQB4 SOST Sclerostin Vascular calcification, Vascular remodeling P05062 ALDOB Fructose-bisphosphate aldolase B Vascular remodeling Q03154 ACY1 Aminoacylase-1 Collagen regulation and TGF-1/Smad3 signaling, glucose and insulin homeostasis P09467 FBP1 Fructose-1,6-bisphosphatase-1 Fibroblast cell regulation, angiogenesis regulation Q7Z3B1 NEGR1 Neuronal growth regulator-1 A cell adhesion molecule linked to...”
- Plasma Proteomic Risk Markers of Incident Type 2 Diabetes Reflect Physiologically Distinct Components of Glucose-Insulin Homeostasis.
Cronjé, Diabetes 2023 - Defining the serum proteomic signature of hepatic steatosis, inflammation, ballooning and fibrosis in non-alcoholic fatty liver disease.
Sanyal, Journal of hepatology 2023 - “...receptor ionotropic, delta-2 O43424 3.86 2.2e-04 CNDP1 Beta-Ala-His dipeptidase Q96KN2 3.62 5.0e-04 Inflammation ACY1 Aminoacylase-1 Q03154 12.12 2.2e-16 TXNRD1 Thioredoxin reductase 1, cytoplasmic Q16881 11.36 2.2e-16 FCGR3B Low affinity immunoglobulin gamma Fc region receptor III-B O75015 8.29 1.5e-15 PCOLCE2 Procollagen C-endopeptidase enhancer 2 Q9UKZ9 6.03 3.5e-09...”
- Proteomic Biomarkers of the Apnea Hypopnea Index and Obstructive Sleep Apnea: Insights into the Pathophysiology of Presence, Severity, and Treatment Response.
Cederberg, International journal of molecular sciences 2022 - “...Q7Z3B1 NEGR1 0.000225 0.018214 SEZ6L Q9BYH1 SEZ6L 0.00033 0.020777 TFPI P10646 TFPI 0.00033 0.029951 Aminoacylase-1 Q03154 ACY1 0.000471 0.075644 P5I11 O14683 TP53I11 0.001001 0.085686 GP116 Q8IZF2 ADGRF5 0.001001 0.051286 NAR3 Q13508 ART3 0.001001 0.033656 IGFBP-5 P24593 IGFBP5 0.001157 0.036965 IGFBP-2 P18065 IGFBP2 0.001182 0.056639 Agrin O00468...”
- Dissecting Regulators of Aging and Age-Related Macular Degeneration in the Retinal Pigment Epithelium.
Karunadharma, Oxidative medicine and cellular longevity 2022 - “...P18669 PGAM1 28.7/6.75 17 3 3 D23 0.0305 3,4 0.0266, 0.0887 I, A Aminoacylase 1 Q03154 ACY1 44.5/6.4 45.9/5.77 13 4 4 Spot number indicated on gel picture in Figure 2 right panel. 3 proteins identifications are listed in this table. The remaining spots are listed...”
- Proteome analysis of urinary biomarkers in a cigarette smoke-induced COPD rat model.
Qin, Respiratory research 2022 - “...member 2 2.73 Q08379 Q63678 Zinc-alpha-2-glycoprotein 2.68 None Q6AYR9 Tetraspanin-1 3.48 O60635 Q6AYS7 Aminoacylase-1A 0.44 Q03154 Q6IRK9 Carboxypeptidase Q 0.62 Q9Y646 Q6TUD4 Protein YIPF3 0.60 Q9GZM5 Q8VD89 Ribonuclease pancreatic gamma-type 5.01 None Q99J86 Attractin 3.02 O75882 Q9JHY1 Junctional adhesion molecule A 0.57 Q9Y624 Q9JI85 Nucleobindin-2 2.59...”
- More
B2FIC0 Succinyl-diaminopimelate desuccinylase from Stenotrophomonas maltophilia (strain K279a)
24% identity, 63% coverage
- Subtractive genomics and molecular docking approach to identify drug targets against Stenotrophomonas maltophilia
Saleem, PloS one 2021 - “...sml00640- Propanoate metabolism sml00620- Pyruvate metabolism Sml00061-Fatty acid biosynthesis sml01200- Carbon metabolism 25 Succinyl-diaminopimelate desuccinylase (B2FIC0) Sml00300- Lysine biosynthesis sml01100-Metabolic pathways sml01120-Microbial metabolism in diverse environments sml01230-Biosynthesis of amino acids 26 4-hydroxy-tetrahydrodipicolinate reductase (B2FQ70) Sml00300- Lysine biosynthesis sml01100-Metabolic pathways sml01120-Microbial metabolism in diverse environments sml01230-Biosynthesis of...”
BG05_RS20350 peptidase from Bacillus mycoides
23% identity, 79% coverage
DVU1827 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase family protein from Desulfovibrio vulgaris Hildenborough
24% identity, 65% coverage
8uw6B / P23908 Acetylornithine deacetylase from escherichia coli, di-zinc form. (see paper)
25% identity, 71% coverage
PH1153 hypothetical protein from Pyrococcus horikoshii OT3
24% identity, 72% coverage
B4DNW0 N-acyl-aliphatic-L-amino acid amidohydrolase from Homo sapiens
25% identity, 49% coverage
PSHAa2292 acetylornithine deacetylase (Acetylornithinase) (AO) (N-acetylornithinase) (NAO) from Pseudoalteromonas haloplanktis TAC125
23% identity, 89% coverage
- Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments
Perrin, Nature communications 2020 - “...0.11 Concerning MetJ regulon, we noticed a group of genes (including PSHAa2222, PSHAa2223, PSHAa0287 and PSHAa2292) whose expression values are negatively correlated with those of genes PSHAa2274-76 and PSHAa1226 (Fig. 3d ). This group of co-regulated genes include those involved in the conversion of homocysteine to...”
- “...PSHAa2223), an L-alanine-DL-glutamate epimerase (PSHAa0287) and a Methylthioribulose-1-phosphate dehydratase involved in the Met salvage pathway (PSHAa2292). Finally, as for TyrR1regulon, PSHAa2042-43, coding for 4a-hydroxytetrahydrobiopterin dehydratase and phenylalanine-4-hydroxylase are negatively correlated to the other genes in the same regulon (Fig. 3e ). PSHAa2043 encodes phhA the gene...”
- Modelling microbial metabolic rewiring during growth in a complex medium
Fondi, BMC genomics 2016 - “...genes Cluster name Motif name Genes Weblogo Cluster 2 ArgR PSHAa0194, PSHAa0698,PSHAa2175, PSHAa2287, PSHAa2290, PSHAa2291, PSHAa2292, PSHAb0333, PSHAb0428, PSHAb0543 Cluster 3 CcpA PSHAa0189, PSHAa0609, PSHAa0740, PSHAa1167, PSHAa1648, PSHAa1649, PSHAa1650, PSHAa1651, PSHAa2167, PSHAb0082, PSHAb0345 Cluster 6 GalR PSHAa0603, PSHAa0871, PSHAa1364, PSHAa1767, PSHAa2301, PSHAb0295 Cluster 2. This cluster,...”
DR_2493 carboxypeptidase G2 from Deinococcus radiodurans R1
27% identity, 69% coverage
Tter_0317 N-acetyl-ornithine/N-acetyl-lysine deacetylase from Thermobaculum terrenum ATCC BAA-798
22% identity, 96% coverage
- Modular architecture of metabolic pathways revealed by conserved sequences of reactions
Muto, Journal of chemical information and modeling 2013 - “...2-aminoadipate lysine M00028 (bsu) BSU11200 BSU11210+BSU11190 BSU11220 glutamate ornithine M00031 (ttr) Tter_0315+Tter_0316 Tter_0320 Tter_0319 Tter_0321 Tter_0317 a KEGG organism codes are shown in parentheses: pfu (T00075), Pyrococcus furiosus DSM 3638; bth (T00122), Bacteroides thetaiotaomicrometer VPI-5482; bsu (T00010), Bacillus subtilis 168; ttr (T01134), Thermobaculum terrenum ATCC BAA-798....”
BC2248 Acetylornithine deacetylase from Bacillus cereus ATCC 14579
23% identity, 79% coverage
ACY1_MOUSE / Q99JW2 Aminoacylase-1; ACY-1; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14 from Mus musculus (Mouse) (see 2 papers)
Q99JW2 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 3.5.1.14) from Mus musculus (see 2 papers)
25% identity, 60% coverage
- function: Catalyzes the hydrolysis of N-acetylated amino acids to acetate and free amino acids.
catalytic activity: an N-acyl-L-amino acid + H2O = an L-alpha-amino acid + a carboxylate (RHEA:15565)
catalytic activity: N(alpha)-acetyl-L-methionine + H2O = L-methionine + acetate (RHEA:67440)
catalytic activity: N-acetyl-L-glutamine + H2O = L-glutamine + acetate (RHEA:67368)
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
subunit: Homodimer (By similarity). Interacts with SPHK1. - Quantitative Proteomic Analysis Indicates That Pggt1b Deficiency Promotes Cytokine Secretion in Resiquimod-Stimulated Bone Marrow-Derived Macrophages via the NF-κB Pathway
Yu, Immunity, inflammation and disease 2025 - “...Myadm Myeloidassociated differentiation marker P15626 Gstm2 Glutathione Stransferase Mu 2 Q6S5C2 Gnptg N acetylglucosamine1phosphotransferase subunit Q99JW2 Acy1 Aminoacylase1 Q9D379 Ephx1 Epoxide hydrolase 1 Q9EPK6 Sil1 Nucleotide exchange factor SIL1 Q9Z1E4 Gys1 Glycogen [starch] synthase, muscle P35175 Stfa1 Stefin1 P25446 Fas Tumor necrosis factor receptor superfamily member...”
- Treatment of microglia with Anti-PrP monoclonal antibodies induces neuronal apoptosis in vitro
Adhikari, Heliyon 2021 - “...Control Q80XC6 Nuclear exosome regulator NRDE2 Nrde2 Nucleus 2 46.5 0.04874164 28.8 Antibody Treatment Control Q99JW2 Aminoacylase-1 Acy1 Extracellular, Cytosol 2 62.7 0.02111784 Infinite Antibody Treatment Control Q499M4 Tigger transposable element derived 5 Tigd5 Nucleus 2 45.2 0.01042085 10.7 Antibody Treatment Control Q02819 Nucleobindin-1 Nucb1 Extracellular,...”
- Renal proteome in mice with different susceptibilities to fluorosis
Carvalho, PloS one 2013 - “...182 Aldose 1-epimerase 40/6.625 37.8/6.3 4/146 129(0.016) Q8K157 Metabolism 210 Aminoacylase-1 42.5/5.94 45.8/5.9 18/831 129(0.013) Q99JW2 Metabolism 221/217 Medium-chain specific acyl-CoA dehydrogenase, mitochondrial 43/8.25 43.6/7.7 15/541 129(0.001) P45952 Metabolism 223 Adenosylhomocysteinase 42.5/6.6 43/6.3 15/559 129(0.047) P50247 Metabolism 261 Fumarate hydratase, mitochondrial 45/5.72 50/7.9 8/142 129(0.015) P97807...”
- “...184 Sorbitol dehydrogenase 40.5/6.805 38.2/6.56 10/586 129(0.003) Q64442 Metabolism 210 Aminoacylase-1 42.5/5.92 45.8/5.9 18/831 129(0.006) Q99JW2 Metabolism 217/221 Medium-chain specific acyl-CoA dehydrogenase, mitochondrial 41.5/8.22 43.6/7.69 15/715 129(0.009) P45952 Metabolism 269 Homogentisate 1,2-dioxygenase 49/7.41 50/6.85 6/105 129(0.002) O09173 Metabolism 280/119 ATP synthase subunit beta, mitochondrial 51/4.345 51.7/5.0...”
- Differentially expressed proteins of gamma-ray irradiated mouse intestinal epithelial cells by two-dimensional electrophoresis and MALDI-TOF mass spectrometry.
Zhang, World journal of gastroenterology 2003
MSMEG_4200 peptidase M20 from Mycobacterium smegmatis str. MC2 155
23% identity, 59% coverage
BUMPUSDA_CDS00542 acetylornithine deacetylase from Buchnera aphidicola str. USDA (Myzus persicae)
23% identity, 70% coverage
- Potato leafroll virus reduces Buchnera aphidocola titer and alters vector transcriptome responses
Patton, Scientific reports 2021 - “...(MYZPE13164_G006_v1.0_000070430.1) and M. persicae cuticle protein5-like ( Mpcp5-like) (MYZPE13164_G006_v1.0_000133030.2), and for the Buchnera genes, argE (BUMPUSDA_CDS00542), dnaK (BUMPUSDA_CDS00441), and groEL (BUMPUSDA_CDS00567), using gene specific primers (Supplementary Table S1 ). qRT-PCR reactions were carried out using SYBR green PCR master mix (Applied Biosystems, Carlsbad, CA, USA), in...”
BJA5080_04943 M20/M25/M40 family metallo-hydrolase from Bradyrhizobium diazoefficiens SEMIA 5080
25% identity, 69% coverage
OFBG_01207 succinyl-diaminopimelate desuccinylase from Oxalobacter formigenes OXCC13
24% identity, 69% coverage
- Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
Ellis, Journal of proteomics & bioinformatics 2016 - “...stationary relative to log (two genes in an operon involved in lysine biosynthesis, OFBG_01202 and OFBG_01207). Lysine is an important component of peptidoglycan and an increase in lysine synthesis may reflect the requirement for structural changes of the periplasm in stationary phase. Biosynthesis of various cofactors...”
c4916 Acetylornithine deacetylase from Escherichia coli CFT073
UTI89_C4548 acetylornithine deacetylase from Escherichia coli UTI89
25% identity, 68% coverage
GLRG_10812 peptidase family M20/M25/M40 from Colletotrichum graminicola M1.001
26% identity, 58% coverage
PA2787 glutamate carboxypepticase from Pseudomonas aeruginosa PAO1
Q9I056 Carboxypeptidase G2 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
24% identity, 71% coverage
BAV3208 amidohydrolase/peptidase from Bordetella avium 197N
25% identity, 56% coverage
BBA_03016 peptidase family protein from Beauveria bassiana ARSEF 2860
25% identity, 59% coverage
EF2578 peptidase from Enterococcus faecalis V583
EF_2578 YgeY family selenium metabolism-linked hydrolase from Enterococcus faecalis V583
24% identity, 76% coverage
- Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
Gilmore, mBio 2020 - “...92 V SAW_02395 EF2575 Potentially Important C Mo UE Carbamate kinase 0.020 79 E SAW_02397 EF2578 Potentially Important C Mo UE Peptidase 0.063 54 E SAW_02400 EF2581 Important AC Mo Se Selenate reductase subunit YgfK 0.047 75 R; E SAW_02526 EF2722 Potentially Important C Fe UE...”
- Tracing the Enterococci from Paleozoic Origins to the Hospital
Lebreton, Cell 2017 - “...genes EF1390, EF1613, EF2559 (6 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...”
- In silico identification of genes involved in selenium metabolism: evidence for a third selenium utilization trait
Zhang, BMC genomics 2008 - “...protein) 4 EF2563 (HP1) EF2565 (Hypothetical protein) EF2566 (SirA-like) 5 EF2565 (Hypothetical protein) EF2566 (SirA-like) EF2578 (Peptidase, M20/M25/M40 family) 6 EF2570 (Aldehyde oxidoreductase, putative) EF2578 (Peptidase, M20/M25/M40 family) EF2567 (SelD) 7 EF2569 (MobA-related protein) EF2577 (Aspartate/ornithine carbamoyltransferase family) EF2570 (Aldehyde oxidoreductase, putative) 8 EF1394 (Hypothetical protein)...”
- Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
Haft, Biology direct 2008 - “...ammonia-lyase 10 b2871 7 EF_2579 7 CD2085 ygeY hydrolase, peptidase M20 family 4 b2872 3 EF_2578 (CD2084) ygeZ phenyl-hydantoinase 19 b2873 (EF_2580) 6 pNG7258 yqeA carbamate kinase 18 b2874 15 EF_2575 yqeB SDMH accessory protein TIGR03309 1 b2875 2 EF_2563 1 pNG7241 1 CD3478 yqeC SDMH...”
PH1715 hypothetical protein from Pyrococcus horikoshii OT3
27% identity, 97% coverage
- The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis
Fondi, BMC evolutionary biology 2007 - “...as in the AAA variant of lysine biosynthesis, and that ORF PH1720, PH1718, PH1716, and PH1715 (Figure 3b ) might be involved in the biosynthesis of both lysine (through the AAA one) and arginine. Even though it cannot be ruled a priori out the possibility that...”
- Functional and evolutionary relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through alpha-aminoadipate
Miyazaki, Journal of bacteriology 2001 - “...Pyrococcus horikoshii, which possesses argDE homologs (PH1716 and PH1715) in a tandem manner at a position distal to the putative lysine biosynthetic gene...”
- “...cluster lacks two genes corresponding to PH1716 and PH1715 in the putative lysine Downloaded from http://jb.asm.org/ on February 12, 2017 by University of...”
PF1185 acetylornithine deacetylase from Pyrococcus furiosus DSM 3638
23% identity, 95% coverage
F6R8T8 N-acyl-aliphatic-L-amino acid amidohydrolase from Equus caballus
25% identity, 59% coverage
- Proteins involved in embryo-maternal interaction around the signalling of maternal recognition of pregnancy in the horse
Smits, Scientific reports 2018 - “...tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) F7E0H3 0,91 0,01211 TUBB* tubulin beta class I F6R8T8 0,90 0,01473 ACY1 aminoacylase 1 F7D9J2 0,90 0,00053 TKT* transketolase F6W039 0,85 0,00024 ARHGDIA* Rho GDP dissociation inhibitor alpha F6ZHQ5 0,83 0,00336 CLIC1 chloride intracellular channel 1 F7D1R1 0,82 0,01371...”
PAB0723 Acetyl ornithine deacetylase from Pyrococcus abyssi GE5
23% identity, 94% coverage
dapE / CAA08876.1 DapE from Bordetella pertussis (see paper)
26% identity, 64% coverage
C9ZBW7 Succinyl-diaminopimelate desuccinylase from Streptomyces scabiei (strain 87.22)
25% identity, 91% coverage
LIC13491 metallopeptidase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
21% identity, 65% coverage
- A comprehensive approach to identification of surface-exposed, outer membrane-spanning proteins of Leptospira interrogans
Pinne, PloS one 2009 - “...the genes in parentheses are: Lic13166 (ompL36) , Lic12263 (ompL37) , Lic13050 (ompL47) , and Lic13491 (ompL54) . The genes encoding the four predicted OMPs were cloned into the expression vector, pET-20b(+) (Novagen). All primer sequences for amplification from Fiocruz L1130 DNA are listed in Table...”
- “...and Methods led to the selection of OmpL36 (LIC13166), OmpL37 (LIC12263), OmpL47 (LIC13050), and OmpL54 (LIC13491) for further study, designated according to their apparent molecular mass determined by gel electrophoresis. All four candidates were predicted to be nonlipoproteins with a Signal peptidase I (SPI) cleavage site...”
LIMLP_17785 M20/M25/M40 family metallo-hydrolase from Leptospira interrogans serovar Manilae
21% identity, 65% coverage
Q6AYS7 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 3.5.1.14) from Rattus norvegicus (see 2 papers)
24% identity, 60% coverage
- Alterations in mitochondrial protein glycosylation in myocardial ischaemia reperfusion injury.
Feng, Biochemistry and biophysics reports 2023 - “...30-min group 1 ischemia 30-min group 2 Q4FZT0 G3V7Y3 Q5RKI1 A0A0G2K7N1 Q7TP75 P61016 D4AB01 D3ZIL6 Q6AYS7 P57093 Q5BK81 Q3MIE0 Q9EPB1 Q3KRE0 D4A9W3 Q7TMB9 G3V879 Q499R7 P29418 M0R544 A0A140TAE0 A0A023ILN9 Q5XI97 P11951 Q4QRB4 O88637 D4ADD7 Q5RKI8 D3ZBS2 D4A8Y1 Q64560 A0A0G2K719 M0R5R0 Q7TQ70 D3ZFJ6 Q5M891 D3ZY96 Q6IFZ5 A0A096P6L8...”
- Melatonin in preservation solutions prevents ischemic injury in rat kidneys.
Coskun, PloS one 2022 - “...Q5BK32 Serum albumin ALBU_RAT Alb P02770 Aspartate-tRNA ligase, cytoplasmic SYDC_RAT Dars P15178 Aminoacylase-1A ACY1A_RAT Acy1a Q6AYS7 Fascin FSCN1_RAT Fscn1 P85845 Transmembrane protein 43 TMM43_RAT Tmem43 Q5XIP9 Fidgeting-like protein 1 FIGL1_RAT Fignl1 Q6GX84 Serotransferrin TRFE_RAT Tf P12346 Transketolase TKT_RAT Tkt P50137 Adenosine monophosphate-protein transferase FICD FICD_RAT Ficd...”
- Proteome analysis of urinary biomarkers in a cigarette smoke-induced COPD rat model.
Qin, Respiratory research 2022 - “...Golgin subfamily A member 2 2.73 Q08379 Q63678 Zinc-alpha-2-glycoprotein 2.68 None Q6AYR9 Tetraspanin-1 3.48 O60635 Q6AYS7 Aminoacylase-1A 0.44 Q03154 Q6IRK9 Carboxypeptidase Q 0.62 Q9Y646 Q6TUD4 Protein YIPF3 0.60 Q9GZM5 Q8VD89 Ribonuclease pancreatic gamma-type 5.01 None Q99J86 Attractin 3.02 O75882 Q9JHY1 Junctional adhesion molecule A 0.57 Q9Y624...”
- Changes in the urinary proteome in rats with regular swimming exercise.
Meng, PeerJ 2021 - “...0.463 P82450 Sialate O-acetylesterase Q9HAT2 0.007297 1.623 0.647 P47820 Angiotensin-converting enzyme P12821 0.018595 0.642 0.303 Q6AYS7 Aminoacylase-1A Q03154 0.023841 0.532 2.322 P02651 Apolipoprotein A-IV P06727 0.029010 0.508 0.362 P13635 Ceruloplasmin P00450 0.002251 0.479 0.501 Q64319 Neutral and basic amino acid transport protein rBAT Q07837 0.025707 0.465...”
- Protection of the transplant kidney during cold perfusion with doxycycline: proteomic analysis in a rat model
Moser, Proteome science 2020 - “...5 98.45 12 46 6.47(5.91)/39.14 (33) Phosphotriesterase-related protein (Q63530) 6 595.06 29 76 6.11(6.00)/45.80(45) Aminoacylase-1A (Q6AYS7) 7 68.57 8 38 5.81(6.90)/31.42(27) N(G),N(G)-dimethylarginine dimethylaminohydrolase (O08557) 8 184.72 17 52 7.56(7.40)/44.54(40) Phosphoglycerate kinase 1 (P16617) a) Exp, experimental b) List of peptides in Additional file 1 Levels of...”
- Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair
Devaux, Molecular & cellular proteomics : MCP 2016 - “...Q5BJP9 Q5PQN7 Q5XI22 Q62952-2 Q66HG4 Q6AY84 Q6AYS7 Q6P502 Q6P9V9 Q7TP98 2650 Protein name Glycerol-3-phosphate dehydrogenase NAD(), cytoplasmic...”
- Proteomic profiling of the retinas in a neonatal rat model of oxygen-induced retinopathy with a reproducible ion-current-based MS1 approach.
Tu, Journal of proteome research 2015 - “...organization P60892 Prps1 ribose-phosphate pyrophospho kinase 1 3 1.39 0.14 0.04 carbohydrate metabolic process; apoptosis Q6AYS7 Acyla aminoacylase-1A 2 1.39 0.08 <0.01 cellular amino acid metabolic process Q9Z1B2 Gstm5 glutathione S -transferase Mu 5 3 1.38 0.25 0.04 metabolic process Q6AXT5 Rab21 Ras-related protein Rab-21 3...”
ACY1B_RAT / Q6PTT0 Aminoacylase-1B; ACY-1B; ACY IB; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14 from Rattus norvegicus (Rat) (see paper)
25% identity, 59% coverage
- function: Involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate).
catalytic activity: an N-acyl-L-amino acid + H2O = an L-alpha-amino acid + a carboxylate (RHEA:15565)
catalytic activity: an N-acetyl-L-cysteine-S-conjugate + H2O = an S-substituted L- cysteine + acetate (RHEA:36855)
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
subunit: Homodimer.
DAPE_HELPY / O25002 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) (see paper)
O25002 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Helicobacter pylori (see paper)
HP0212 succinyl-diaminopimelate desuccinylase (dapE) from Helicobacter pylori 26695
26% identity, 57% coverage
- function: Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminopimelate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso- diaminopimelic acid, an essential component of bacterial cell walls.
catalytic activity: N-succinyl-(2S,6S)-2,6-diaminopimelate + H2O = (2S,6S)-2,6- diaminopimelate + succinate (RHEA:22608)
cofactor: Zn(2+) Co(2+) (Binds 2 Zn(2+) or Co(2+) ions per subunit.)
subunit: Homodimer. - Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
Thiele, Journal of bacteriology 2005 - “...18 7 3 HP0112 HP0121 HP0191 to HP0193 HP0197 HP0212 HP0215 HP0255 HP0293 HP0329 HP0360 HP0372 HP0380 HP0381 HP0389 HP0476 HP0509 HP0512 HP0588 to HP0591 fucA...”
- Characterization of a bordetella pertussis diaminopimelate (DAP) biosynthesis locus identifies dapC, a novel gene coding for an N-succinyl-L,L-DAP aminotransferase
Fuchs, Journal of bacteriology 2000 - “...influenzae (GenBank accession number P444514), and H. pylori (36) (HP0212) (B) to the product of ORF3 (DapE B. pertussis). Amino acids identical or similar in...”
MSMEG_2491 acetylornithine deacetylase from Mycobacterium smegmatis str. MC2 155
23% identity, 73% coverage
- Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture
Petridis, BMC genomics 2015 - “...2.35 1.43E-04 nitrilase 2 msmeg_0443 d 2.28 1.82E-02 carbon-nitrogen hydrolase msmeg_3397 2.26 3.75E-04 acetylornithine deacetylase msmeg_2491 2.25 3.45E-02 acetylornithine deacetylase Nitrate/Nitrite msmeg_0427 4.42 1.52E-03 nitrite reductase, large subunit msmeg_0332 d 0.16 7.18E-10 2-nitropropane dioxygenase CoA biosynthesis msmeg_6097 d 0.49 9.14E-05 pantoate--alanine ligase a Locus number of...”
Q5LPN6 Acetylornithine deacetylase from Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)
23% identity, 87% coverage
OEOE_RS04760 ArgE/DapE family deacylase from Oenococcus oeni PSU-1
26% identity, 48% coverage
Q59284 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Corynebacterium glutamicum (see paper)
NCgl1064 succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum ATCC 13032
25% identity, 71% coverage
- Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum
Kim, International journal of molecular sciences 2016 - “...them, 9 genes (NCgl0247; lysC , NCgl0248; asd , NCgl1058; dapC , NCgl1061; dapD , NCgl1064; dapE , NCgl1868; dapF , NCgl1896; dapA , NCgl1898; dapB , and NCgl2528; ddh ) were slightly upregulated and 2 genes (NCgl1133; lysA and NCgl1214; lysE ) were slightly downregulated...”
- Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum
Brunger, Acta crystallographica. Section D, Biological crystallography 2012 - “...method (Klock et al. , 2008 ). The gene encoding Cgl1109 (GenBank NP_600337, gi|19552335; UniProt Q59284) was PCR-amplified from C.glutamicum 534 genomic DNA using PfuTurbo DNA polymerase (Stratagene) and I-PIPE primers (forward primer, 5-ctgtacttccagggcCTGTACTTCCAGGGCATGAACTCTGAACTCAAACCAGGATTAG-3; reverse primer, 5-aattaagtcgcgttaAATTAAGTCGCGTTACTCGCTCAGGTACTGCTTCAAAATTGC-3; target sequence in upper case) that included sequences for...”
- “...the production of theflavoring agent monosodium glutamate. Cgl1109 (NCBI reference sequence identifier NP_600337; UniProt identifier Q59284) is a putative succinyl-diaminopimelate desuccinylase (DapE) from C. glutamicum consisting of two domains: a peptidase domain belonging to family PF01546 (Peptidase_M20) in clan CL0035 of zinc metallopeptidases (30000 proteins in...”
W6QQU2 Acetylornithine deacetylase from Ectopseudomonas oleovorans (strain CECT 5344)
22% identity, 60% coverage
BA2297 peptidase, M20/M25/M40 family from Bacillus anthracis str. Ames
22% identity, 79% coverage
XP_030032986 aminoacylase-1 from Manduca sexta
25% identity, 51% coverage
- Knock-Out of ACY-1 Like Gene in Spodoptera litura Supports the Notion that FACs Improve Nitrogen Metabolism
Maruoka, Journal of chemical ecology 2024 - “...Heliothis subflexa , AET43037; Spodoptera frugiperda , AET43033; Spodoptera litura , XP_022815042; Manduca sexta , XP_030032986; Pieris rapae , XP_022115118; Plutella xylostella , XP_048480360; Amyelois transitella , XP_013187319; Papilio xuthus , KPI96806. CRISPR/Cas9-Mediated Targeted Gene Mutagenesis of the Sl-ACY-1 To disrupt the Sl-ACY-1 gene, we designed...”
Rv2141c hypothetical protein from Mycobacterium tuberculosis H37Rv
22% identity, 50% coverage
- Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains
Ullah, Pathogens (Basel, Switzerland) 2021 - “...to compare the proteome of DS, RR, MDR, and XDR clinical strains. We found iniC, Rv2141c, folB, and Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS...”
- “...C). Importantly, both RR and MDR strains showed a high expression of 4 proteins: iniC, Rv2141c, folB, and Rv2561 ( Figure 1 D). In addition, 10 proteins were increased in the RR and XDR strains, while 6 proteins were increased in the MDR and XDR strains...”
- Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment
Fernandez, BMC infectious diseases 2021 - “...we found miss-sense mutations and InDels related to intermediary metabolism and respiration ( oplA V674fs, Rv2141c T178A), a stress protein ( Rv1636 D15A), lipid metabolism ( pks6 G807C), and information pathways ( recC A773D) (Supplementary Table 1 ), reinforcing the idea of within-host coexistence of different...”
- Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes
Modlin, mSystems 2021 - “...Conserved hypothetical alanine- and proline-rich protein Conserved hypothetical alanine- and proline-rich protein Oxidoreductase More specific Rv2141c M20 family metallopeptidase 20 0.82 2pok Putative linear amide hydrolase Conserved protein Conserved protein FIG016551: putative peptidase Affirmatory Rv1775 2,4-Diacetylphloroglucinol hydrolase 29 0.82 3hwp Putative 3-oxo-carboxylic acid hydrolase Conserved hypothetical...”
- Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam
Hang, Scientific reports 2019 - “...No No No Yes Yes Yes ctpB, drrA, ethA, fhaA, PPE19, PPE60, Rv0094c, Rv1945, Rv2019, Rv2141c, Rv3921c 11 No Yes Yes No No No accD2, eccC3, eccC4, fadE7, fas, glfT1, icd1, lepB, lprN, mbtJ, mce1R, menA, mez, PE_PGRS42, PPE30, PPE4, PPE54, rbsK, Rv1106c, Rv1147, Rv1215c, Rv1747,...”
- Genomic Insight into Mechanisms of Reversion of Antibiotic Resistance in Multidrug Resistant Mycobacterium tuberculosis Induced by a Nanomolecular Iodine-Containing Complex FS-1
Ilin, Frontiers in cellular and infection microbiology 2017 - “...N/D T/C 39.80 1.93 39.84 0.03 40.57 1.91 46.59 2.07 Non-coding Possible promoter of peptidase Rv2141c 2397748 SNV T/C 38.62 0.23 37.45 0.09 AFL40_2592 Type V PE_PGRS43 protein; similar to Rv2490c 2800107 SNV A/C 44.89 8.05 AFL40_3034 Phenolpthiocerol synthesis type-I polyketide synthase; similar to Rv2931 3237781...”
- Inhibition of apoptosis by Rv2456c through Nuclear factor-κB extends the survival of Mycobacterium tuberculosis
Jurcic, International journal of mycobacteriology 2016 - “...membrane protein, similarity to nuoK 13 Rv1781c malQ Probable 4-alpha-glucanotransferase 14 Rv2663 Hypothetical protein 15 Rv2141c Conserved protein 16 Rv3738c PPE66 Unknown 17 Rv1704c cycA Probable D-serine/alanine/glycine transporter 18 Rv1737c narK2 Possible nitrate/nitrite transporter 19 Rv2456c Probable conserved integral membrane transport protein 20 Rv2054 Conserved protein...”
- Production of recombinant proteins in Mycobacterium smegmatis for structural and functional studies
Bashiri, Protein science : a publication of the Protein Society 2015 - “...Rv1212c Rv1213 Rv1601 Rv1665 Rv1886c Rv1980c Rv1991c Rv2141c Rv2220 Rv2245 Rv2420c Rv2611c Rv2903c Rv2924c Rv3127 Rv3177 Rv3248c Rv3490 Rv3547 Rv3565 Rv3713...”
- Comparative genomics of cell envelope components in mycobacteria
Banerjee, PloS one 2011 - “...Mycolate pathway genes MI co-expression PCC Predicted domain in hypothetical protein Mutant studies Supporting literature Rv2141c Rv0636 0.992774 0.41302 0.872206 Peptidase family M20/M25/M40 Non-essential Probable dapE2 Soluble protein [90] Rv1784 Rv0503c 0.934068 0.45765 0.909174 FtsK/SpoIIIE family no data available Rv1784 is a split gene; supposed to...”
- More
PITG_00577 uncharacterized protein from Phytophthora infestans T30-4
23% identity, 30% coverage
CCNA_00277 succinyl-diaminopimelate desuccinylase from Caulobacter crescentus NA1000
24% identity, 67% coverage
WP_003970135 M20/M25/M40 family metallo-hydrolase from Streptomyces sp. SID724
22% identity, 58% coverage
- Perspectives of aminoacylases in biocatalytic synthesis of N-acyl-amino acids surfactants
Haeger, Applied microbiology and biotechnology 2024 - “...aminoacylase from Streptomyces ambofaciens ATCC 23877 (GenBank: AKZ54783); SgAA, aminoacylase from Streptomyces griseus (accession number: WP_003970135); PmAcy, aminoacylase from Paraburkholderia monticola (GenBank: KXU85199); BurkAcy, aminoacylase from Burkholderia sp. LP5_18B (GenBank: BBI47489); Sgx9260b, amidohydrolase (PDB: 3MKV); Sgx9260c, prolidase (PDB: 3N2C); IADA, isoaspartyl dipeptidase from E. coli (UniProt...”
LOC110768015 acetylornithine deacetylase from Prunus avium
29% identity, 46% coverage
XP_048480360 aminoacylase-1 from Plutella xylostella
24% identity, 73% coverage
CG6465 uncharacterized protein from Drosophila melanogaster
24% identity, 70% coverage
- Daily Regulation of Phototransduction, Circadian Clock, DNA Repair, and Immune Gene Expression by Heme Oxygenase in the Retina of Drosophila
Damulewicz, Genes 2018 - “...CG10116, MtnD , Crz , Acox57D-d , Pepck , Cyp6a14 , fng , CG10512, CG7059, CG6465, AcCoAS , dob , Cyp9h1 , CG11236, CG18170, S6k , CG11425, CG3397, Jhe , CG6415, CG14688, Gnmt , Prx2540-2 , CG7724, Sk1 , ade3 , Cyp4p2 , CG14630, Sodh-2 ,...”
- Genetic basis of thermal plasticity variation in Drosophila melanogaster body size
Lafuente, PLoS genetics 2018 - “...int, ups T28C YES (KD) NO T28C CG14688 SNP 3R:10678848 mis T28C YES (MR) NA CG6465 ups CR44230 Optix SNP 2R:8032561 int T17C YES (KD) NA Wapl SNP X:2152985 int A28C NO (KD) NA 1 Putatively affected gene given as ID gene symbol. 2 Type of...”
- Transcriptome Analysis of Male Drosophila melanogaster Exposed to Ethylparaben Using Digital Gene Expression Profiling
Xue, Journal of insect science (Online) 2017 - “...5-GCATCAGATACTGTCCCTTGAAGC-3 ToA -F 5-TCAATAGCACCCAG GAACTAC-3 ToA -R 5-AGAATCCAGTTGCAAGGC-3 Sqz -F 5-CGAGC AGCAGGAACAGAAGT-3 Sqz -R 5-TCGCAAAACAATCCGAAGCA-3 CG6465 -F 5-TCGCAAAACAATCCGAAGCA-3 CG9465 -R 5-TTGTTTC GGGACATGACTGC-3 CG9468 -F 5-ATTTGTGCGGCATTGTGCTT-3 CG9468 -R 5-TCCTGTCGCATTCTGGCATT-3 Fig. 3. qRT-PCR validations of expression levels of candidate genes from DGE analysis. Quantitative RT-PCR validation of differentially...”
- Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles
Huang, G3 (Bethesda, Md.) 2015 - “...and MT 3.55 Irk3 Potassium channel Brain and MT 3.46 Tdc2 Tyrosine decarboxylase Brain-specific 3.44 CG6465 Peptidase Brain and other tissues 3.37 CG15201 Unknown Brain and other tissues 3.22 CG12269 Sterol binding Brain and eye 3.06 Hsp23 Chaperone Brain and other tissues 3.01 CG32195,CG7341 Protein kinase-like...”
- Genome of Drosophila suzukii, the spotted wing drosophila
Chiu, G3 (Bethesda, Md.) 2013 - “...CG14022, CG9391, ApepP, primo-2, CG14034, SPE, cathD, kraken, mag, CG2680, CG42264, CG31272, gd, LysC, Mdr49, CG6465, sda GOTERM MF GO:0008233 peptidase activity 12 2.21E03 CG31821, CG30049, ApepP, CG42264, S-Lap7, gd, SPE, CG6465, cathD, Ance, sda, PGRP-SA 3 2.54 SwissProt PIR Disulfide bond 9 1.56E03 crq, Adk2,...”
- “...15 1.10E03 lwr, CG31821, S-Lap7, Roc1a, SPE, cathD, CG11864, CG30049, CG42264, CG32486, Nedd8, Prosbeta3, gd, CG6465, Ance GOTERM MF GO:0008233 peptidase activity 13 3.84E03 CG31821, ApepP, S-Lap7, SPE, cathD, CG11864, CG30049, CG42264, Prosbeta3, gd, CG6465, PGRP-SA, Ance 3 2.09 SwissProt PIR Glycoprotein 14 1.64E03 PGRP-LE, CG4928,...”
- Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
Berman, Genome biology 2004 - “...Cyp4ac1 -7804 6 9 6 9 4.1 65 PCE8511 3R 6,469,170 6,470,599 1,430 hth -4766 CG6465 +32311 7 10 5 7 4.0 66 PCE8512 pdm2 neurogenic 2L 12,663,453 12,664,721 1,269 pdm2 +2754 pdm2 +2754 5 12 4 9 4.0 67 PCE8513 3L 14,550,945 14,551,746 802 HGTX...”
VV1_1370 acetylornithine deacetylase from Vibrio vulnificus CMCP6
23% identity, 71% coverage
V9KNP8 N-acyl-aliphatic-L-amino acid amidohydrolase from Callorhinchus milii
23% identity, 78% coverage
- Mass Spectrometry Analysis of Shark Skin Proteins
Bachar-Wikstrom, International journal of molecular sciences 2023 - “...A0A401RNN1 Branched-chain amino acid aminotransferase A0A401SFZ0 LRRcap domain-containing protein A0A401SLZ2 2-oxoisovalerate dehydrogenase subunit alpha (fragment) V9KNP8 N-acyl-aliphatic-L-amino acid amidohydrolase A0A401NQW3 P/Homo B domain-containing protein A0A401T7U8 FGE-sulfatase domain-containing protein (fragment) A0A401S584 Inter-alpha-trypsin inhibitor heavy chain H3 A0A401RY12 CYTOSOL_AP domain-containing protein A0A401T3E2 CYTOSOL_AP domain-containing protein A0A401NQA1 GADL1 decarboxylase...”
ACBG90_06555 acetylornithine deacetylase from Stutzerimonas kunmingensis
20% identity, 83% coverage
CKY39_29385 glutamate carboxypeptidase from Variovorax boronicumulans
29% identity, 44% coverage
DAPE_MYCS2 / A0R2G4 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
24% identity, 97% coverage
- function: Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls.
catalytic activity: N-succinyl-(2S,6S)-2,6-diaminopimelate + H2O = (2S,6S)-2,6- diaminopimelate + succinate (RHEA:22608)
cofactor: Zn(2+) Co(2+) (Binds 2 Zn(2+) or Co(2+) ions per subunit.)
subunit: Homodimer.
disruption phenotype: Cells lacking this gene show multiple auxotrophy (Met, Thr, Lys and DAP).
Mrub_0027 N-acetyl-ornithine/N-acetyl-lysine deacetylase from Meiothermus ruber DSM 1279
23% identity, 95% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...scotoductus TSC_c05810 TSC_c20650 TSC_c03550 TSC_c3520 TSC_c01940* TSC_c01930* TSC_c01920* TSC_c01890* TSC_c01880* TSC_c01850* Meiothermus ruber Mrub_0871 Mrub_2738 Mrub_0027 Mrub_2721* Mrub_2723* Mrub_2724* Mrub_2727* Mrub_2728* Meiothermus silvanus Mesil_2567 Mesil_1337 Mesil_0348 Mesil_0347 Mesil_0435* Mesil_0436* Mesil_0438* Mesil_0441* Mesil_0442* Oceanithermus profundus Ocepr_1387 Ocepr_1797* Ocepr_1798* Ocepr_1796* Ocepr_1788* Ocepr_1784* Ocepr_1781* Ocepr_1780* Ocepr_1779* Marinithermus hydrothermalis Marky_1533...”
CBG17687 Protein CBG17687 from Caenorhabditis briggsae
26% identity, 63% coverage
- Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes
Beadell, Genome biology and evolution 2014 - “...Leucine-rich repeat NA WBGene00026898 Cbr-dnc-6 Dynactin complex subunit 6 0.085 WBGene00033866 Cbr-lir-1 LIN-26-related 2.800 WBGene00037251 CBG17687 Peptidase M20 0.459 WBGene00026895 CBG04168 DOMON domain 0.782 WBGene00039610 Cbr-csc-1 Chromosome segregation and cytokinesis factor NA WBGene00033472 CBG12532 Myb DNA-binding domain, associated with splicing NA N ote .Only genes whose...”
7m6uB / P06621 Crystal structure of a circular permutation and computationally designed pro-enzyme of carboxypeptidase g2 (see paper)
29% identity, 47% coverage
CBPG_PSES6 / P06621 Carboxypeptidase G2; CPDG2; Folate hydrolase G2; Glutamate carboxypeptidase; Pteroylmonoglutamic acid hydrolase G2; Glucarpidase; EC 3.4.17.11 from Pseudomonas sp. (strain RS-16) (see paper)
P06621 glutamate carboxypeptidase (EC 3.4.17.11) from Pseudomonas sp. (see 2 papers)
cpg / AAA62842.1 carboxypeptidase G2 precursor from Variovorax paradoxus (see 2 papers)
29% identity, 44% coverage
- function: Catalyzes the hydrolysis of reduced and non-reduced folates to pteroates and L-glutamate. This enzyme has a broad specificity
catalytic activity: Release of C-terminal glutamate residues from a wide range of N-acylating moieties, including peptidyl, aminoacyl, benzoyl, benzyloxycarbonyl, folyl and pteroyl groups.
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
subunit: Homodimer. - Considerations on the Rational Design of Covalently Conjugated Cell-Penetrating Peptides (CPPs) for Intracellular Delivery of Proteins: A Guide to CPP Selection Using Glucarpidase as the Model Cargo Molecule
Behzadipour, Molecules (Basel, Switzerland) 2019 - “...amino acid sequence from Pseudomonas sp. strain RS-16 was retrieved from Uniprot (Uniprot ID # P06621) to build protein conjugates. The nucleotide sequence of the cpg2 gene was then codon-optimized by the codon usage wrangler server ( https://www.mrc-lmb.com.ac.uk/ms/methods/codon.html ). 3.2. Penetration Prediction of CPPs The uptake...”
- Comparison of Substrate Specificity of Escherichia Coli p-Aminobenzoyl-Glutamate Hydrolase with Pseudomonas Carboxypeptidase G
Larimer, Advances in enzyme research 2014 - “...E. coli AbgA (P77357), E. coli AbgB (P76052), and Pseudomonas sp. RS-16 carboxypeptidase G 2 (P06621) were obtained from the UniProt website. 2.3. Enzyme Assays Continuous spectrophotometric assays were used to measure the ability of CPG and PGH to utilize a variety of folates and anti-folates...”
1cg2A / P06621 Carboxypeptidase g2 (see paper)
29% identity, 47% coverage
7t1qA / A3M8H2 Crystal structure of the succinyl-diaminopimelate desuccinylase (dape) from acinetobacter baumannii in complex with succinic acid
23% identity, 58% coverage
A1S_2810 succinyl-diaminopimelate desuccinylase from Acinetobacter baumannii ATCC 17978
23% identity, 62% coverage
SCO1676 hypothetical protein from Streptomyces coelicolor A3(2)
22% identity, 58% coverage
argE / CAB95019.1 acetylornithinase (n2-acetyl-l-ornithine amidohydrolase) from Moritella abyssi (see paper)
21% identity, 84% coverage
A0J47_RS07600 M20 family metallopeptidase from Photobacterium damselae subsp. damselae
27% identity, 53% coverage
SAM23877_1734 M20/M25/M40 family metallo-hydrolase from Streptomyces ambofaciens ATCC 23877
21% identity, 58% coverage
SSO1007 Acetylornithine deacetylase (argE-2) from Sulfolobus solfataricus P2
27% identity, 36% coverage
PD0292 acetylornithine deacetylase from Xylella fastidiosa Temecula1
24% identity, 55% coverage
MMJJ_14410 M20 family metallo-hydrolase from Methanococcus maripaludis
26% identity, 50% coverage
- Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis
Fonseca, Molecular genetics and genomics : MGG 2023 - “...with hypothesized DNA/RNA binding proteins, possibly involved in transcription or translation (MMJJ_01810, MMJJ_13210, MMJJ_17710, and MMJJ_14410). Lastly, we identified multiple independent transposon mutant strains with insertions in a two gene operon containing a predicted MinD/ParA ATPase (MMJJ_11080) and a hypothetical protein (MMJJ_11090). Fig. 2 Schematic representation...”
- “...1,193,041; 1,193,089 MMJJ_13030 Tripartite tricarboxylate transporter TctA family protein 1,194,079 MMJJ_13210 Peptidase family M50 1,210,579 MMJJ_14410 Putative succinyl-diaminopimelate desuccinylase 1,306,596 1,306,596; 1,306,683 MMJJ_16440 Thermonuclease 1,499,668 MMJJ_17200 Archaeosortase family protein ArtE 1,571,918 MMJJ_17710 Uncharacterized protein 1,619,404; 1,619,626 Developing a screen for transformation defects with integrating plasmids There...”
PAB0581 hypothetical protein from Pyrococcus abyssi GE5
35% identity, 19% coverage
Q9C5C4 acetylornithine deacetylase (EC 3.5.1.16) from Arabidopsis thaliana (see 2 papers)
AT4G17830 peptidase M20/M25/M40 family protein from Arabidopsis thaliana
27% identity, 46% coverage
- N2-Acetylornithine deacetylase functions as a Cys-Gly dipeptidase in the cytosolic glutathione degradation pathway in Arabidopsis thaliana
Miyaji, The Plant journal : for cell and molecular biology 2024 (PubMed) (secret) - Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions
Nose, PloS one 2023 - “...three sites. Probe Sequence ID Arabidopsis ID e-value Symbol Description Parameter Pearson r CUST_8719_PI429951308 reCj23354:MSWR:isotig23206 AT4G17830 0.0 - Peptidase M20/M25/M40 family protein temp-7d -0.97 CUST_12145_PI429951308 reCj26834:--WR:isotig26686 AT5G14800 4.0E-113 P5CR pyrroline-5- carboxylate (P5C) reductase temp-7d -0.96 CUST_10209_PI429951308 reCj24864:MSW-:isotig24716 AT3G04790 9.5E-47 EMB3119 Ribose 5-phosphate isomerase, type A pro...”
- Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation
Félix, International journal of molecular sciences 2023 - “...Table S1 ). In the MPT coconut, DAPs included polyadenylate-binding protein 5 (A0A8B7MTK7), acetylornithine deacetylase (AT4G17830), putative isopentenyl-diphosphate delta-isomerase I (AT5G16440), mitochondrial gamma-aminobutyrate transaminase 1 (AT3G22200), actin-101 (AT5G09810), two-component response regulator 24 (A0A8B7D411), which were down-accumulated throughout ripening ( Table S1 ). On the contrary, DAPs...”
- Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis
Zhu, The Plant cell 2022 - “...(At1g10070), ALANINE:GLYOXYLATE AMINOTRANSFERASE 2 ( AGT2 ; At4g39660), TyrDC (At4g28680), P5CS1 (At2g39800), LACS9 (At1g77590), NAOD (At4g17830), ARGINASE 1 (At4g08900), SHN2 (At5g11190), CHY4 (At4g31810), ProDH (At3g30775), AO/FDH (At5g14760/At5g14780), KCS4 (At1g19440), PLD2 (At4g11830), TAG1 (At2g19450), KCS13 (At2g46720), ACX3/6 (At1g06290/At1g06310), LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE 1 ( LPCAT1 ; At1g12640), DELTA9 DESATURASE...”
- Identification of DIR1-Dependant Cellular Responses in Guard Cell Systemic Acquired Resistance
David, Frontiers in molecular biosciences 2021 - “...guard cells in the amino acid biosynthesis metabolic pathways included AGD2, CYSC1, CBL, MS2, MTO1, AT4G17830, and AQI, and decreased metabolites in these pathways included gly-leu, niacin, acetyl-leucine, desaminotyrosine, and pyroglutamic acid. One increased metabolite in dir1-1 guard cells in the arginine biosynthesis pathway was aminolevulinic...”
- The Arabidopsis N-Acetylornithine Deacetylase Controls Ornithine Biosynthesis via a Linear Pathway with Downstream Effects on Polyamine Levels
Molesini, Plant & cell physiology 2017 (PubMed)- “...2016; Accepted September 22, 2016) Arabidopsis thaliana At4g17830 codes for a protein showing sequence similarity with the Escherichia coli N-acetylornithine...”
- “...(PAs). Here, we showed the direct connection between At4g17830 function and Orn biosynthesis, demonstrating biochemically that At4g17830 codes for a NAOD. These...”
- PGPR strain Paenibacillus polymyxa SQR-21 potentially benefits watermelon growth by re-shaping root protein expression
E, AMB Express 2017 - “...GDH1, At1g64190, NADP-ME3 and A0A0A0LEK8 etc.; biosynthesis of amino acids contain At3g58610, CSY4, At3g08590, ENO1, At4g17830 and CICDH; carbon fixation in photosynthetic organisms contain At2g36460, MDH1 and NADP-ME3; glutathione metabolism contain GSTF7, GSTU22, GSTF10, At1g64190, CICDH and ACG12; glycolsis/gluconeogenesis contain ADH2, At3g08590, At2g36460, PGI1 and ENO1;...”
- “...pathway contain At2g36460, PGI1, At1g64190 and ACG12; 2-Oxocarboxylic acid metabolism contain At3g58610, CSY4, CICDH and At4g17830; phenylpropanoid biosynthesis contain PER54, PER72, PER47 and PER55; Citrate cycle (TCA cycle) contain CSY4, MDH1 and CICDH; Proteasome contain RPN3, ARPN1A and ARPN2B (Additional file 1 : Table S1). Fig.6...”
- Physiological implications of arginine metabolism in plants
Winter, Frontiers in plant science 2015 - “...et al. (2015) analyzed the NAOD-activity in Arabidopsis after downregulation of the putative NAOD gene (At4g17830) by using RNA silencing and T-DNA insertion mutants. All analyzed NAOD-suppressed plants showed consistently reduced ornithine content compared with wild-type plants, suggesting that in addition to NAOGAcT action, NAOD contributes...”
- More
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
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.
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