PaperBLAST
PaperBLAST Hits for tr|Q9HWM9|Q9HWM9_PSEAE Probable hydrolase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA4152 PE=4 SV=1 (370 a.a., MSRIHTLTMP...)
Show query sequence
>tr|Q9HWM9|Q9HWM9_PSEAE Probable hydrolase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA4152 PE=4 SV=1
MSRIHTLTMPKWGLSMTEGRVDAWLKEEGAHIEKGDEVLDVETDKISSSVEAPFSGVLRR
KVAREDETLAVGALLGVVVEGEASDEEIDALVQRFQAEFVPADEDAGDSGPAPRKVELDG
RLLRYFDRGEGDPALLLIHGFGGDLNNWLFNHEALAAERRVIALDLPGHGESGKALVRGD
LDELSGSVLALLDHLDLEQVHLAGHSMGGAVALNCARLAPQRVLSLSLIGSAGLGEEING
DYLRGFVEAANRNALKPQLVQLFSDPALVTRQMLEDMLRYKRLEGVDAALRQLLDNLFAD
GRQRNDLRAVANEGRQPVLAIWGSDDAIIPARHAEGLPAQVEIIPGQAHMVQMEAAEQVN
RLLLDFLRQH
Running BLASTp...
Found 261 similar proteins in the literature:
PA4152 probable hydrolase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
PA14_10240 putative hydrolase from Pseudomonas aeruginosa UCBPP-PA14
CIA_04250 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas aeruginosa PA14
99% identity, 100% coverage
- Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
Thöming, NPJ biofilms and microbiomes 2020 - “...exaD 3.0 PA14_06680 PA0512 nirH 3.2 PA14_10200 PA4156 2.8 PA14_38920 4.1 PA14_06690 PA0513 nirG 2.9 PA14_10240 PA4152 acoC 2.8 PA14_38970 PA1976 2.9 PA14_06700 PA0514 nirL 3.3 PA14_10250 PA4151 acoB 3.0 PA14_38990 PA1975 3.1 PA14_06710 PA0515 nirD 3.3 PA14_10260 PA4150 acoA 3.1 PA14_39000 PA1974 4.9 PA14_06720 PA0516...”
- The novel type II toxin-antitoxin PacTA modulates Pseudomonas aeruginosa iron homeostasis by obstructing the DNA-binding activity of Fur
Song, Nucleic acids research 2022 - “...dehydratase PrpD, succinate dehydrogenase SdhD, 3-hydroxybutyrate dehydrogenase BdhA, amino acid dehydrogenase CIA_03490, 2,3-butanediol catabolism dehydrogenase CIA_04250, Glycolate oxidase subunit GlcF, formiminoglutamate deiminase HutF, aspartate aminotransferase IlvE, nucleotide hydrolases dgt2, 3-butanediol catabolism dehydrogenase CIA_04250. Furthermore, the proteins involved in transport process were also reduced, including peptide transporter...”
AXG94_01195 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas corrugata
78% identity, 100% coverage
A0U95_29285 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas brassicacearum
78% identity, 100% coverage
ELZ14_17090 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas brassicacearum
77% identity, 100% coverage
PP0553, PP_0553 acetoin dehydrogenase, dihydrolipoamide acetyltransferase component from Pseudomonas putida KT2440
75% identity, 100% coverage
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440
Liu, Frontiers in bioengineering and biotechnology 2021 - “...PAO1 ( Liu et al., 2018 ). Comparative genomics analysis indicated that PP0555, PP0554, and PP0553 exhibit strikingly high homology to AcoA, AcoB, and AcoC in AC dehydrogenase enzyme system (AoDH ES) of P. aeruginosa PAO1. R , R -BDH and (2 S ,3 S )-2,3-BDO...”
- “...with 2gL 1 mixed 2,3-BDO as the sole carbon source. Since pp0555 , pp0554 , pp0553 and pp0552 were located adjacent to acoX ( pp0556 ) and acoR ( pp0557 ) gene homologues of AC utilization operons in other bacteria, we hypothesized that these genes may...”
- Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog
Sumi, Journal of bacteriology 2020 (secret) - Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Beckers, Microbial cell factories 2016 - “...Pyruvate dehydrogenase 1.16 1.86 1.03 0.33 acoB PP0554 Pyruvate dehydrogenase 1.5 1.88 1.04 0.66 acoC PP0553 Pyruvate dehydrogenase 1.57 1.81 0.96 0.72 PP0545 Aldehyde dehydrogenase 0.2 0.11 0.91 1.01 acsA PP4487 Acetyl-CoA synthetase 0.13 0.23 0.15 3.56 accC - 2 PP5347 Pyruvate carboxylase 0.22 0.27 0.12...”
- Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
Borrero-de, Microbial cell factories 2014 - “...Pyruvate metabolism acoA PP0555 Pyruvate dehydrogenase 12.4 5.3 acoB PP0554 Pyruvate dehydrogenase 1.5 1.0 acoC PP0553 Pyruvate dehydrogenase 0.7 0.7 PP0545 Aldehyde dehydrogenase 0.1 -1.0 acsA PP4487 Acetyl-CoA synthetase 0.8 1.4 accC-2 PP5347 Pyruvate carboxylase 0.5 0.2 ppsA PP2082 Phosphoenolpyruvate synthase 0.5 0.4 ppc PP1505 Phosphoenolpyruvate...”
- “...Pyruvate metabolism acoA PP0555 Pyruvate dehydrogenase 1.3 -2.7 acoB PP0554 Pyruvate dehydrogenase 0.7 -0.8 acoC PP0553 Pyruvate dehydrogenase 0.5 -1.2 PP0545 Aldehyde dehydrogenase 0.5 -0.9 acsA PP4487 Acetyl-CoA synthetase -0.3 -0.6 accC-2 PP5347 Pyruvate carboxylase 0.8 2.3 ppsA PP2082 Phosphoenolpyruvate synthase 0.2 -0.1 ppc PP1505 Phosphoenolpyruvate...”
- The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
Poblete-Castro, Microbial cell factories 2012 - “...-6.7 -8.3 PP0556 Acetoin catabolism protein -3.7 -4.6 PP0554 Acetoin dehydrogenase beta subunit -4.6 -4.2 PP0553 Acetoin dehydrogenase dihydrolipoamide -5.3 -4.0 PP0557 Acetoin catabolism regulatory protein -3.4 -3.6 PP2149 Glyceraldehyde 3-phospate dehydrogenase 1.5 -3.7 PP4715 Triosephosphate isomerase 1.9 -3.3 PP4737 D-lactate dehydrogenase putative -2.6* -3.1 PP0545...”
- “...-4.0 7 -8.3 0 Acetoin dehydrogenase -sub PP0554 AcoB -5.6 23 -4.2 0 Acetoin dehydrogenase PP0553 AcoC -3.7 10 -4.0 0 Nitrogen metabolism Nitrogen regulatory protein P-II PP5234 GlnK only in CN 6 10.4 0 Protein synthesis Elongation factor Tu PP0452 TUF-2 only in CN 16...”
- Transcriptome dynamics of Pseudomonas putida KT2440 under water stress
Gülez, Applied and environmental microbiology 2012 - “...PP_4034 PP_0103 PP_0104 PP_0105 PP_0106 PP_0490 PP_0552 PP_0553 PP_0554 PP_0555 PP_0556 PP_0557 PP_0596 PP_0989 PP_0999 PP_1000 PP_1001 PP_1157 PP_2351 PP_2422...”
Pden_4983 alpha/beta hydrolase fold from Paracoccus denitrificans PD1222
50% identity, 99% coverage
- H-NOX Influences Biofilm Formation, Central Metabolism, and Quorum Sensing in Paracoccus denitrificans
Islam, Journal of proteome research 2024 - “...gene whose expression was constitutive at the protein level (A1B5X4, see Table S1 ). Pden_4985, Pden_4983, and Pden_1517 are annotated as the / hydrolase fold enzyme (A/B), pyruvate dehydrogenase E1 subunit (PDH), and XRE family transcriptional regulator (TR), respectively. All are downregulated comparably at both the...”
- “...Further, we see a downregulation in proteins annotated as E1 (Pden_4984 and Pden_4985) and E2 (Pden_4983) components of PDH. This is counterintuitive, given that downregulation of these proteins would presumably lead to an increase of the substrate pyruvate in the hnox strain. However, it is unknown...”
WP_095844694 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Gibbsiella quercinecans
50% identity, 97% coverage
JV35_11985 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pectobacterium betavasculorum
49% identity, 98% coverage
acoC / AAA21950.1 FMP from Cupriavidus necator (see paper)
47% identity, 96% coverage
APA386B_2085 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Acetobacter pasteurianus 386B
42% identity, 95% coverage
C7JDV2 Esterase/lipase from Acetobacter pasteurianus (strain NBRC 105184 / IFO 3283-01)
41% identity, 95% coverage
O66382 Esterase2 from Acetobacter pasteurianus
38% identity, 90% coverage
BAB2_1042 Alpha/beta hydrolase fold:Biotin/lipoyl attachment:Esterase/lipase/thioesterase, active site:2-oxo acid dehydrogenase, acyltr... from Brucella melitensis biovar Abortus 2308
26% identity, 81% coverage
pRL80081 putative hydrolase from Rhizobium leguminosarum bv. viciae 3841
32% identity, 67% coverage
Ngar_c35080 alpha/beta fold hydrolase from Candidatus Nitrososphaera gargensis Ga9.2
33% identity, 68% coverage
- The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1
Chow, Scientific reports 2018 - “.... e . estN1 ), Ngar_c30910 ( i . e . estN2 ), Ngar_c32780 and Ngar_c35080, which could possibly encode a BioH analogue, were amplified with specific primers, cloned into pDrive (PCR Cloning Kit, Qiagen, Hilden, Germany) and transformed into competent E . coli DH5 cells....”
- “...BioH-activities. According to a conserved domain search, three of the candidate enzymes (Ngar_c21820, Ngar_c24650 and Ngar_c35080) showed domains for being members of the /-hydrolase superfamily (e-values between 1.9e 44 and 2.1e 17 ), while three others even showed possible pimeloyl-ACP methyl ester carboxylesterase domains [Ngar_c14400 (...”
acoC / AAA18917.1 dihydrolipoamide acetyltransferase from Pelobacter carbinolicus (see paper)
49% identity, 22% coverage
acoC / Q3A7N9 dihydrolipoamide acetyltransferase subunit from Syntrophotalea carbinolica (strain DSM 2380 / NBRC 103641 / GraBd1) (see paper)
Pcar_0345 dihydrolipoamide acetyltransferase from Pelobacter carbinolicus str. DSM 2380
49% identity, 22% coverage
- Constraint-based modeling analysis of the metabolism of two Pelobacter species
Sun, BMC systems biology 2010 - “...the reaction was associated with the acoA (Pcar_0343 & Ppro_1131), acoB (Pcar_0344 & Ppro_1132), acoC (Pcar_0345 & Ppro_1133), and acoL (Pcar_0347 & Ppro_1137) genes. In the P. carbinolicus model, the resulting acetaldehyde is reduced to ethanol by alcohol dehydrogenase, whereas acetyl-CoA is converted into acetate by...”
ACIAD1019 dihydrolipoamide acetyltransferase from Acinetobacter sp. ADP1
48% identity, 20% coverage
H0N28_08825, KZA74_09665 2-oxo acid dehydrogenase subunit E2 from Acinetobacter baumannii
43% identity, 23% coverage
- Antibacterial activity and mechanism of X33 antimicrobial oligopeptide against Acinetobacter baumannii
Lu, Synthetic and systems biotechnology 2024 - “...peroxidase H0N28_07425 glutathione peroxidase 2.57 1.72E-100 down H0N28_18175 glutathione peroxidase 2.13 2.85E-101 down TCA cycle H0N28_08825 2-oxo acid dehydrogenase subunit E2 1.45 6.06E-54 down lldD FMN-dependent l-lactate dehydrogenase LldD 1.02 3.36E-11 down gltA citrate (Si)-synthase 1.13 2.58E-45 down lpdA dihydrolipoyl dehydrogenase 3.02 1.53E-250 down lpdA dihydrolipoyl...”
- “...phosphorylation genes, and 17 genes involved in glycolysis/gluconeogenesis. The rate-limiting enzymes in the pyruvate pathway, H0N28_08825 encoding pyruvate dehydrogenase subunit E2, and lldD encoding FMN-dependent l -lactate dehydrogenase LldD, were considerably downregulated in pyruvate metabolism [ 33 ]. In addition, the expression of genes related to...”
- DNA damage response coregulator <i>ddrR</i> affects many cellular pathways and processes in <i>Acinetobacter baumannii</i> 17978
Cook, Frontiers in cellular and infection microbiology 2023 - “...NSC KZA74_08660 NSC NSC 28 A1S_1843/KZA74_08665 NSC R KZA74_08665 NSC NSC 29 A1S_1701/KZA74_09665 R R KZA74_09665 NSC NSC 30 A1S_1700/KZA74_09670 NSC R KZA74_09670 NSC NSC 31 A1S_1699/KZA74_09675 R NSC KZA74_09675 NSC NSC 32 A1S_1679/KZA74_09805 NSC NSC KZA74_09805 NSC NSC 33 A1S_1671/KZA74_09845 NSC NSC KZA74_09845 NSC NSC...”
DJ41_569 2-oxo acid dehydrogenase subunit E2 from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
43% identity, 23% coverage
G8E09_10090 2-oxo acid dehydrogenase subunit E2 from Acinetobacter pittii
42% identity, 23% coverage
- Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii
Zhang, Frontiers in microbiology 2020 - “...dehydrogenase 2.35 0.0000 0.0013 G8E09_14960 Trehalose-6-phosphate synthase 2.33 0.0012 0.0314 G8E09_12910 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylatedehydrogenase 2.25 0.0000 0.0009 G8E09_10090 2-oxo acid dehydrogenase subunit E2 2.24 0.0000 0.0012 G8E09_07160 Type 1 glutamine amidotransferase 2.23 0.0001 0.0076 G8E09_14205 Non-heme iron oxygenase ferredoxin subunit 2.22 0.0004 0.0151 G8E09_08630 Nuclear transport factor 2...”
NTE_01571 alpha/beta fold hydrolase from Candidatus Nitrososphaera evergladensis SR1
28% identity, 69% coverage
Q1LNT5 2-hydroxymuconic semialdehyde hydrolase (HMSH)-alpha/beta hydrolase superfamily (Belongs to CMGI-2) from Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)
KZ686_10070 alpha/beta fold hydrolase from Cupriavidus cauae
33% identity, 71% coverage
AGH13449.1 hybrid C-C meta-cleavage hydrolase-carboxylesterase from Cycloclasticus zancles (see paper)
28% identity, 66% coverage
CC2395 acetoin dehydrogenase E2 component, putative from Caulobacter crescentus CB15
31% identity, 67% coverage
- The metabolic enzyme CTP synthase forms cytoskeletal filaments
Ingerson-Mahar, Nature cell biology 2010 - “...cell periphery is marked with a gfp fusion (green) to the periplasmic protein encoded by CC2395. (g) ECT filaments in creS cells (ZG17). Arrows point to filaments ends. (hi) Co-localization of Caulobacter mCherry-CtpS (red) and CreS-tc (green) in both Caulobacter (h, ZG218) and upon heterologous co-expression...”
Q73ZZ9 AB hydrolase-1 domain-containing protein from Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)
31% identity, 69% coverage
ABO_1197 carboxylic ester hydrolase from Alcanivorax borkumensis SK2
40% identity, 35% coverage
- Plastic-Degrading Enzymes from Marine Microorganisms and Their Potential Value in Recycling Technologies
Ruginescu, Marine drugs 2024 - “...T agg (<50 C), suggesting the adaptability to function under moderate temperatures. Moreover, three (i.e., ABO_1197, ABO_1251, and MGS0010) exhibited remarkable salt tolerances of up to 3.5 M NaCl [ 42 ]. However, detailed quantitative assays using various types of PLA substrates are necessary to fully...”
- “...PDLLA (Mw: 2 kDa) after 24 h at 30 C, pH 8.0 [ 42 ] ABO_1197 Alcanivorax borkumensis Seawater metagenome T agg = 47.0 The PLA-degrading activity was confirmed through a qualitative assay on agar plates containing emulsified PDLLA (Mw: 2 kDa) after 24 h at...”
- Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase
Placido, Applied microbiology and biotechnology 2015 - “...coli BL21(DE3) Protein expression strain harbouring LIPESV12_26 This study E. coli NovaBlue Transformant strain harbouring ABO_1197 This study E. coli BL21(DE3) Protein expression strain harbouring ABO_1197 This study E. coli NovaBlue Transformant strain harbouring ABO_1251 This study E. coli BL21(DE3) Protein expression strain harbouring ABO_1251 This...”
- “...the conditions described in the Materials and methods , the other three, LIPESV12_24, LIPESV12_26, and ABO_1197, were significantly activated also in the hydrolysis of the long-chain ester p -NP-C16 and released approx. 128.0, 554.0, and 12.0mol p -NPpermg protein, respectively. Further, to study the substrate specificities...”
- Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics
Alcaide, Applied and environmental microbiology 2015 - “...388 Le PLEe MGS-M1f MGS-M2f MGS-B1f MGS-K1f MGS-MT1f ABO_1197, ABO_1251, MGS0010, MGS0105, and MGS0109g R. exoculata enzymes 47.6 53.3 42.0 ND/NA 53.0 ND ND/NA...”
- “...obtained via genomic mining of marine bacteria (ABO_1197, ABO_1251, CCSP0084, CCSP0211, CCSP0528, and CCSP2178) or via metagenomic approaches of communities...”
hbpD / O06648 2-hydroxy-6-oxo-6-phenyl-2,4-hexadienoate hydrolase [multifunctional] (EC 3.7.1.8) from Pseudomonas nitroreducens (see 2 papers)
31% identity, 67% coverage
G5B91_07370 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Pseudomonas nitroreducens
32% identity, 67% coverage
b0349 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase from Escherichia coli str. K-12 substr. MG1655
28% identity, 68% coverage
- RNA stability is regulated by both RNA polyadenylation and ATP levels, linking RNA and energy metabolisms in <i>Escherichia coli</i>
Roux, mBio 2025 - “...membrane maeA b1479 Malate dehydrogenase Energy production and conversion 1698 No 61 2.4 Cytosol mhpC b0349 2-hydroxy-6-oxononatrienedioate hydrolase NA 867 Yes 1 3.4 Cytosol purL b2557 Phosphoribosylformylglycinamide synthetase Nucleotide transport and metabolism 3888 No 195 1.1 Cytosol torS b0993 Sensor histidine kinase TorS Signal transduction mechanisms...”
- Bioinformatic prediction reveals posttranscriptional regulation of the chromosomal replication initiator gene dnaA by the attenuator sRNA rnTrpL in Escherichia coli
Li, RNA biology 2021 (secret) - Cloning, screening and characterization of enantioselective ester hydrolases from Escherichia coli K-12
Tang, World journal of microbiology & biotechnology 2011 - Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
Mariño-Ramírez, Journal of bacteriology 2004 - “...b1517 b1512 b2463 b1620 b4037 b4346 b4119 b3929 b3939 b0349 b0783 b4351 b0091 b2733 b2286 b1393 b1396 b0134 b3019 b2564 b4100 b1020 b3724 b0951 b4201 b0467...”
- Definition of the Escherichia coli MC4100 genome by use of a DNA array
Peters, Journal of bacteriology 2003 - “...yagF cynR, lacA, lacI, lacZ, mhpB, yagG, yeiQ, b0271, b0349 cynS, cynT, yagC, yagE, yagT, ykfD,a b0331, b0333 eaeH b0323, b0324, b0325, b0350a yagA, yagB, yagJ,...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...pin rplD b2667 rplC rplY rpmC rpsJ trmD b2797 b2796 b0349 b0699 b1759 b3983 b0218 b3984 b3184 b0574 b1445 b1035 b4162 b3986 b3316 b3985 b3313 b3314 b0719 b3317...”
- Sequence analysis of Tn10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction
Nichols, Journal of bacteriology 1998 - “.... , . , thrA carB leuO yadC yafC proA lacI b0349 b0374 tsx b0441 gsk purK b0604 ybeG asnB nadA ig,e b0786-b0787 potI ig, ycaD-b0899 b0940 yccE yceG b1160 fadR...”
AT4G36530 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
28% identity, 66% coverage
- Development of a Target Enrichment Probe Set for Conifer (REMcon)
Khan, Biology 2024 - “...768 60 MA_225872 AT5G14260 456 61 MA_224167 AT2G20790 900 62 MA_199851 AT3G01660 350 63 MA_196209 AT4G36530 273 64 MA_187402 AT4G31460 471 65 MA_173127 AT4G28740 548 66 MA_159115 AT2G27600 1191 67 MA_159115 AT4G27600 1056 68 MA_127668 AT3G15290 465 69 MA_123340 AT2G19870 1137 70 MA_121485 AT1G02410 749 71...”
- HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight
Zupanska, International journal of molecular sciences 2019 - “...AT1G78980 SRF5 STRUBBELIG-receptor family 5 2.4 X AT1G78080 WIND1 related to AP2 4 1.2 X AT4G36530 alpha/beta-Hydrolases superfamily protein 1.2 X CC endomembrane system GO:0012505 Golgi apparatus GO:0005794 At3g18260 Reticulon family protein 3.1 X At1g77510 PDIL1-2 PDI-like 1-2 protein disulfide isomerase-like 1-2 1.2 X At2g03760 ST1...”
- Catalytic and structural properties of pheophytinase, the phytol esterase involved in chlorophyll breakdown
Guyer, Journal of experimental botany 2018 - “..., 2016 ) were retrieved from TAIR ( http://www.arabidopsis.org/, last accessed 6 September 2017 ): At4g36530; At5g19850; At5g38520. Multiple sequence alignment of these proteins was generated and phylogenetic analysis (Supplementary Fig. S5B) performed with the neighbor-joining method using MEGA7 ( Kumar et al. , 2016 )....”
- Accumulation of high OPDA level correlates with reduced ROS and elevated GSH benefiting white cell survival in variegated leaves
Sun, Scientific reports 2017 - “...OPDA production in VMW. In addition, two DEGs (contig_4904 and_10685) to alpha/beta hydrolases (AT5G17780 and AT4G36530) known to be responsible for fatty acid accumulation 59 were also up-regulated ~3-fold ( Supplementary Table S3 ). These genes might facilitate the production and accumulation of fatty acids in...”
- Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
Wan, Genome biology 2015 - “...AT4G39100, AT4G20860, AT3G23560, AT2G01830 [ 73 , 76 78 ] Redox process AT3G50440, AT4G34900, AT2G07785, AT4G36530, AT4G20860 [ 18 , 79 ] Differentially or specifically expressed during flowering AT3G23450, AT1G44890, AT5G44110, AT1G18370, AT1G05070, AT3G04620, AT5G62580, AT2G27380, AT2G45730, AT3G23560, [ 18 , 80 83 ] Response to...”
- “...AT2G27900, AT2G14080, AT2G01830 [ 78 , 88 ] Carbohydrate metabolism or energy release AT3G22210, AT1G22940, AT4G36530 [ 18 ] sn (o) RNA or other ncRNA AT3G57645 a Suggests the function of RNA itself, for example, rRNA, or the functions in its expressed proteins b The functions...”
- Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses
Zhang, BMC bioinformatics 2012 - “...-9.82 ATP-dependent Clp protease ATP-binding subunit ClpX, putative AT3G53520 -8.90 -11.20 NAD-dependent epimerase/dehydratase family protein AT4G36530 -10.08 -4.63 hydrolase, alpha/beta fold family protein AT5G22880 -26.74 -4.23 histone H2B, putative *IDs in bold are genes with opposite regulation Cluster analysis of zeatin and BR treated sample Besides...”
- Reduced expression of the genes encoding chloroplast-localized proteins in a cold-resistant bri1 (brassinosteroid-insensitive 1) mutant
Kim, Plant signaling & behavior 2010 (secret)
MhpC / b0349 2-hydroxy-6-ketonona-2,4-dienedioate hydrolase (EC 3.7.1.14) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
mhpC / P77044 2-hydroxy-6-ketonona-2,4-dienedioate hydrolase (EC 3.7.1.14) from Escherichia coli (strain K12) (see 10 papers)
MHPC_ECOLI / P77044 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase; 2-hydroxy-6-ketonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; EC 3.7.1.14 from Escherichia coli (strain K12) (see 4 papers)
P77044 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase (EC 3.7.1.14) from Escherichia coli (see 4 papers)
NP_414883 2-hydroxy-6-ketonona-2,4-dienedioate hydrolase from Escherichia coli str. K-12 substr. MG1655
28% identity, 68% coverage
- function: Catalyzes the cleavage of the C5-C6 bond of 2-hydroxy-6- oxononadienedioate and 2-hydroxy-6-oxononatrienedioate, a dienol ring fission product of the bacterial meta-cleavage pathway for degradation of phenylpropionic acid. MhpC shows some selectivity for the carboxylate of the side chain.
catalytic activity: (2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2Z)-2- hydroxypenta-2,4-dienoate + succinate + H(+) (RHEA:34187)
catalytic activity: (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate + H(+) (RHEA:34191)
subunit: Homodimer. - Evidence for a gem-diol reaction intermediate in bacterial C-C hydrolase enzymes BphD and MhpC from 13C NMR spectroscopy.
Li, Biochemistry 2006 (PubMed)- GeneRIF: A new line-broadened signal was observed upon incubation of the (13)C-labeled substrate with an H114A MhpC mutant, which is able to accept the 6-phenyl-containing substrate, on a shorter time scale.
- Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD.
Li, Biochemistry 2006 (PubMed)- GeneRIF: Replacement of Arg-188 in MhpC with Gln and Lys led to 200- and 40-fold decreases, respectively, in k(cat).
- Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants.
Li, Journal of molecular biology 2005 (PubMed)- GeneRIF: A catalytic mechanism is proposed involving stabilisation of reactive intermediates and activation of a nucleophilic water molecule by Ser110
- The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism.
Dunn, Journal of molecular biology 2005 (PubMed)
MSMEG_2900 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Mycobacterium smegmatis str. MC2 155
A0QWD3 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_2900, MSMEI_2827 alpha/beta fold hydrolase from Mycolicibacterium smegmatis MC2 155
30% identity, 69% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...N -acetyltransferase MSMEG_3513 (EC 2.3.1.) 0.05 0.04 A0QV52 MSMEG_2450, MSMEI_2388 Adenosylmethionine-8-amino-7-oxononanoate transaminase 0.03 0.02 A0QWD3 MSMEG_2900, MSMEI_2827 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.) 0.03 0.02 0.27 0.24 A0QZ01 lipT , MSMEG_3848, MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...Uncharacterized N -acetyltransferase MSMEG_3513 (EC 2.3.1.) 0.05 0.04 A0QV52 MSMEG_2450, MSMEI_2388 Adenosylmethionine-8-amino-7-oxononanoate transaminase 0.03 0.02 A0QWD3 MSMEG_2900, MSMEI_2827 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.) 0.03 0.02 0.27 0.24 A0QZ01 lipT , MSMEG_3848, MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...-acetyltransferase MSMEG_3513 (EC 2.3.1.) 0.05 0.04 A0QV52 MSMEG_2450, MSMEI_2388 Adenosylmethionine-8-amino-7-oxononanoate transaminase 0.03 0.02 A0QWD3 MSMEG_2900, MSMEI_2827 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.) 0.03 0.02 0.27 0.24 A0QZ01 lipT , MSMEG_3848, MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD ,...”
TOL_0906 alpha/beta fold hydrolase from Thalassolituus oleivorans MIL-1
29% identity, 66% coverage
B5SU85 2,6-dioxo-6-phenylhexa-3-enoate hydrolase (EC 3.7.1.8) from Dyella ginsengisoli (see paper)
30% identity, 67% coverage
MAB_3810 Putative hydrolase, alpha/beta fold from Mycobacterium abscessus ATCC 19977
29% identity, 69% coverage
- The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus
Crowe, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...two candidates, each encoding proteins with 40% amino acid sequence identity to HsaD Mtb : Mab_3810 and Mab_4366c. The former, identified henceforth as hsaD , occurs in a predicted single gene operon, 1.8 Mb from the hsaACB operon. Interestingly, a mycobacterial KstR-binding site as defined by...”
- “...plasmids for HsaD Mtb were described previously ( 7 ). The hsaD Mab gene ( mab_3810 ) was amplified from M. abscessus ATCC 19977 (ASM6918v1) genomic DNA using oligonucleotides MabhsaD_NdeI_F and MabhsaD_HindIII_R ( SI Appendix , Table S4 ). The amplicon was digested with NdeI and...”
GSU3157 hydrolase, alpha/beta fold family from Geobacter sulfurreducens PCA
32% identity, 68% coverage
plu2202 No description from Photorhabdus luminescens subsp. laumondii TTO1
29% identity, 68% coverage
- Cinnamic acid, an autoinducer of its own biosynthesis, is processed via Hca enzymes in Photorhabdus luminescens
Chalabaev, Applied and environmental microbiology 2008 - “...MhpC, and MhpD homologs in P. luminescens are Plu2208, Plu2202, and Plu2201, respectively, with amino acid identities of 41% (e-value of 5e-73), 28% (e-value of...”
- “...Dotted arrows indicate homology between plu2201 and mhpD, plu2202 and mhpC, and plu2208 and mhpB. For hca genes, genes with similar shadings encode subunits...”
2og1A / P47229 Crystal structure of bphd, a c-c hydrolase from burkholderia xenovorans lb400 (see paper)
30% identity, 58% coverage
BPHD_PARXL / P47229 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Paraburkholderia xenovorans (strain LB400) (see 2 papers)
P47229 2,6-dioxo-6-phenylhexa-3-enoate hydrolase (EC 3.7.1.8) from Paraburkholderia xenovorans (see 2 papers)
BphD / CAA46911.1 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate hydrolase from Pseudomonas sp (see paper)
WP_011494293 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Cupriavidus necator H850
30% identity, 58% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer. - The lid domain of the MCP hydrolase DxnB2 contributes to the reactivity toward recalcitrant PCB metabolites.
Ruzzini, Biochemistry 2013 - GeneRIF: Data indicate that the chlorine substituent is accommodated by a hydrophobic pocket that is larger than the homologous site in BphDLB400 from Burkholderia xenovorans LB400.
- Evidence for a gem-diol reaction intermediate in bacterial C-C hydrolase enzymes BphD and MhpC from 13C NMR spectroscopy.
Li, Biochemistry 2006 (PubMed)- GeneRIF: Site-directed single mutants of BphD in which catalytic residues His-265 and Ser-112 were replaced with Ala possessed 10(4)-fold reduced k(cat) values, and in each case, the C-C cleavage step was rate-limiting.
- Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD.
Li, Biochemistry 2006 (PubMed)- GeneRIF: replacements with Gln and Lys for Arg-190 of BphD led to 400- and 700-fold decreases, respectively, in k(cat)
PFLU_1856 alpha/beta fold hydrolase from Pseudomonas [fluorescens] SBW25
30% identity, 68% coverage
Q8KRR8 2-hydroxymuconic semialdehyde hydrolase from Pseudomonas fluorescens
33% identity, 72% coverage
Ngar_c14400 alpha/beta fold hydrolase from Candidatus Nitrososphaera gargensis Ga9.2
27% identity, 69% coverage
- The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1
Chow, Scientific reports 2018 - “...possible candidates that could serve as bioC analogues ( bioC1-4 ). The ORFs Ngar_c21820, Ngar_c24650, Ngar_c14400 ( i . e . estN1 ), Ngar_c30910 ( i . e . estN2 ), Ngar_c32780 and Ngar_c35080, which could possibly encode a BioH analogue, were amplified with specific primers,...”
- “...in E . coli Rosetta-gami 2 (DE3) and enzyme purification As mentioned above, thegene estN1 (Ngar_c14400) encoding an active esterasewas cloned into the pET21a expression vector (Table S1). The plasmid was transformed into E . coli BL21 [DE3; F ompT hsdS g (r g m g...”
PSPTO_0675 arylesterase from Pseudomonas syringae pv. tomato str. DC3000
31% identity, 67% coverage
BPHD_PSEPU / Q52036 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see paper)
30% identity, 67% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer. - Metabolic perceptrons for neural computing in biological systems
Pandi, Nature communications 2019 - “...sp.) identifier: UniProtKB - P17297 bphD (2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC: 3.7.1.8), Pseudomonas putida) identifier: UniProtKB - Q52036 Benzamide transforming enzyme (Amidase (EC: 3.5.1.4), Rhodococcus erythropolis) identifier: UniProtKB - B4XEY3 Sequence and source of all the genes and parts are available in Supplementary Table 5 and the plasmids...”
RHA1_RS28300 alpha/beta fold hydrolase from Rhodococcus jostii RHA1
RHA1_ro05797 alpha/beta-fold C-C bond hydrolase from Rhodococcus sp. RHA1
31% identity, 69% coverage
- Degradation of Bile Acids by Soil and Water Bacteria
Feller, Microorganisms 2021 - “...-steroid dioxygenase C211_RS11215 CTCNB1_RS06510 (TesB) RHA1_RS28330 (HsaC3) Nov2c350 4,5,9,10-di seco -steroid hydroxylase C211_RS11155 CTCNB1_RS06910 (TesD) RHA1_RS28300 (HsaD3) Nov2c348 C/D-ring (HIP) side-chain degradation CoA-ligase C211_RS11045 (StdA3 *) CTCNB1_RS06940 (ScdA) RHA1_RS22410 ** (FadD3) Nov2c359 ACAD C211_RS11065 (Scd3A) CTCNB1_RS06570 (ScdC1) RHA1_RS22390 ** Nov2c367 C211_RS11070 (Scd3B) CTCNB1_RS06575 (ScdC2) RHA1_RS22415 **...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352 RHA1_ro05800 RHA1_ro04534 Rv3535c Propanol...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...(RHA1_RS28325) (RHA1_RS22125) HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG...”
MAV_2517 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase from Mycobacterium avium 104
30% identity, 68% coverage
EstN1 / K0IAM1 pimeloyl-[acyl-carrier protein] methyl ester esterase (EC 3.1.1.85) from Nitrososphaera gargensis (strain Ga9.2) (see paper)
27% identity, 68% coverage
hppC / AAB81313.1 2-hydroxy-6-ketonona-2,4-dienoate hydrolase from Rhodococcus globerulus (see paper)
31% identity, 67% coverage
Q9KJG6 triacylglycerol lipase (EC 3.1.1.3) from Pseudomonas aeruginosa (see paper)
PA2949 probable lipase from Pseudomonas aeruginosa PAO1
32% identity, 62% coverage
- Mining bacterial genomes for novel arylesterase activity
Wang, Microbial biotechnology 2010 - “...purified carboxylic ester hydrolases. Property PaEST1 PpEST1 PpEST2 PpEST3 RpEST1 RpEST2 RpEST3 SavEST1 UniProt ID Q9KJG6 Q88QX0 Q88CC8 Q88GS3 Q6NCW9 Q6N0W4 Q6N4A9 Q82QJ4 MW a 34.8 26.3 30 31.1 32.4 26.2 27.2 28.5 pI a 6.1 5.0 4.9 5.1 5.3 5.3 5.6 5.4 pH optimum 79...”
- Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-Regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa
Gentile, JACS Au 2024 - “...procedures. 6 For obtaining PlaF variants of the lid-like domain, site-directed mutagenesis of plaF ( pa2949 ) was carried out using the Quik-Change PCR method with the Phusion DNA polymerase and the pET_pa2949 plasmid. 74 Similarly, mutants located in the T3 tunnel were generated through site-directed...”
- “...Gohlke H. ; Batra-Safferling R. ; Jaeger K. E. ; Kovacic F. Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization . Acta Crystallogr. F Struct. Biol. 2019 , 75 ( 4 ), 270 7 . 10.1107/S2053230X19002152 ....”
- Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa
Bleffert, eLife 2022 - “...P. aeruginosa PAO1 (WT) cells transformed ( Choi et al., 2006 ) with plasmid pBBR- pa2949 ( Kovacic et al., 2016 ), here abbreviated as p- plaF , were grown overnight at 37C in lysogeny broth (LB) medium supplemented with tetracycline (100 g/ml) ( Bleffert et...”
- “...F Granzin J Gohlke H Batra-Safferling R Jaeger KE Kovacic F 2019 Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization Acta Crystallographica. Section F, Structural Biology Communications 75 270 277 10.1107/S2053230X19002152 30950828 Bleves S Lazdunski A Filloux...”
- Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization
Bleffert, Acta crystallographica. Section F, Structural biology communications 2019 - “...2053-230X International Union of Crystallography 6450514 aq5005 10.1107/S2053230X19002152 ACSFEN S2053230X19002152 Research Communications Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization Pseudomonas aeruginosa esterase PA294 Bleffert Florian a Granzin Joachim b Gohlke Holger b c d Batra-Safferling Renu...”
- “...of this article is available from Crystallography Journals Online. Homologous expression of the membrane-bound esterase PA2949 from Pseudomonas aeruginosa PA01 and the purification of detergent-solubilized enzyme resulted in stable PA2949 protein that crystallized. The crystals obtained were used for X-ray analysis and diffracted to a resolution...”
- Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates
Siebers, PloS one 2018 - “...as the amount of enzyme releasing 1.0 mol min -1 of lauric acid. Phospholipase A PA2949 from Pseudomonas aeruginosa was used as control [ 35 ]. Protease activity was determined by degradation of fluorescein-tagged casein using the Thermo fluorescent protease assay kit (Thermo Scientific) with 25...”
- “..., Wilhelm S , Granzin J , Batra-Safferling R , et al A membrane-bound esterase PA2949 from Pseudomonas aeruginosa is expressed and purified from Escherichia coli . FEBS Open Bio . 2016 ; 6 ( 5 ): 484 93 . doi: 10.1002/2211-5463.12061 27419054 36 Grosser K...”
- Additive Effects of Quorum Sensing Anti-Activators on Pseudomonas aeruginosa Virulence Traits and Transcriptome
Asfahl, Frontiers in microbiology 2017 - “...) 1.5 NC NC NC PA2939 probable aminopeptidase ( pepB ) 2.7 4.1 9.1 11.5 PA2949 probable lipase 1.4 NC NC NC PA3326 clpP2 ClpP2 2.5 7.2 7.3 7.0 PA3327 probable non-ribosomal peptide synthetase 3.3 16.1 8.1 3.5 PA3328 probable FAD-dependent monooxygenase 4.5 21.9 12.4 5.4...”
- A membrane-bound esterase PA2949 from Pseudomonas aeruginosa is expressed and purified from Escherichia coli
Kovacic, FEBS open bio 2016 - “...Wiley and Sons Inc. Hoboken 4856427 10.1002/2211-5463.12061 FEB412061 Research Article Research Articles A membranebound esterase PA2949 from Pseudomonasaeruginosa is expressed and purified from Escherichiacoli F. Kovacic etal . Kovacic Filip 1 Bleffert Florian 1 Caliskan Muttalip 1 Wilhelm Susanne 1 Granzin Joachim 2 BatraSafferling Renu 2...”
- “...a precursor of captopril, a drug used for treatment of hypertension. We show here that PA2949 from P.aeruginosa PA01, a homologue of EstA, can efficiently be expressed in an enzymatically active form in E.coli . The enzyme is membraneassociated as demonstrated by cell fractionation studies. PA2949...”
- Sequence- and activity-based screening of microbial genomes for novel dehalogenases
Chan, Microbial biotechnology 2010 - “...activity pNPpalmitate PalmitoylCoA pNPP+Mg 2+ pNPP+cations ABH PA5513 High 0.76 3.2 1.0 1.2 Thioesterase ABH PA2949 Low 2.6 2.2 0.92 0.92 Esterase ABH PP4164 High 0.83 2.8 0.90 0.95 Thioesterase ABH PP2567 High 0.88 2.4 0.95 0.99 Thioesterase ABH PP2083 High 0.74 2.1 0.92 0.96 Thioesterase...”
- In vivo evidence of Pseudomonas aeruginosa nutrient acquisition and pathogenesis in the lungs of cystic fibrosis patients
Son, Infection and immunity 2007 - “...Phospholipases and lipases PA0843 PA0844 PA2862 PA2863 PA2949 PA4813 Gene VOL. 75, 2007 P. AERUGINOSA NUTRIENT ACQUISITION AND PATHOGENESIS 5321 material)....”
- More
6i8wB / Q9KJG6 Crystal structure of a membrane phospholipase a, a novel bacterial virulence factor (see paper)
33% identity, 62% coverage
- Ligand: undecanoic acid (6i8wB)
F1721_00695 alpha/beta fold hydrolase from Saccharopolyspora hirsuta
30% identity, 69% coverage
P96965 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) from Pseudomonas fluorescens (see 2 papers)
cumD / BAA12150.1 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase from Pseudomonas fluorescens (see paper)
28% identity, 68% coverage
BPHD_METFU / Q52011 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Metapseudomonas furukawaii (Pseudomonas furukawaii) (see paper)
bphD / BAA12881.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid hydrolase from Pseudomonas oleovorans (see paper)
31% identity, 58% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer.
YP_001188192 alpha/beta hydrolase fold from Pseudomonas mendocina ymp
29% identity, 66% coverage
- Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment
Jeon, Evidence-based complementary and alternative medicine : eCAM 2011 - “...acyl hydrolase from Moritella marina ; YP_001530963, an / hydrolase fold from Desulfococcus oleovorans Hxd3; YP_001188192, an / hydrolase fold from Pseudomonas mendocina ymp (YP_001188192). (c) EstD2 family including EM3L2: ZP_01915829, a hypothetical protein from Limnobacter sp. MED105; ADN26553, an EstD2 from uncultured bacterium; ZP_00952831, a...”
nahN / BAE92169.1 2-hydroxymuconic semialdehyde hydrolase NahN from Pseudomonas putida (see 2 papers)
32% identity, 72% coverage
RSPO_c00415 alpha/beta fold hydrolase from Ralstonia solanacearum Po82
30% identity, 70% coverage
- A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum
Castillo, BMC evolutionary biology 2019 - “...precursor transmembrane protein IIB/chromosome RSPO_c00179 gcl 1 0.0240** 2.1552** 1.5475** Tartronate-semialdehyde synthase (glyoxylate carboligase) IIB/chromosome RSPO_c00415 RSPO_c00416 1 0.0352** 2.0846** 1.4063** b-ketoadipate enol-lactone hydrolase protein and 3-ketoacyl-(acyl-carrier-protein) reductase IIB/chromosome RSPO_c00497 secY 1 0.0282** 1.9898** 1.5826** Preprotein translocase (membrane subunit) IIB/chromosome RSPO_c00765 phcB 1 0.0240** 2.1264** 1.5475**...”
hsaD / P9WNH5 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase monomer (EC 3.7.1.17) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 3 papers)
HSAD_MYCTU / P9WNH5 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase; 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; Meta-cleavage product hydrolase; MCP hydrolase; EC 3.7.1.17; EC 3.7.1.8 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 4 papers)
P9WNH5 2,6-dioxo-6-phenylhexa-3-enoate hydrolase (EC 3.7.1.8) from Mycobacterium tuberculosis (see paper)
Rv3569c 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD from Mycobacterium tuberculosis H37Rv
Mb3600c 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD from Mycobacterium bovis AF2122/97
29% identity, 68% coverage
- function: Catalyzes the hydrolysis of a carbon-carbon bond in 4,5: 9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate (4,9- DSHA) to yield 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oate (DOHNAA) and 2-hydroxy-hexa-2,4-dienoate (HHD). Is also able to catalyze the hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) and the synthetic analog 8-(2-chlorophenyl)-2-hydroxy-5- methyl-6-oxoocta-2,4-dienoic acid (HOPODA).
catalytic activity: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta- 1(10),2-dien-4-oate + H2O = 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo- octahydro-1H-inden-4-yl]propanoate + (2Z,4Z)-2-hydroxyhexa-2,4- dienoate + H(+) (RHEA:32035)
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer. - Novel target and cofactor repertoire for the transcriptional regulator JTY_0672 from <i>Mycobacterium bovis</i> BCG
Wang, Frontiers in microbiology 2024 - “...under H 2 O 2 stress ( Li et al., 2020 ). The binding of Rv3569c with Ser has shown to result in the reduced activity of enzymes involved in lipid metabolism in Mtb ( Barelier et al., 2023 ). Rv1460 is a repressor of the...”
- “...Roig-Zamboni V. Poncin I. ( 2023 ). Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis. FEBS J. 290 1563 1582 . 10.1111/febs.16645 36197115 Bharati B. K. Sharma I. M. Kasetty S. Kumar M. Mukherjee R. Chatterji D. ( 2012 ). A full-length...”
- Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis
Barelier, The FEBS journal 2023 (PubMed)- “...many of them involved in lipid or steroid metabolisms. One of the captured enzymes, HsaD (Rv3569c), is required for the survival of M. tb within macrophages and is thus a potential therapeutic target. This prompted us to further explore and validate, through a combination of biochemical...”
- The Prospect of Repurposing Immunomodulatory Drugs for Adjunctive Chemotherapy against Tuberculosis: A Critical Review
Lee, Antibiotics (Basel, Switzerland) 2021 - “...in vitro whole-cell screens but are critical in vivo, such as mycobacterial HsaD. The hsaD (Rv3569c) gene is found to be essential for mycobacterial cholesterol metabolism within macrophages, and its hypomorphs have been used to identify and develop novel chemical leads in antibiotic discovery [ 91...”
- Comprehensive Comparative Analysis of Cholesterol Catabolic Genes/Proteins in Mycobacterial Species
van, International journal of molecular sciences 2019 - “...probable acyl-CoA dehydrogenase fadE32 Rv3563 a,b,c probable acyl-CoA dehydrogenase hsaC Rv3568c a,c,d 3,4-DHSA dioxygenase hsaD Rv3569c b,c,d 4,9-DHSA hydrolase hsaA Rv3570c b,c,d 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione hydroxylase (3-HSA hydroxylase, reductase) kshB Rv3571 a,c,d ketosteroid-9-hydroxylase, reductase mce4F Rv3494c c,d Mce4 transport system mce4D Rv3496c c,d Mce4 transport system mce4B Rv3498c...”
- More than cholesterol catabolism: regulatory vulnerabilities in Mycobacterium tuberculosis
Bonds, Current opinion in chemical biology 2018 - “...Cholesterol CD Ring Degradation Acyl-CoA dehydrogenase (-subunit) Rv3568c HsaC Cholesterol AB Ring Degradation 3,4-DHSA dioxygenase Rv3569c HsaD Cholesterol AB Ring Degradation 4,9-DHSA hydrolase RV3570c HsaA Cholesterol AB Ring Degradation 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione hydroxylase 1 Red circle: acetylation; yellow star: succinylation; SS : disulfide formation. Highlights Cholesterol is important...”
- Cyclipostins and Cyclophostin analogs as promising compounds in the fight against tuberculosis
Nguyen, Scientific reports 2017 - “...32.1 Lipase/esterase LM 43 Mycolic acid synthase UmaA Rv0469 33.1 Methyltransferase LM 34 Hydrolase hsaD Rv3569c 32.1 Macrophages and growth on cholesterol Hydrolase IM/R 53 , 54 7 Monoglyceride lipase Rv0183 30.2 Lipase/esterase IM/R 39 , 40 Thioesterase tesA Rv2928 29.1 in vitro Lipase/esterase LM 48...”
- “...and Ag85C (Rv0129c), the thioesterase TesA (Rv2928), the carboxylesterase CaeA (Rv2224c) and the hydrolase HsaD (Rv3569c); the latter two proteins being annotated as essential enzymes 44 . Ag85A and Ag85C express both a mycolyl transferase activity. They catalyze the transfer of mycolic acids from trehalose monomycolate...”
- Cholesterol metabolism: a potential therapeutic target in Mycobacteria
Abuhammad, British journal of pharmacology 2017 - “...facilitate the optimization of these inhibitors. HsaD HsaD (Rv3569c) was identified as a meta-cleavage product (MCP) hydrolase. It catalyses the hydrolysis of a...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352...”
- More
- Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosis
Lack, Acta crystallographica. Section F, Structural biology and crystallization communications 2008 - “...and Rv3566c . The corresponding genes in M. bovis BCG have accession numbers Mb3601c , Mb3600c , Mb3599c , Mb3598c , Mb3597c and Mb3596c . Figure 2 Sequence alignment of the HsaD protein from M. tuberculosis with BphDs from B. xenovorans (PDB code 2og1 ) and...”
- Characterization of the putative operon containing arylamine N-acetyltransferase (nat) in Mycobacterium bovis BCG
Anderton, Molecular microbiology 2006 (PubMed)- “...operon. Two genes in the operon, Mb3599c and Mb3600c, are predicted to encode homologues of enzymes annotated as a 2,3-dihydroxybiphenyl 1,2-dioxygenase (bphC5)...”
- “...A2, A3, A4, A5 and A6 correspond to Mb3601c, Mb3600c, Mb3599c, Mb3568c, Mb3567c and Mb3566c respectively, using either cDNA (+) and mock cDNA produced without...”
WP_042686824 alpha/beta fold hydrolase from Candidatus Nitrosotenuis chungbukensis
24% identity, 69% coverage
5jz9A / P9WNH5 Crystal structure of hsad bound to 3,5-dichloro-4- hydroxybenzenesulphonic acid (see paper)
29% identity, 68% coverage
- Ligand: 3,5-dichloro-4-hydroxybenzene-1-sulfonic acid (5jz9A)
G3KFX4 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) from Pseudomonas sp. (see paper)
32% identity, 69% coverage
1iunB / P96965 Meta-cleavage product hydrolase from pseudomonas fluorescens ip01 (cumd) s103a mutant hexagonal (see paper)
28% identity, 68% coverage
- Ligand: acetate ion (1iunB)
MXAN_0220 hydrolase, alpha/beta fold family from Myxococcus xanthus DK 1622
28% identity, 59% coverage
MHPC_COMTE / Q8KZP5 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase; 2-hydroxy-6-ketonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; EC 3.7.1.14 from Comamonas testosteroni (Pseudomonas testosteroni) (see paper)
30% identity, 65% coverage
- function: Catalyzes the cleavage of the C5-C6 bond of 2-hydroxy-6- oxononadienedioate, and probably also 2-hydroxy-6-oxononatrienedioate, a dienol ring fission product of the bacterial meta-cleavage pathway for degradation of phenylpropionic acid.
catalytic activity: (2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2Z)-2- hydroxypenta-2,4-dienoate + succinate + H(+) (RHEA:34187)
catalytic activity: (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate + H(+) (RHEA:34191)
subunit: Homodimer.
BCG_2728 putative hydrolase from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv2715 POSSIBLE HYDROLASE from Mycobacterium tuberculosis H37Rv
29% identity, 61% coverage
- Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target
Xu, PLoS pathogens 2022 - “...), and BCG_0695c (64.6% identity with MSMEG_1352, bioH2 ). In contrast, the most similar one, BCG_2728 displayed only 14.9% identity with MSMEG_6710 ( bioH3 ). Thus, they also were genetically amenable to functional assays. To extend biochemical assays, a panel of engineering E . coli strains...”
- Biochemical characterisation of pimelate biosynthetic genes of Mycobacterium tuberculosis
Gugu, 2019 - Oxidative Phosphorylation as a Target Space for Tuberculosis: Success, Caution, and Future Directions
Cook, Microbiology spectrum 2017 - “...is easily identifiable as encoding a protein with similar function to MenH. Rv0045c, Rv1938 and Rv2715 are all potential candidates, although none encode a protein with a high degree of similarity to MenH from E. coli . The isoprenoid tail of the menaquinone must be generated...”
- “...( 87 ), suggesting other non-specific thioesterase activities can compensate. Similarly Rv0045c , Rv1938 and Rv2715 encode potential, but low probability, candidates for 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH) in M. tuberculosis , none of which are predicted to be essential. In this case it should be noted that...”
- Structural Analysis of Mycobacterium tuberculosis Homologues of the Eukaryotic Proteasome Assembly Chaperone 2 (PAC2)
Bai, Journal of bacteriology 2017 - “...eukaryotic system, we 75 asked if Rv2125 or Rv2715 might function as bacterial proteasome assembly 76 chaperones. We conducted biochemical and structural...”
- Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence
Ortega, Cell chemical biology 2016 - “...hydrolase Rv1769 Rv1770 peptidase peptidase Rv1794 other c Rv2061c other Rv2204c other Rv2695 hydrolase hydrolase Rv2715 hydrolase hydrolase hydrolase Rv3311 poor prediction Rv3312c hydrolase hydrolase hydrolase Rv3401 hydrolase hydrolase hydrolase Rv3528c other Rv3591c hydrolase hydrolase Rv3722c other Rv3802c lipase cutinase hydrolase a PDB: 3P2M. b Phosphoserine...”
- Partial Saturation of Menaquinone in Mycobacterium tuberculosis: Function and Essentiality of a Novel Reductase, MenJ
Upadhyay, ACS central science 2015 - “...biosynthetic pathway enzyme M. tuberculosis gene ref chorismate MenF Rv3215 isochorismate MenD Rv0555 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate MenH Rv2715 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate MenC Rv0553 2-succinylbenzoic acid MenE Rv0166 ( 37 ) 2-succinylbenzoyl-CoA MenB Rv0548c ( 34 ) 1,4-dihydroxy-2-naphthoate-CoA MenI Rv1847 1,4-dihydroxy-2-naphthoate MenA Rv0534c ( 48 ) demethylmenaquinone MenG Rv0558 , Rv0560c...”
- Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig
Kato-Maeda, Clinical and vaccine immunology : CVI 2012 - “...Rv0634c Rv1009 Rv1140 Rv1207 Rv1638 Rv1665 Rv2416c Rv2715 Rv3167c Rv3665c Rv3886c Rv0775 Rv0826 Rv0989c Rv1152 Rv1295 Rv1317c Rv1502 Rv1811 Rv2124c Rv2394...”
- Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis
Shi, Journal of the American Chemical Society 2011 - “...type II pathway along with BioC ( Mtb ortholog: Rv0089) and BioH ( Mtb ortholog: Rv2715) for synthesis of pimeloyl-ACP, which is proposed as the physiologically relevant substrate for BioF. 7 Amiclenomycin (ACM) isolated from Streptomyces lavendulae subsp. amiclenomycini and its simplified amino-alcohol analogue ACM-OH are...”
TTE0552 predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) from Thermoanaerobacter tengcongensis MB4
29% identity, 69% coverage
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...210 GISGN Thermoanaerobacter tengcongensis TTE0035 AAM23348 Hypothetical protein 237 GDSIS TTE0419 AAM23703 Lysophospholipase 314 GHSFG TTE0552 AAM23828 Predicted hydrolase 279 GVSMG TTE0556 AAM23832 Predicted hydrolase 298 GWSMG TTE1809 AAM25001 Alpha/beta hydrolase 258 GLSMG TTE2321 AAM25462 Alpha/beta hydrolase 414 CHSMG TTE2547 AAM25672 Alpha/beta hydrolase 285 AHSFG Thermococcus...”
BPHD_PSES1 / P17548 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Pseudomonas sp. (strain KKS102) (see paper)
31% identity, 57% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer.
KR76_14475 4,5:9,10-diseco-3-hydroxy-5,9, 17-trioxoandrosta-1(10),2-diene-4-oate hydrolase from Pimelobacter simplex
28% identity, 67% coverage
flnE / BAC75995.1 meta cleavage compound hydrolase from Terrabacter sp. DBF63 (see paper)
Q83ZF0 2-hydroxy-6-oxo-6-(2'-carboxyphenyl)-hexa-2,4-dienoate hydrolase from Terrabacter sp. (strain DBF63)
28% identity, 66% coverage
ABHD6_MOUSE / Q8R2Y0 Monoacylglycerol lipase ABHD6; 2-arachidonoylglycerol hydrolase; Abhydrolase domain-containing protein 6; EC 3.1.1.23 from Mus musculus (Mouse) (see 4 papers)
27% identity, 64% coverage
- function: Lipase that preferentially hydrolysis medium-chain saturated monoacylglycerols including 2-arachidonoylglycerol (PubMed:18096503, PubMed:20657592). Through 2-arachidonoylglycerol degradation may regulate endocannabinoid signaling pathways (PubMed:18096503, PubMed:20657592). Also has a lysophosphatidyl lipase activity with a preference for lysophosphatidylglycerol among other lysophospholipids (PubMed:24095738). Also able to degrade bis(monoacylglycero)phosphate (BMP) and constitutes the major enzyme for BMP catabolism (PubMed:26491015). BMP, also known as lysobisphosphatidic acid, is enriched in late endosomes and lysosomes and plays a key role in the formation of intraluminal vesicles and in lipid sorting (PubMed:26491015).
catalytic activity: Hydrolyzes glycerol monoesters of long-chain fatty acids.
catalytic activity: 2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = glycerol + (5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) (RHEA:26132)
catalytic activity: 1-octanoylglycerol + H2O = octanoate + glycerol + H(+) (RHEA:44328)
catalytic activity: 1-decanoylglycerol + H2O = decanoate + glycerol + H(+) (RHEA:44320)
catalytic activity: 1-dodecanoylglycerol + H2O = dodecanoate + glycerol + H(+) (RHEA:44316)
catalytic activity: 1-tetradecanoylglycerol + H2O = tetradecanoate + glycerol + H(+) (RHEA:44312)
catalytic activity: 2-hexadecanoylglycerol + H2O = glycerol + hexadecanoate + H(+) (RHEA:39963)
catalytic activity: 2-(9Z-octadecenoyl)-glycerol + H2O = glycerol + (9Z)- octadecenoate + H(+) (RHEA:38491)
catalytic activity: 1-(9Z-octadecenoyl)-glycerol + H2O = glycerol + (9Z)- octadecenoate + H(+) (RHEA:38487)
catalytic activity: 2-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:44732)
catalytic activity: 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = glycerol + (5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) (RHEA:44728)
catalytic activity: 1-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:48428)
catalytic activity: 3-(9Z-octadecenoyl)-sn-glycero-1-phospho-(3'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = 3-(9Z-octadecenoyl)-sn-glycero- 1-phospho-(1'-sn-glycerol) + (9Z)-octadecenoate + H(+) (RHEA:55712)
catalytic activity: (S,S)-2-(9Z-octadecenoyl)-sn-glycero-1-phospho-(2'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = (S,S)-2-(9Z-octadecenoyl)-sn- glycero-1-phospho-(1'-sn-glycerol) + (9Z)-octadecenoate + H(+) (RHEA:55716)
catalytic activity: (R,R)-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(2'-(9Z- octadecenoyl)-3'-sn-glycerol) + H2O = (R,R)-2-(9Z-octadecenoyl)-sn- glycero-3-phospho-(3'-sn-glycerol) + (9Z)-octadecenoate + H(+) (RHEA:55804)
disruption phenotype: Abhd6 partial knockdown inducing a stronger depletion in liver, kidney and white adipose tissues protects mice against hight-fat diet-induced metabolic disorder and obesity. De novo lipogenesis in liver is reduced and associated with a reduced expression of lipogenic genes. Accumulation of phospholipids and lysophospholipds in the liver is also observed. - Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach.
Zhou, Oncotarget 2016 - “...0.0253 (23) [ 69 ] Q27757 Luciferin 4-monooxygenase Firefly 0.0239 (20) 0.0153 (14) 0.0241 (20) Q8R2Y0 Monoacylglycerol lipase ABHD6 Mouse 0.0245 (21) 0.0272 (29) - [ 70 ] P49286 Melatonin receptor type 1B Human 0.0247 (22) 0.0245 (24) 0.0247 (22) [ 53 ] P35968 Vascular endothelial...”
RSP_1258 putative hydrolase from Rhodobacter sphaeroides 2.4.1
29% identity, 66% coverage
- Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
Dufour, PLoS genetics 2012 - “...Detoxification RSP_1057, RSP_2389, RSP_2693, RSP_3263 Toxin production and resistance RSP_2803 Central intermediary metabolism Other RSP_0897, RSP_1258, RSP_1397, RSP_3072 Phosphorus compounds RSP_0782 Protein synthesis/fate Amino acid biosynthesis RSP_0398 Degradation of proteins, peptides, and glycopeptides RSP_0686, RSP_1490 Protein folding and stabilization RSP_1219 tRNA and rRNA base modification RSP_2971...”
Q2VLB9 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Burkholderia cepacia
29% identity, 65% coverage
estRB8 / CAE54381.1 carboxylesterase, partial from Oleispira antarctica (see paper)
estRB8 / CAE54384.1 carboxylesterase from Oleispira antarctica (see paper)
24% identity, 66% coverage
pRL100243 putative hydrolase from Rhizobium leguminosarum bv. viciae 3841
30% identity, 69% coverage
cbzF / AAX50133.1 CbzF from Pseudomonas putida (see paper)
29% identity, 63% coverage
Alide2_0281, Alide_0336 alpha/beta fold hydrolase from Alicycliphilus denitrificans BC
32% identity, 66% coverage
- Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.)
Oosterkamp, PloS one 2013 - “...to 2-oxopent-4-enoate. The enzyme catalyzing this conversion is a 2-hydroxymuconic semialdehyde hydrolase (Alide_0336 in BC; Alide2_0281 in K601 T ). Methyl-catechol and catechol are converted to 2-oxopent-4-enoate using the oxalocrotonate branch of the meta-cleavage pathway, which proceeds via a dehydrogenase, tautomerase and decarboxylase (Alide_0335+0340+0342 in BC;...”
- “...of 2-hydroxymuconic semialdehyde to 2-oxopent-4-enoate. The enzyme catalyzing this conversion is a 2-hydroxymuconic semialdehyde hydrolase (Alide_0336 in BC; Alide2_0281 in K601 T ). Methyl-catechol and catechol are converted to 2-oxopent-4-enoate using the oxalocrotonate branch of the meta-cleavage pathway, which proceeds via a dehydrogenase, tautomerase and decarboxylase...”
PA0829 probable hydrolase from Pseudomonas aeruginosa PAO1
28% identity, 69% coverage
- Recent advances in therapeutic targets identification and development of treatment strategies towards Pseudomonas aeruginosa infections
Sanya, BMC microbiology 2023 - “...also positively monitors the expression of genes in a second putative operon, comprising genes PA0807 PA0829 , to facilitate the survival of P. aeruginosa cells in the host [ 48 ]. On the other hand, P. aeruginosa contains some rhamnolipids (glycolipids molecules) forming micelles that transport...”
- Control of a programmed cell death pathway in Pseudomonas aeruginosa by an antiterminator
Peña, Nature communications 2021 - “...regulates the expression of all of the genes on the positive strand between PA0807 and PA0829 (i.e. PA0807 ( ampDh3 ), PA0808 , PA0815 , PA0817 , PA0819 , PA0820 , PA0828 , and PA0829 ) (Fig. 1a, b ), a finding we confirmed using quantitative...”
- “...(Supplementary Table 1 ). These findings suggest that AlpA exerts its regulatory effects on PA0807 PA0829 directly. AlpA did not detectably associate with the alpB promoter region as assessed by ChIP-Seq (Supplementary Table 1 ). AlpR binding to the alpB promoter region during our ChIP-Seq studies...”
TGND_ACIAD / Q6F9F4 (E)-2-((N-methylformamido)methylene)succinate hydrolase; MFMS hydrolase; EC 3.5.1.- from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (see paper)
ACIAD2545 conserved hypothetical protein; putative hydrolase from Acinetobacter sp. ADP1
27% identity, 67% coverage
- function: Involved in the degradation of the pyridine ring of trigonelline (TG; N-methylnicotinate) into succinate and methylamine as carbon and nitrogen sources, respectively. Catalyzes the hydrolysis of (E)-2-((N-methylformamido)methylene)succinate (MFMS) into formic acid, succinate semialdehyde (SSA), methylamine and carbon dioxide.
catalytic activity: (E)-2-((N-methylformamido) methylene)succinate + 2 H2O + H(+) = succinate semialdehyde + methylamine + formate + CO2 (RHEA:57032)
subunit: Monomer. - Elucidation of the trigonelline degradation pathway reveals previously undescribed enzymes and metabolites
Perchat, Proceedings of the National Academy of Sciences of the United States of America 2018 - “...0.5 ACIAD2539 0.0 0.0 0.5 ACIAD2544 ACIAD2541 1.0 ACIAD2545 1.5 2.0 OD600 (succinate + NH4Cl) ACIAD2543 ACIAD2542 Fig. 1. Phenotyping of the genome-scale ADP1...”
- “...is provided in Table 1. Perchat et al. ACIAD2545 ACIAD2546 Sma0792 Sma0791 Sma0790 Sma0789 PNAS PLUS ACIAD2544 Sma0793 ACIAD2548 ACIAD2543 Sma0794 ACIAD2547...”
NP_001007681 monoacylglycerol lipase ABHD6 from Rattus norvegicus
Q5XI64 Monoacylglycerol lipase ABHD6 from Rattus norvegicus
27% identity, 69% coverage
F1SGJ4 acylglycerol lipase from Sus scrofa
27% identity, 66% coverage
BC4345 Lipase from Bacillus cereus ATCC 14579
26% identity, 60% coverage
A1S_1701 dihydrolipoamide acetyltransferase from Acinetobacter baumannii ATCC 17978
39% identity, 21% coverage
BCAS0226 putative hydrolase from Burkholderia cenocepacia J2315
33% identity, 68% coverage
CBL13_01858 alpha/beta fold hydrolase from Pseudomonas putida
32% identity, 66% coverage
todF / P23133 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase (EC 3.7.1.25) from Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1) (see paper)
TODF_PSEP1 / P23133 2-hydroxy-6-oxo-2,4-heptadienoate hydrolase; HOHH; EC 3.7.1.25 from Pseudomonas putida (strain ATCC 700007 / DSM 6899 / JCM 31910 / BCRC 17059 / LMG 24140 / F1) (see 2 papers)
30% identity, 65% coverage
ABHD6_HUMAN / Q9BV23 Monoacylglycerol lipase ABHD6; 2-arachidonoylglycerol hydrolase; Abhydrolase domain-containing protein 6; EC 3.1.1.23 from Homo sapiens (Human) (see 2 papers)
NP_001307055 monoacylglycerol lipase ABHD6 from Homo sapiens
26% identity, 69% coverage
- function: Lipase that preferentially hydrolysis medium-chain saturated monoacylglycerols including 2-arachidonoylglycerol (PubMed:22969151). Through 2-arachidonoylglycerol degradation may regulate endocannabinoid signaling pathways (By similarity). Also has a lysophosphatidyl lipase activity with a preference for lysophosphatidylglycerol among other lysophospholipids (By similarity). Also able to degrade bis(monoacylglycero)phosphate (BMP) and constitutes the major enzyme for BMP catabolism (PubMed:26491015). BMP, also known as lysobisphosphatidic acid, is enriched in late endosomes and lysosomes and plays a key role in the formation of intraluminal vesicles and in lipid sorting (PubMed:26491015).
catalytic activity: Hydrolyzes glycerol monoesters of long-chain fatty acids.
catalytic activity: 1-octanoylglycerol + H2O = octanoate + glycerol + H(+) (RHEA:44328)
catalytic activity: 1-decanoylglycerol + H2O = decanoate + glycerol + H(+) (RHEA:44320)
catalytic activity: 1-dodecanoylglycerol + H2O = dodecanoate + glycerol + H(+) (RHEA:44316)
catalytic activity: 1-tetradecanoylglycerol + H2O = tetradecanoate + glycerol + H(+) (RHEA:44312)
catalytic activity: 2-hexadecanoylglycerol + H2O = glycerol + hexadecanoate + H(+) (RHEA:39963)
catalytic activity: 2-(9Z-octadecenoyl)-glycerol + H2O = glycerol + (9Z)- octadecenoate + H(+) (RHEA:38491)
catalytic activity: 1-(9Z-octadecenoyl)-glycerol + H2O = glycerol + (9Z)- octadecenoate + H(+) (RHEA:38487)
catalytic activity: 2-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:44732)
catalytic activity: 2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = glycerol + (5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) (RHEA:26132)
catalytic activity: 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = glycerol + (5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) (RHEA:44728)
catalytic activity: 1-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:48428)
catalytic activity: 3-(9Z-octadecenoyl)-sn-glycero-1-phospho-(3'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = 3-(9Z-octadecenoyl)-sn-glycero- 1-phospho-(1'-sn-glycerol) + (9Z)-octadecenoate + H(+) (RHEA:55712)
catalytic activity: (S,S)-2-(9Z-octadecenoyl)-sn-glycero-1-phospho-(2'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = (S,S)-2-(9Z-octadecenoyl)-sn- glycero-1-phospho-(1'-sn-glycerol) + (9Z)-octadecenoate + H(+) (RHEA:55716)
catalytic activity: (R,R)-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(2'-(9Z- octadecenoyl)-3'-sn-glycerol) + H2O = (R,R)-2-(9Z-octadecenoyl)-sn- glycero-3-phospho-(3'-sn-glycerol) + (9Z)-octadecenoate + H(+) (RHEA:55804) - Refining S-acylation: Structure, regulation, dynamics, and therapeutic implications.
Anwar, The Journal of cell biology 2023 - “...Q9UMR5 70,881 ABHD2 P08910 4,273 ABHD3 Q8WU67 1,825 ABHD4 Q8TB40 9,544 ABHD5 Q8WTS1 9,921 ABHD6 Q9BV23 21,560 ABHD10 Q9NUJ1 197,249 ABHD11 Q8NFV4 157,176 ABHD12 Q8N2K0 55,135 ABHD13 Q7L211 4,159 ABHD14A Q9Y3T7 2,545 ABHD14B Q96IU4 607,032 ABHD15 Q96EC5 3,469 ABHD16A O95870 25,149 ABHD17A Q96GS6 27,342 ABHD17B Q5VST6...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Enzymes.
Alexander, British journal of pharmacology 2017 - “...Hydrolase 6 HGNC, UniProt DAGLA , Q9Y4D2 DAGLB , Q8NCG7 MGLL , Q99685 ABHD6 , Q9BV23 EC number 3.1.1. 3.1.1. 3.1.1.23 3.1.1.23 Common abreviation DAGL DAGL MAGL ABHD6 Endogenous substrates diacylglycerol diacylglycerol 2oleoyl glycerol = 2arachidonoylglycerol anandamide [ 181 ] 1arachidonoylglycerol > 2arachidonoylglycerol > 1oleoylglycerol >...”
- The Concise Guide to PHARMACOLOGY 2015/16: Enzymes.
Alexander, British journal of pharmacology 2015 - “...been reported to be hydrolysed by multiple enzyme activities from neural preparations, including ABHD6 ( Q9BV23 ) [ 41 ], ABHD12 ( 8N2K0 ) [ 41 ], neuropathy target esterase ( PNPLA6 , Q8IY17 [ 316 ]) and carboxylesterase 1 ( CES1 , P23141 [ 533...”
- A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs.
Dingerdissen, Biology direct 2014 - “...P18900 Q9UQB9 P38991 Q99447 P33412 P04180 P40345 O14734 P41903 P30793 P51601 Q9Y3Q0 P47161 P14550 P14065 Q9BV23 P53750 O43175 P40054 P08243 P49090 P56937 Q12452 P22830 P16622 Q86V88 P40081 Q16769 P43599 O95336 P38858 Q8IXB1 P40564 Q15386 P53119 Q969P6 P04786 Q9Y3B8 P54964 Q9Y2H1 P53894 Q9Y2Z4 P48527 P00813 P53909 Q9UI42...”
- Highly predictive ligand-based pharmacophore and homology models of ABHD6.
Bowman, Chemical biology & drug design 2013 - “...sequence for human ABHD6 was taken from the SWISSPROT protein sequence database (primary accession number Q9BV23). Initial analysis of the ABHD6 sequence indicates that first ~9 residues are extracellular, the next ~30 residues are involved in a transmembrane helix, and the remaining ~290 residues are intracellular....”
- “...5 a non-selective ABHD6 inhibitor. Figure 2 Modeling alignment for the sequences of human ABHD6 (Q9BV23) and BphD from Burkholderia xenovorans LB400 (PDB ID: 2OG1). Aligned query and template residues that are identical are highlighted in black; conserved residues (according to the BLOSUM62 scoring matrix), in...”
- ABHD6 suppresses colorectal cancer progression via AKT signaling pathway.
Xiong, Molecular carcinogenesis 2024 (PubMed)- GeneRIF: ABHD6 suppresses colorectal cancer progression via AKT signaling pathway.
- Enhanced monoacylglycerol lipolysis by ABHD6 promotes NSCLC pathogenesis.
Tang, EBioMedicine 2020 - GeneRIF: Enhanced monoacylglycerol lipolysis by ABHD6 promotes NSCLC pathogenesis.
- Cutting Edge: Dysregulated Endocannabinoid-Rheostat for Plasmacytoid Dendritic Cell Activation in a Systemic Lupus Endophenotype.
Rahaman, Journal of immunology (Baltimore, Md. : 1950) 2019 (PubMed)- GeneRIF: We discovered a regulatory role of ABHD6 in human plasmacytoid dendritic cells (pDCs) through modulating the local abundance of its substrate, the endocannabinoid 2-arachidonyl glycerol (2-AG), and elucidated a hitherto unknown cannabinoid receptor 2-mediated regulatory role of 2-AG on IFN-alpha induction by pDCs.
- Metabolic disease and ABHD6 alter the circulating bis(monoacylglycerol)phosphate profile in mice and humans.
Grabner, Journal of lipid research 2019 - GeneRIF: It demonstrate that ABHD6 affect Bis(monoacylglycerol)phosphate (BMP) metabolism in mice and humans.
- Monoacylglycerol signalling and ABHD6 in health and disease.
Poursharifi, Diabetes, obesity & metabolism 2017 (PubMed)- GeneRIF: Data suggest that ABHD6 plays important role in regulation of signaling via monoacylglycerols (MAGs) in both central and peripheral tissues; alterations in MAG signaling are involved in type 2 diabetes, obesity, and metabolic syndrome. [REVIEW]
- α/β-Hydrolase domain-containing 6 (ABHD6) negatively regulates the surface delivery and synaptic function of AMPA receptors.
Wei, Proceedings of the National Academy of Sciences of the United States of America 2016 - GeneRIF: The hydrolase activity of ABHD6 was not required for the effects of ABHD6 on AMPAR function in either neurons or transfected HEK293T cells. Thus, these findings reveal a novel and unexpected mechanism governing AMPAR trafficking at synapses through ABHD6.
- PXK locus in systemic lupus erythematosus: fine mapping and functional analysis reveals novel susceptibility gene ABHD6.
Oparina, Annals of the rheumatic diseases 2015 (PubMed)- GeneRIF: Results confirm the genetic association of the locus 3p14.3 with systemic lupus erythematosus in Europeans and point to the ABHD6 and not PXK, as the major susceptibility gene in the region.
- α/β Hydrolase Domain-containing 6 (ABHD6) Degrades the Late Endosomal/Lysosomal Lipid Bis(monoacylglycero)phosphate.
Pribasnig, The Journal of biological chemistry 2015 - GeneRIF: data suggest that ABHD6 controls BMP catabolism and is therefore part of the late endosomal/lysosomal lipid-sorting machinery
- More
ACIAD1121 lipase from Acinetobacter sp. ADP1
28% identity, 65% coverage
P19076 2-hydroxymuconate semialdehyde hydrolase from Pseudomonas sp. (strain CF600)
32% identity, 65% coverage
ESTE_PSEFL / P22862 Arylesterase; Aryl-ester hydrolase; Carboxylic acid perhydrolase; PFE; Putative bromoperoxidase; EC 3.1.1.2; EC 1.-.-.- from Pseudomonas fluorescens (see 8 papers)
GI|951089 arylesterase; EC 1.-.-.-; EC 3.1.1.2 from Pseudomonas fluorescens (see 3 papers)
AAB60168.1 esterase from Pseudomonas fluorescens (see 2 papers)
29% identity, 69% coverage
- function: Hydrolyzes phenolic esters, such as phenyl acetate, nitrophenyl acetate and naphtyl acetate (PubMed:1368608, PubMed:15803517, PubMed:7704276, PubMed:9571805). Can act on a wide range of esters, but reaction rate and enantioselectivity differ significantly depending on the substrate (PubMed:1368608, PubMed:9571805). Shows a preference for esters with small acyl groups (PubMed:15213385). Also shows low perhydrolase activity, and catalyzes the reversible formation of peroxycarboxylic acids from carboxylic acids and hydrogen peroxide (PubMed:15803517, PubMed:20112920, PubMed:22618813). In vitro, enzyme-generated peracetic acid oxidizes bromide ion to bromonium, which reacts with monochlorodimedone to form bromochlorodimedone (PubMed:20112920, PubMed:22618813, PubMed:7704276).
catalytic activity: a phenyl acetate + H2O = a phenol + acetate + H(+) (RHEA:17309)
catalytic activity: peracetic acid + H2O = acetate + H2O2 + H(+) (RHEA:68392)
catalytic activity: a percarboxylic acid + H2O = a carboxylate + H2O2 + H(+) (RHEA:68396)
subunit: Dimer of trimers. - Crystal Structure and Functional Characterization of an Esterase (EaEST) from Exiguobacterium antarcticum
Lee, PloS one 2017 - “...of Ea EST (NCBI reference sequence number WP_014970431.1), aryl esterase (PDB code 3HEA; UniProtKB code P22862), bromoperoxidase (PDB code 3FOB; UniProtKB code Q81NM3), haloperoxidase (PDB code 1A8S; UniProtKB code O31158), chloroperoxidase (PDB code 4DGQ; UniProtKB code B4EA96), and esterase (PDB code 1ZOI; UniProtKB code Q3HWU8). Secondary...”
- Mining bacterial genomes for novel arylesterase activity
Wang, Microbial biotechnology 2010 - “...looked for preferential substitutions in the thermal stable enzymes characterized in this study (relative to P22862) that were previously found to occur in other thermophilic enzymes; the abundance of amino acids that typically occur at increased frequency in thermal stable enzymes was also determined ( Argos...”
- “...36 active bacterial enzymes purified in this study and the characterized arylesterase from Pseudomonas fluorescens P22862 (Fig.S3). Overall sequence comparison did not cluster the proteins according to measured enzyme activities, nor did comparison of sequences to the Lipase Engineering Database, although like P22862, sequence similarity between...”
RPA3430 possible hydrolase from Rhodopseudomonas palustris CGA009
Q6N4A9 Alpha/beta hydrolase from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
33% identity, 61% coverage
A1YV97 Lipase (Fragment) from Fervidobacterium changbaicum
26% identity, 69% coverage
- Role of the NC-loop in catalytic activity and stability in lipase from Fervidobacterium changbaicum
Li, PloS one 2012 - “...Server ( http://www.sbg.bio.ic.ac.uk/phyre/ ) was used to derive the 3D structure of FClip1 (UniProt accession: A1YV97). The aryl esterase PFE from Pseudomonas fluorescens (PDB code: 1VA4) [42] was chosen as the template. Structural qualities of the generated models were evaluated using Protein Structure Validation Software [43]...”
- “...repesented by the accession numbers were the same as in figure 1 . Although FClip1 (A1YV97) belongs to the lipase family, it situates at the root of the lipases branch and is near the perhydrolases branch. It might be an evolutionary intermediate between lipases and perhydrolases...”
Q88GS3 L-proline amide hydrolase from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
32% identity, 66% coverage
- Mining bacterial genomes for novel arylesterase activity
Wang, Microbial biotechnology 2010 - “...hydrolases. Property PaEST1 PpEST1 PpEST2 PpEST3 RpEST1 RpEST2 RpEST3 SavEST1 UniProt ID Q9KJG6 Q88QX0 Q88CC8 Q88GS3 Q6NCW9 Q6N0W4 Q6N4A9 Q82QJ4 MW a 34.8 26.3 30 31.1 32.4 26.2 27.2 28.5 pI a 6.1 5.0 4.9 5.1 5.3 5.3 5.6 5.4 pH optimum 79 89 9 89...”
B7D75_07235 alpha/beta fold hydrolase from Pseudomonas paraeruginosa
31% identity, 71% coverage
KR76_27085 alpha/beta fold hydrolase from Pimelobacter simplex
27% identity, 71% coverage
C7W88_RS19345 dihydrolipoamide acetyltransferase family protein from Novosphingobium sp. THN1
40% identity, 22% coverage
8pi1B / P22862 Bicyclic incypro pseudomonas fluorescens esterase (see paper)
29% identity, 69% coverage
- Ligand: n-[2-[3,5-bis[2-(2-iodanylethanoylamino)ethanoyl]-1,3,5-triazinan-1-yl]-2-oxidanylidene-ethyl]-2-iodanyl-ethanamide (8pi1B)
bphD / BAM76235.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Janibacter sp. TYM3221 (see paper)
27% identity, 69% coverage
PSPPH_0033 3-oxoadipate enol-lactonase, putative from Pseudomonas syringae pv. phaseolicola 1448A
28% identity, 68% coverage
ABUW_2914 alpha/beta fold hydrolase from Acinetobacter baumannii
27% identity, 64% coverage
MSMEG_6037 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase from Mycobacterium smegmatis str. MC2 155
29% identity, 64% coverage
- Pathogen roid rage: cholesterol utilization by Mycobacterium tuberculosis
Wipperman, Critical reviews in biochemistry and molecular biology 2014 - “...Rv3567c MSMEG_6035 hsaB 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione 4-hydroxylase reductase component KstR1 Rv3568c MSMEG_6036 hsaC 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase KstR1 Rv3569c MSMEG_6037 hsaD 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase Essential KstR1 Rv3570c MSMEG_6038 hsaA 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione 4-monooxygenase component Essential KstR1 Rv3571 MSMEG_6039 kshB 3-ketosteroid 9-hydroxylase reductase component Induced KstR1 Rv3572 MSMEG_6040 conserved hypothetical protein ? KstR1 Rv3573c...”
Q0SH24 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) from Rhodococcus jostii (see paper)
RHA1_ro01338 3-oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylase from Rhodococcus sp. RHA1
32% identity, 60% coverage
XCV1928 hydrolase of the alpha/beta fold superfamily from Xanthomonas campestris pv. vesicatoria str. 85-10
31% identity, 70% coverage
BPSL3337 putative hydrolase from Burkholderia pseudomallei K96243
29% identity, 68% coverage
- Phenotypic and genetic alterations of Burkholderia pseudomallei in patients during relapse and persistent infections
Seng, Frontiers in microbiology 2023 - “...non-synonymous mutations in 5 different genes, including chromate transporter ( chr, BPSL0285 ), hydrolase ( BPSL3337 ), NAD (P) transhydrogenase subunit alpha ( BPSL2887 ), ferric uptake regulator ( fur , BPSL2943 ), and type VI secretion system (T6SS-5) protein TssB-5 ( tssB-5 , BPSS1496 )...”
- Evolutionary analysis of Burkholderia pseudomallei identifies putative novel virulence genes, including a microbial regulator of host cell autophagy
Singh, Journal of bacteriology 2013 - “...Hypothetical protein Putative hydrolase 4.34E50 6.09E06 BPSL3229 BPSL3337 181.4097 30.67755 Dispersed with clusters throughout the cell 20 21 Phosphoesterase...”
TTE2547 predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) from Thermoanaerobacter tengcongensis MB4
27% identity, 70% coverage
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...hydrolase 298 GWSMG TTE1809 AAM25001 Alpha/beta hydrolase 258 GLSMG TTE2321 AAM25462 Alpha/beta hydrolase 414 CHSMG TTE2547 AAM25672 Alpha/beta hydrolase 285 AHSFG Thermococcus kodakaraensis TK0522 BAD84711 Carbohydrate esterase 449 GSSLG Thermotoga maritima TM1022 AAD36099 Esterase 253 GLSMG TM1160 AAD36236 Esterase 306 GLSAG TM1350 AAD36421 Lipase, putative 259...”
ACICU_01737 pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component from Acinetobacter baumannii ACICU
44% identity, 16% coverage
- Colistin Resistant A. baumannii: Genomic and Transcriptomic Traits Acquired Under Colistin Therapy
Cafiso, Frontiers in microbiology 2018 - “...RefGen, i.e. Butanoate metabolism (4 genes: ACICU_01343, ACICU_01342, ACICU_01735, ACICU_01767); Glycolysis/Gluconeogenesis (3 genes: ACICU_02656, ACICU_01735, ACICU_01737); Benzoate degradation via CoA ligation (3genes: ACICU_01343, ACICU_01342, ACICU_01767); Pyruvate metabolism (3 genes: ACICU_01735, ACICU_01737, ACICU_01767); Valine, leucine and isoleucine degradation (3 genes: ACICU_01408, ACICU_01342, ACICU_01767). Similarly, the enrichment analysis...”
PP5253 arylesterase, putative from Pseudomonas putida KT2440
Q88CC8 Arylesterase from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
PPUBIRD1_5047 alpha/beta fold hydrolase from Pseudomonas putida BIRD-1
30% identity, 69% coverage
- Genetic differences between blight-causing Erwinia species with differing host specificities, identified by suppression subtractive hybridization
Triplett, Applied and environmental microbiology 2006 - “...T3SS invasion protein 2E EP3b Pseudomonas putida, Pp5253 Putative arylesterase 7 E28 NP_747354 47 NP_458840 YP_237843 EP4 Salmonella enterica, CysQ Ammonium...”
- Mining bacterial genomes for novel arylesterase activity
Wang, Microbial biotechnology 2010 - “...ester hydrolases. Property PaEST1 PpEST1 PpEST2 PpEST3 RpEST1 RpEST2 RpEST3 SavEST1 UniProt ID Q9KJG6 Q88QX0 Q88CC8 Q88GS3 Q6NCW9 Q6N0W4 Q6N4A9 Q82QJ4 MW a 34.8 26.3 30 31.1 32.4 26.2 27.2 28.5 pI a 6.1 5.0 4.9 5.1 5.3 5.3 5.6 5.4 pH optimum 79 89 9...”
- Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria
Lidbury, Environmental microbiology 2016 - “...PPUBIRD1_4925 2.04 ND Fe3+ ABC transporter, ATPbinding domain ADR62478 PPUBIRD1_4927 2.85 ND Arylesterase, putative ADR62594 PPUBIRD1_5047 3.47 ND Winged helix family regulator phoB ADR62659 PPUBIRD1_5112 4.38 ND Phosphate regulon sensor protein phoR ADR62660 PPUBIRD1_5113 4.64 ND Phosphate ABC transporter, ATPbinding domain pstB2 ADR62665 PPUBIRD1_5118 5.16 ND...”
MXAN_0201 hydrolase, alpha/beta fold family from Myxococcus xanthus DK 1622
28% identity, 70% coverage
- The lethal cargo of Myxococcus xanthus outer membrane vesicles
Berleman, Frontiers in microbiology 2014 - “...domain protein OMV ENRICHED 62 loci Unknown 38 loci Putative lipoproteins 43 loci Other functions MXAN_0201 Hydrolase, alpha/beta fold family MXAN_0533 NAD dependent epimerase/dehydratase family MXAN_0886 Metal dependent amidohydrolase MXAN_1389 Putative alkaline phosphatase MXAN_1394 Metallo-beta-lactamase family protein MXAN_1564 Alkyl hydroperoxide reductase C MXAN_1623 Peptidase, M16 (pitrilysin)...”
- “...in OMV than in the corresponding OM samples, i.e., lipoproteins (MXAN_6367 and MXAN_7333), a hydrolase (MXAN_0201) and a hypothetical protein (MXAN_5453). The other two, chaperonins GroEL1 (MXAN__4895) and GroEL2 (MXAN__4467) ranked as the first and third most abundant protein in OMV, albeit were present at ~50%...”
WP_024569139 alpha/beta fold hydrolase from Cupriavidus metallidurans H1130
40% identity, 32% coverage
CBL13_02626 alpha/beta fold hydrolase from Pseudomonas putida
38% identity, 31% coverage
PP4540 hydrolase, alpha/beta fold family from Pseudomonas putida KT2440
38% identity, 31% coverage
PA3586 probable hydrolase from Pseudomonas aeruginosa PAO1
31% identity, 69% coverage
- Global transcriptome analysis of Pseudomonas aeruginosa NT06 response to potassium chloride, sodium lactate, sodium citrate, and microaerophilic conditions in a fish ecosystem
Tomaś, FEMS microbiology letters 2024 - “...hutU , and PA0747), carbohydrate metabolism ( pgl, glcD , and PA3516), and lipid degradation (PA3586, PA3226, and PA1628). DEGs classified into the cell maintenance and division group Although not the most numerous, very important DEGs were classified as cell maintenance and division, which included the...”
- “...observed (Wang et al. 2018 ). In KCl-treated cells, genes associated with lipid degradation, e.g. PA3586 and PA3226, encoding hydrolases, and PA1628, encoding dehydrogenase, were downregulated. Validation of RNA-Seq by RTqPCR The transcriptome sequencing results were validated by performing RTqPCR analyses of the selected genes from...”
- LipG a bifunctional phospholipase/thioesterase involved in mycobacterial envelope remodeling
Santucci, Bioscience reports 2018 - “...sequence identity with the EstB protein from Acinetobacter calcoaceticus and 43% with the putative hydrolase PA3586 from Pseudomonas aeruginosa PAO1. Interestingly, the Rv0646c gene has been annotated as essential for M. tuberculosis H 37 Rv survival within primary murine cells by transposon site hybridization [ 26...”
- Swarming of Pseudomonas aeruginosa is controlled by a broad spectrum of transcriptional regulators, including MetR
Yeung, Journal of bacteriology 2009 - “...minimal medium. Interestingly, the gene adjacent to metR, PA3586, which encodes a putative hydrolase and is transcribed divergently from metR, was highly...”
- “...less under liquid swarming medium conditions (2-fold). PA3586 was, however, not required for swarming. A large number of virulence-related genes were...”
hsaD / Q9KWQ6 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase monomer (EC 3.7.1.17) from Rhodococcus jostii (strain RHA1) (see paper)
HSAD_RHOJR / Q9KWQ6 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase; Meta-cleavage product hydrolase; MCP hydrolase; EC 3.7.1.17 from Rhodococcus jostii (strain RHA1) (see 2 papers)
RHA1_RS22130 4,5:9,10-diseco-3-hydroxy-5,9, 17-trioxoandrosta-1(10),2-diene-4-oate hydrolase from Rhodococcus sp. DK17
RHA1_ro04540 4,9-DSHA hydrolase from Rhodococcus sp. RHA1
30% identity, 66% coverage
- function: Catalyzes the hydrolysis of a carbon-carbon bond in 4,5: 9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate (4,9- DSHA) to yield 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oate (DOHNAA) and 2-hydroxy-hexa-2,4-dienoate (HHD). Also involved in biphenyl and polychlorinated biphenyls (PCBs) degradation.
catalytic activity: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta- 1(10),2-dien-4-oate + H2O = 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo- octahydro-1H-inden-4-yl]propanoate + (2Z,4Z)-2-hydroxyhexa-2,4- dienoate + H(+) (RHEA:32035)
subunit: Homodimer. - Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352 RHA1_ro05800 RHA1_ro04534 Rv3535c Propanol dehydrogenase...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...(RHA1_RS22125) HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF...”
AT4G33180 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
26% identity, 64% coverage
MAB_1945c Probable dihydrolipoamide succinyltransferase from Mycobacterium abscessus ATCC 19977
48% identity, 13% coverage
- Evolution of Mycobacterium abscessus in the human lung: Cumulative mutations and genomic rearrangement of porin genes in patient isolates
Shallom, Virulence 2023 - “...ORFs in isolate 2B7, 2B9, and 2B11 Frameshift sucB dihydrolipoyllysine- residue succinyltransferase dihydrolipoyllysine-residue succinyltransferase activity MAB_1945c MM2B0626_1741 (2B1)/MM2B0107_1078 and MM2B0107_1079 (2B11) 572 (2B1) 241 and 305 (2B11) 2 ORFs in isolates 2B4, 2B5, 2B6, 2B9, and 2B11 Stop codon mutation 3.6. Other genomic changes Further, we...”
- Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing
Rifat, mBio 2021 - “...MAB_1918 Conserved hypothetical protein (possible hydrolase) GA MAB_1933c Probable glutamine synthetase, type I GlnA1 ES MAB_1945c 2-Oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase GD MAB_2124 Putative phenyloxazoline synthase MbtB NE MAB_2140 NADH-quinone oxidoreductase, G subunit NuoG NE MAB_2231c Hypothetical PE family protein NE MAB_2262c Hypothetical ABC transporter...”
CtCNB1_1354 alpha/beta hydrolase fold protein from Comamonas testosteroni CNB-2
CTCNB1_RS06910 alpha/beta fold hydrolase from Comamonas thiooxydans
29% identity, 72% coverage
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...(CTCNB1_RS06920) (RHA1_RS28325) (RHA1_RS22125) HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105)...”
- Degradation of Bile Acids by Soil and Water Bacteria
Feller, Microorganisms 2021 - “...9,10- seco -steroid dioxygenase C211_RS11215 CTCNB1_RS06510 (TesB) RHA1_RS28330 (HsaC3) Nov2c350 4,5,9,10-di seco -steroid hydroxylase C211_RS11155 CTCNB1_RS06910 (TesD) RHA1_RS28300 (HsaD3) Nov2c348 C/D-ring (HIP) side-chain degradation CoA-ligase C211_RS11045 (StdA3 *) CTCNB1_RS06940 (ScdA) RHA1_RS22410 ** (FadD3) Nov2c359 ACAD C211_RS11065 (Scd3A) CTCNB1_RS06570 (ScdC1) RHA1_RS22390 ** Nov2c367 C211_RS11070 (Scd3B) CTCNB1_RS06575 (ScdC2)...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352 RHA1_ro05800 RHA1_ro04534 Rv3535c...”
cmpF / CAB06612.1 2-hydroxymuconic semialdehyde hydrolase from Sphingomonas sp (see 2 papers)
28% identity, 68% coverage
tesD / Q83VZ6 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (EC 3.7.1.17) from Comamonas testosteroni (see 3 papers)
29% identity, 72% coverage
NSU_pLA1124 alpha/beta fold hydrolase from Novosphingobium pentaromativorans US6-1
29% identity, 69% coverage
pcaL / AAC38246.1 3-oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylase from Rhodococcus opacus (see paper)
32% identity, 60% coverage
WSS_A28595 3-oxoadipate enol-lactonase from Rhodococcus opacus M213
31% identity, 60% coverage
lmo1374 similar to branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) from Listeria monocytogenes EGD-e
Q8Y7B2 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
40% identity, 20% coverage
- A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites
Dienemann, Angewandte Chemie (International ed. in English) 2023 (secret) - Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
Pinilla, Data in brief 2022 - “...into large acid- insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides Q8Y7B2 lmo1374 lmo1374 Nis / LNis Annotation not available Q8Y6J3 lmo1691 lmo1691 Nis / LNis Deoxyuridine triphosphate nucleotidohydrolase; enzyme involved in nucleotide metabolism, produces dUMP, the immediate precursor of thymidine nucleotides and...”
- The Characteristics and Function of Internalin G in Listeria monocytogenes
Gou, Polish journal of microbiology 2022 - “...no 1.88 up propanediol dehydratase subunit alpha lmo2720 no 2.02 down AMP-binding enzyme C-terminal domain lmo1374 no 1.52 down biotin-requiring enzyme lmo1371 no 1.28 down pyridine nucleotide-disulphide oxidoreductase Valine, leucine, nd isoleucine degradation lmo1373 no 1.86 down transketolase, pyrimidine binding domain lmo1374 no 1.52 down biotin-requiring...”
- A complex lipoate utilization pathway in Listeria monocytogenes
Christensen, The Journal of biological chemistry 2011 - “...(lmo2425), lipL (lmo2566), and the lipoyl domain of bkdB (lmo1374 or E2BkdB) were placed under the control of a T7 promoter for heterologous expression in E....”
- Identification of a sigma B-dependent small noncoding RNA in Listeria monocytogenes
Nielsen, Journal of bacteriology 2008 - “...Length B promoterb sbrA sbrB sbrC sbrD lmo1374 lmo1375 lmo1251 lmo1252 lmo1515 lmo1516 atpI lmo1537 70 168 73 68 TAAAAATGTTTTAATCTAGGTTTAGCGGGTATTGTTTAGT...”
- “...a 70-nucleotide B-dependent sRNA encoded by the IGR between lmo1374 and lmo1375. Furthermore, we note that no potential open reading frames are likely to be...”
- Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
Pinilla, Data in brief 2022 - “...DNA into large acid- insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides Q8Y7B2 lmo1374 lmo1374 Nis / LNis Annotation not available Q8Y6J3 lmo1691 lmo1691 Nis / LNis Deoxyuridine triphosphate nucleotidohydrolase; enzyme involved in nucleotide metabolism, produces dUMP, the immediate precursor of thymidine nucleotides...”
H16_A3742 Lipase from Ralstonia eutropha H16
H16_A3742 alpha/beta fold hydrolase from Cupriavidus necator H16
28% identity, 69% coverage
SMc01944 PUTATIVE HALOPEROXIDASE PROTEIN from Sinorhizobium meliloti 1021
28% identity, 69% coverage
- OxyR-Dependent Transcription Response of Sinorhizobium meliloti to Oxidative Stress
Lehman, Journal of bacteriology 2018 - “...1 mM CL150 0.5 mM CL150 SMc00819 SMc01944 SMb20054 SMb20964 SMc00818 Catalase Nonheme chloroperoxidase F (chloride peroxidase; CPO-F) Chloride peroxidase...”
- “...set also included a gene encoding a secreted peroxidase (SMc01944) and a gene of unknown function (SMc01113) whose expression has been previously shown to be...”
- Formation of chloroform and tetrachloroethene by Sinorhizobium meliloti strain 1021
Weigold, Letters in applied microbiology 2015 (PubMed)- “...chloroform, chloroperoxidases, Sinorhizobium meliloti, Smc01944, tetrachloroethene, volatile organohalogen compounds. Correspondence Sebastian Behrens,...”
- “...meliloti can be attributed to one of its chloroperoxidases (Smc01944) that is highly expressed in the presence of H2O2. However, addition of 10 mmol l1 H2O2 to...”
- Resistance to organic hydroperoxides requires ohr and ohrR genes in Sinorhizobium meliloti
Fontenelle, BMC microbiology 2011 - “...presents 40% identity with OhrR of X. campestris [ 11 ]; the adjacent gene cpo (SMc01944) has been shown to encode a secreted peroxidase. Co-localisation on the genome of ohr and ohrR was found in all bacteria in which these genes were investigated [ 20 ,...”
- “...2003 16 3 217 225 10.1094/MPMI.2003.16.3.217 12650453 Barloy-Hubler F Cheron A Hellegouarch A Galibert F Smc01944, a secreted peroxidase induced by oxidative stresses in Sinorhizobium meliloti 1021 Microbiology 2004 150 Pt 3 657 664 14993315 Baker CJ Orlandi EW Active oxygen in plant pathogenesis Annu Rev...”
- Molecular determinants of a symbiotic chronic infection
Gibson, Annual review of genetics 2008 - “...genes include an extracellular peroxidase (Smc01944), a bacteriocuprein-family superoxide dismutase (sodC), and an alkylhydroperoxidase (ahpC), each...”
- “...F, Cheron A, Hellegouarch A, Galibert F. Smc01944, a secreted peroxidase induced by oxidative stresses in Sinorhizobium meliloti 1021. Microbiology...”
- How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model
Jones, Nature reviews. Microbiology 2007 - “...a predicted sodM (Smc00911) or a secreted chloroperoxidase (Smc01944) have not yet been analysed57. Further work is therefore required to elucidate how ROS,...”
- “...F., Cheron, A., Hellegouarch, A. & Galibert, F. Smc01944, a secreted peroxidase induced by oxidative stresses in Sinorhizobium meliloti 1021. Microbiology 150,...”
- Smc01944, a secreted peroxidase induced by oxidative stresses in Sinorhizobium meliloti 1021
Barloy-Hubler, Microbiology (Reading, England) 2004 (PubMed)- “...Smc01944, a secreted peroxidase induced by oxidative stresses in Sinorhizobium meliloti 1021 Frederique Barloy-Hubler, Angelique Cheron, Adeline Hellegouarch and Francis Galibert Laboratoire de Genetique et...”
- “...identified new genes induced by exogenous H2O2. The smc01944 gene was the most strongly induced: quantitative PCR showed that the amount of smc01944 mRNA...”
xylF / P23106 2-hydroxymuconic semialdehyde hydrolase (EC 3.7.1.9) from Pseudomonas putida (see paper)
XYLF_PSEPU / P23106 2-hydroxymuconate semialdehyde hydrolase; HMSH; 2-hydroxymuconic semialdehyde hydrolase; EC 3.7.1.9 from Pseudomonas putida (Arthrobacter siderocapsulatus)
31% identity, 69% coverage
- function: Catalyzes the conversion of 2-hydroxymuconate semialdehyde to 2-hydroxypent-2,4-dienoate.
catalytic activity: (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = 2-oxopent-4- enoate + formate + H(+) (RHEA:14549)
SMa0792 hypothetical protein with local similarity from Sinorhizobium meliloti 1021
27% identity, 69% coverage
P23974 Putative 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase from Bacillus subtilis (strain 168)
BSU30810 putative esterase from Bacillus subtilis subsp. subtilis str. 168
30% identity, 63% coverage
- Novel Cold-Adapted Esterase MHlip from an Antarctic Soil Metagenome
Berlemont, Biology 2013 - “...aureofaciens , and with the crystallized esterase YTXM from Bacillus subtilis (id. 26%, acc. no. P23974). We constructed a phylogenetic tree using the MHlip sequence and some sequences derived from various esterase-related families [ 25 ]. Next, Pfam numbers were assigned to each sequence using Pfam_scan...”
- The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...BSU30790 BSU30800 BSU30820 Yes Yes Yes Yes ytxM menF BSU30810 BSU30830 No No BSU31600 BSU31610 BSU31620 BSU31630 BSU31640 BSU31650 BSU31660 Yes Yes Yes Yes No...”
IM701_21000 alpha/beta fold hydrolase from Novosphingobium sp. ES2-1
28% identity, 69% coverage
BJN34_29740 3-oxoadipate enol-lactonase from Cupriavidus necator
29% identity, 68% coverage
Rmet_4875 3-oxoadipate enol-lactonase from Cupriavidus metallidurans CH34
Rmet_4875 3-oxoadipate enol-lactonase from Ralstonia metallidurans CH34
28% identity, 67% coverage
slr1235 unknown protein from Synechocystis sp. PCC 6803
25% identity, 70% coverage
- Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis
Shahbazi, 3 Biotech 2021 - “...protein, sll0355 fus, slr1105 hypothetical protein, slr1235 hypothetical protein, slr0957 hypothetical protein, slr0320 ssyA, sll1383 ycf21, sll1797 probable...”
- Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. strain PCC 6803
Li, Journal of bacteriology 2004 - “...Berkeley slr0270 sll1620 slr1215 sll0185 slr0967 slr1235 slr0888 sll0939 Other categories Adaptations and atypical conditions sll0947 P(treatment) Function...”
- Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light
Huang, Journal of bacteriology 2002 - “...slr0852 slr0863 slr0959 slr0967 slr1074 slr1119 slr1205 slr1235 slr1259 slr1293 slr1322 slr1383 slr1397 slr1413 slr1512 slr1513 slr1544 slr1557 slr1603 slr1674...”
GBAA1019 hydrolase, alpha/beta fold family from Bacillus anthracis str. 'Ames Ancestor'
BA1019 hydrolase, alpha/beta fold family from Bacillus anthracis str. Ames
34% identity, 32% coverage
ECA2972 alpha/beta fold hydrolase from Pectobacterium atrosepticum SCRI1043
29% identity, 54% coverage
A9762_00985 alpha/beta fold hydrolase from Pandoraea sp. ISTKB
30% identity, 68% coverage
Q8IUS5 Epoxide hydrolase 4 from Homo sapiens
NP_775838 epoxide hydrolase 4 from Homo sapiens
26% identity, 69% coverage
LMOf2365_1391 2-oxoisovalerate dehydrogenase E2 component, dihydrolipamide acetyltransferase from Listeria monocytogenes str. 4b F2365
33% identity, 33% coverage
MAB_3034 alpha/beta fold hydrolase from Mycobacteroides abscessus ATCC 19977
MAB_3034 Probable hydrolase from Mycobacterium abscessus ATCC 19977
32% identity, 54% coverage
- Genetic diversification of persistent Mycobacterium abscessus within cystic fibrosis patients
Lewin, Virulence 2021 - “...protein 4014-1 MAB_3029 HIFIHNKG_02972 ideR Iron-dependent repressor [K] 6516-20, 7716-4 Iron acquisition [ 48 ] MAB_3034 HIFIHNKG_02977 Alpha/beta hydrolase fold family hydrolase [I] 6516-20, 7716-4 MAB_3036c HIFIHNKG_02979 nrdR Transcriptional repressor NrdR [K] 4014-3 MAB_3404c HIFIHNKG_03344 nrdF Ribonucleoside-diphosphate reductase subunit beta [F] 7416-1, 10317-1 No homolog HIFIHNKG_03363...”
RPA1568 possible carboxylesterase from Rhodopseudomonas palustris CGA009
29% identity, 62% coverage
YP_003372868 alpha/beta hydrolase fold protein from Pirellula staleyi DSM 6068
27% identity, 70% coverage
MSMEG_4707 non-heme bromoperoxidase BPO-A2 from Mycobacterium smegmatis str. MC2 155
30% identity, 65% coverage
HVO_0666 dihydrolipoamide S-acyltransferase from Haloferax volcanii DS2
38% identity, 22% coverage
H16_A2213 Non-heme haloperoxidase from Ralstonia eutropha H16
29% identity, 68% coverage
bpdF / AAB17100.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Rhodococcus sp. M5 (see paper)
28% identity, 67% coverage
bphD / BAA25612.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Rhodococcus erythropolis (see paper)
27% identity, 69% coverage
AT5G19850 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
27% identity, 68% coverage
- Catalytic and structural properties of pheophytinase, the phytol esterase involved in chlorophyll breakdown
Guyer, Journal of experimental botany 2018 - “...2016 ) were retrieved from TAIR ( http://www.arabidopsis.org/, last accessed 6 September 2017 ): At4g36530; At5g19850; At5g38520. Multiple sequence alignment of these proteins was generated and phylogenetic analysis (Supplementary Fig. S5B) performed with the neighbor-joining method using MEGA7 ( Kumar et al. , 2016 ). Bootstrap...”
- Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification
Velanis, Plant molecular biology 2016 - “...Major facilitator superfamily protein Ch5 AT5G17780 Alpha/beta-Hydrolases superfamily protein Chr3 AT3G10910 RING/U-box superfamily protein Ch5 AT5G19850 Alpha/beta-Hydrolases superfamily protein Chr3 AT3G14770 Nodulin MtN3 family protein Ch5 AT5G23730 RUP2 Transducin/WD40 repeat-like superfamily protein Chr3 AT3G17609 HYH HY5-homologue Ch5 AT5G24120 Sigma factor E Chr3 AT3G21560 UGT84A2 UDP-glycosyltransferase superfamily...”
- Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis
Ashelford, Genome biology 2011 - “...sine wave in constant dark and was therefore a strong potential candidate. Two other genes, At5g19850, a predicted hydrolase, and At5g12470, an organelle protein of unknown function, had good correlation with a cosine wave but only in one set of the constant light data. All other...”
4uhfA / A0A0M3KKY6 Structural studies of a thermophilic esterase from thermogutta terrifontis (l37a mutant with butyrate bound) (see paper)
28% identity, 67% coverage
- Ligand: butanoic acid (4uhfA)
JJQ59_26420 3-oxoadipate enol-lactonase from Cupriavidus necator
29% identity, 67% coverage
MSMEG_4283, MSMEI_4182 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Mycolicibacterium smegmatis MC2 155
A0R072 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_4283 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Mycobacterium smegmatis str. MC2 155
45% identity, 14% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...0.17 0.16 0.06 0.03 A0R266 MSMEG_5002, MSMEI_4876 AAA_27 domain-containing protein 0.06 0.01 A0R072 sucB , MSMEG_4283, MSMEI_4182 Dihydrolipoamide acetyltransferase component of PDH complex 0.1 0.14 A0R729 glpK , MSMEG_6759, MSMEI_6577 Glycerol kinase (EC 2.7.1.30) 0.17 0.25 0.22 0.13 A0QT08 sdhA , MSMEG_1670, MSMEI_1630 Succinate dehydrogenase flavoprotein...”
- “...0.16 0.06 0.03 A0R266 MSMEG_5002, MSMEI_4876 AAA_27 domain-containing protein 0.06 0.01 A0R072 sucB , MSMEG_4283, MSMEI_4182 Dihydrolipoamide acetyltransferase component of PDH complex 0.1 0.14 A0R729 glpK , MSMEG_6759, MSMEI_6577 Glycerol kinase (EC 2.7.1.30) 0.17 0.25 0.22 0.13 A0QT08 sdhA , MSMEG_1670, MSMEI_1630 Succinate dehydrogenase flavoprotein subunit...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...Acetamidase/formamidase family protein 0.17 0.16 0.06 0.03 A0R266 MSMEG_5002, MSMEI_4876 AAA_27 domain-containing protein 0.06 0.01 A0R072 sucB , MSMEG_4283, MSMEI_4182 Dihydrolipoamide acetyltransferase component of PDH complex 0.1 0.14 A0R729 glpK , MSMEG_6759, MSMEI_6577 Glycerol kinase (EC 2.7.1.30) 0.17 0.25 0.22 0.13 A0QT08 sdhA , MSMEG_1670, MSMEI_1630...”
- An in vivo crosslinking system for identifying mycobacterial protein-protein interactions.
Lougheed, Journal of microbiological methods 2014 - “...Pyruvate dehydrogenase E1 component (AceE homologue) 22 A0QQW8 lpdA (MSMEG_0903) Dihydrolipoyl dehydrogenase (LpdC homologue) 5 A0R072 sucB (MSMEG_4283) 2-Oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase (DlaT homologue) 3 A0QTE1 MSMEG_1807 Acetyl-/propionyl-coenzyme A carboxylase alpha chain a 21 A0QS98 Tuf Elongation factor Tu 12 A0QQC8 dnaK Chaperone protein...”
- Spatiotemporal localization of proteins in mycobacteria
Zhu, Cell reports 2021 - “...are more evenly allocated to the two polar (e.g., TtfA, MSMEG_0736) or peri-polar (e.g., DlaT, MSMEG_4283) regions. The complete set of encoding matrices for the MSR-Dendra library are included in Table S1 . To assess whether GEMATRIA faithfully represents the known structural properties of a mycobacterial...”
- Protein Composition of Mycobacterium smegmatis Differs Significantly Between Active Cells and Dormant Cells With Ovoid Morphology
Trutneva, Frontiers in microbiology 2018 - “...as enzymes inactivating active nitrogen compounds [alkylhydroperoxide reductase (MSMEG_4891), dihydrolipoamide dehydrogenase (MSMEG_0903), dihydro lipoamide succinyltransferase (MSMEG_4283), and alkyl hydroperoxidase (MSMEG_4890)]. The dormant proteome also contains an enzyme responsible for detoxification of oxidized lipids (glutathione S-transferase; MSMEG_5695, unique; Supplementary Table S2 ). Chaperones In addition to the...”
- Lack of mycothiol and ergothioneine induces different protective mechanisms in Mycobacterium smegmatis
Singh, Biochemistry and biophysics reports 2016 - “...with protection against oxidative stress are up-regulated in S24. One of these upregulated proteins is MSMEG_4283 (Spot 18), dihydrolipoamide acyltransferase (DlaT), which is the E2 component of pyruvate dehydrogenase complex, and contains a lipoyl binding site [14] . M. tuberculosis dlat mutant has severe growth defect...”
- “...and mshC mutant, S24. Table 3 Spot S24/wt M. smegmatis M. tuberculosis Description 18 8.12 MSMEG_4283 Rv2215 SucB/DlaT dihydrolipoamide acyltransferase 14 4.5 MSMEG_4688 Rv2466c Thiol peroxidase 11 8.8 MSMEG_3084 Rv1436 Glyceraldehyde-3-phosphate dehydrogenase 12 4.68 24 7.63 MSMEG_2027 Rv1558 Coenzyme F420 dependent quinone reductase 16 5.15 MSMEG_1996...”
- An in vivo crosslinking system for identifying mycobacterial protein-protein interactions
Lougheed, Journal of microbiological methods 2014 - “...(Rv2241), E2:DlaT (Rv2215) and E3:LpdC (Rv0462). In M. smegmatis , their homologues are MSMEG_4323, SucB (MSMEG_4283) and LpdA (MSMEG_0903). The aceE (Rv2241) gene from M. tuberculosis was amplified and inserted into pENTR/D/TOPO (Invitrogen) to construct an entry vector that can be used with any of the...”
- “...E1 component (AceE homologue) 22 A0QQW8 lpdA (MSMEG_0903) Dihydrolipoyl dehydrogenase (LpdC homologue) 5 A0R072 sucB (MSMEG_4283) 2-Oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase (DlaT homologue) 3 A0QTE1 MSMEG_1807 Acetyl-/propionyl-coenzyme A carboxylase alpha chain a 21 A0QS98 Tuf Elongation factor Tu 12 A0QQC8 dnaK Chaperone protein DnaK 9...”
DR0791, DR_0791 chloride peroxidase, putative from Deinococcus radiodurans R1
27% identity, 68% coverage
catD / BAA75208.1 b-ketoadipate enol-lactone hydrolase from Frateuria sp. ANA-18 (see paper)
catD / BAC82535.1 b-ketoadipate enol-lactone hydrolase from Frateuria sp. ANA-18 (see 3 papers)
28% identity, 68% coverage
BC4904 Alpha/beta hydrolase fold protein from Bacillus cereus ATCC 14579
26% identity, 66% coverage
- BC4707 is a major facilitator superfamily multidrug resistance transport protein from Bacillus cereus implicated in fluoroquinolone tolerance
Simm, PloS one 2012 - “...described as a bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrase II protein, involved in riboflavin synthesis; and bc4904 , annotated as a hydrolase of the alpha/beta fold family. Furthermore, the cold shock protein CspD ( bc4859 ), was down regulated in the bc4707 mutant compared to the wild...”
- “...protein 1.51 bc4707 drug resistance transporter, EmrB/QacA family 0.32 bc4859 Cold shock protein CspD 0.61 bc4904 Hydrolase, alpha/beta fold family 1.96 BC4707 is not involved in the acid stress defense of B. cereus According to Mols et al. bc4707 is slightly up-regulated under sub-lethal acetic acid...”
Q8DTD0 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
SMU_1421 dihydrolipoamide acetyltransferase family protein from Streptococcus mutans UA159
30% identity, 41% coverage
- Staphylococcus aureus Interferes with Streptococci Spatial Distribution and with Protein Expression of Species within a Polymicrobial Oral Biofilm
Schnurr, Antibiotics (Basel, Switzerland) 2021 - “...upregulated. Two S. mutans proteins were detected only in the 6S + USA300-MRSA MSCRAMM samples: Q8DTD0, related to acyl-groups transferase, and Q8DUL2, glutamate dehydrogenase. As no uniquely or overlapped protein was characterized from S. mutans while in the 6S + USA300-MRSA WT, we assume that the...”
- Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability
Naka, Frontiers in cellular and infection microbiology 2022 - “...ABC transporter ATP-binding protein 1029549 SMU_1068c 2.328 pdhC Branched-chain alpha-keto acid dehydrogenase E2 subunit 1028680 SMU_1421 2.319 lacE PTS system lactose-specific transporter subunit IIBC 1028733 SMU_1491 2.306 oadB Oxaloacetate decarboxylase, sodium ion pump subunit 1028350 SMU_1017 2.285 SMU_1934c Cobalt ABC transporter ATP-binding protein 1029130 SMU_1934c 2.216...”
- Understanding the Streptococcus mutans Cid/Lrg System through CidB Function
Ahn, Applied and environmental microbiology 2016 - “...SMU_574c SMU_1396 SMU_1914c SMU_423 SMU_490 SMU_1752 SMU_191 SMU_40 SMU_1421 SMU_609 SMU_41 SMU_82 SMU_925 SMU_508 SMU_940c tpn lrgB gbpC cipB nlmD pflC NA NA...”
- A five-species transcriptome array for oral mixed-biofilm studies
Redanz, PloS one 2011 - “...Metabolism SMU_1140c conserved hypothetical protein 2.11 down SMU_1322 budC - putative acetoin dehydrogenase 2.78 down SMU_1421 pdhC - putative dihydrolipoamide acetyltransferase, E2 component 2.78 up SMU_1422 pdhB - putative pyruvate dehydrogenase E1 component subunit beta 2.32 up SMU_1424 pdhD - putative dihydrolipoamide dehydrogenase 2.54 up SMU_1493...”
SCAB_13661 putative 3-oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylase from Streptomyces scabiei 87.22
31% identity, 65% coverage
- The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway
Khalil, Frontiers in microbiology 2019 - “...Predicted function of the corresponding protein Primer sets (53) SCAB_13631 Protocatechuate-3,4-dioxygenase beta subunit For:CACATCCACTTCTCGCTCTT Rev:ACTGGATGATCGGGTCGTA SCAB_13661 3-oxoadipate enol-lactone hydrolase For:CGCTTCCAGGACTTCATCTC Rev:CATGGCCAGTTCGTCGTAG SCAB_15301 Vanillate monooxygenase alpha subunit For:CAACCACACGGTCGTCAT Rev:GATGTTGATGCTCAGCTCCT SCAB_15321 Iron-sulfur oxidoreductase beta subunit For:CTACGTGCACACGGAGTT Rev:GGTTCCAGGGCGAAGTT SCAB_15331 IclR-family transcriptional regulator For:GAGCATCCCGCACTGAC Rev:CGAGCGTGAGCAGGAAG SCAB_15591 Feruloyl-CoA hydratase For:CACCCTGTCGCTGTTCAT Rev:CCTTGTTGAGGCCGTAGTT...”
- “...gene located in the vicinity of SCAB_15301 and SCAB_15321), SCAB_2141 (2,3-dihydroxy-2,3-dihydro-phenylpropionate dehydrogenase encoding gene) and SCAB_13661 (3-oxoadipate enol-lactone hydrolase-encoding gene). All genes tested were overexpressed in the presence of at least one of the two cinnamic acids ( trans -ferulic acid or p -coumaric acid) (...”
JJQ59_30925 3-oxoadipate enol-lactonase from Cupriavidus necator
30% identity, 63% coverage
Rmet_4016 3-oxoadipate enol-lactonase from Cupriavidus metallidurans CH34
Rmet_4016 3-oxoadipate enol-lactonase from Ralstonia metallidurans CH34
29% identity, 63% coverage
LOC103509850 epoxide hydrolase 4-like from Diaphorina citri
25% identity, 63% coverage
- The Chorion Proteome of Diaphorina citri, the Vector of Huanglongbing Disease in Citrus
Santos-Ortega, Insects 2021 - “...QUALITY PROTEIN myosin-II-like LOC103524911 A0A3Q0IIF7_DIACI 151 (R)SDSLTNVLNTTSSLNSSSLSNRSLNSSGLSNR(S) (R)ITRVTNDAPIMEVNSNSLGR(R) 3.91 Gene expression regulation Epoxide hydrolase 4-like LOC103509850 A0A1S3D296_DIACI 46 (K)VKDERENAPTCLVDNSFGQHLYVK(L) (K)QVNQQTGLVGKMYGAVSNTVK(Y) (K)QVNQQTGLVGKMYGAVSNTVKYGNHYK(M) 12.80 Hydrolase activity Dynein heavy chain 2, axonemal-like LOC103509704 A0A3Q0IU47_DIACI 538 (K)SETVKDLGKCMAYLVVITNCSDSLDYK(S) (K)DLGKCMAYLVVITNCSDSLDYKSLAR(M) (K)VIVEQMKVEMEENQVLVENYKK(E) 1.14 Microtubule-based movement Odorant binding protein 1 A0A2Z2GYV0_DIACI 16 (K)CKTELNSPPEAVALLGAK(S) (K)TELNSPPEAVALLGAK(S)...”
AF2336 carboxylesterase (est-3) from Archaeoglobus fulgidus DSM 4304
28% identity, 64% coverage
MXAN_1644 putative epoxide hydrolase from Myxococcus xanthus DK 1622
28% identity, 69% coverage
- Biotransformation of polyunsaturated fatty acids to bioactive hepoxilins and trioxilins by microbial enzymes
An, Nature communications 2018 - “...comparison with the sequences of human corresponding genes. The genes of MXAN_1744 , MXAN_1745 , MXAN_1644 , MXAN_5137 , MXAN_5217 , MXAN_0683 , MXAN_2304 and MXAN_3623 in M . xanthus were predicted to be the genes encoding LOX, LOX, EH, EH, COX, twothromboxane A (TXA) synthases...”
- “...The putative LOX enzymes expressed from MXAN_1745 and MXAN_1744 , and the putative EH from MXAN_1644 were purified from crude cell extracts as single soluble proteins using His-Trap affinity chromatography (Supplementary Fig. 4 ). The substrate specificity and products of these purified enzymes are summarized in...”
SACE_1638 dihydrolipoamide succinyltransferase from Saccharopolyspora erythraea NRRL 2338
42% identity, 12% coverage
- Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea
Karničar, Microbial cell factories 2016 - “...biosynthesis. Notably, several proteins of the carbohydrate metabolism (e.g. succinyl-CoA synthetase subunit, SACE_6668; dihydrolipoamide succinyltransferase, SACE_1638; phosphogluconate dehydratase, SACE_1740; 6-phosphofructokinase, SACE_1704; ribose-phosphate pyrophosphokinase, SACE_0816) and nucleotide metabolism (inosine-5-monophosphate dehydrogenase, SACE_6708; phospho-2-dehydro-3-deoxyheptonate aldolase, SACE_1708; phosphoribosylaminoimidazolecarboxamide formyltransferase, SACE_6664) were observed in the WT strain, but not in the...”
- “...than one spot on the gel was found to belong to some of these proteins (SACE_1638, SACE_6668). Three glycolytic enzymes (glucose-6-phosphate isomerase, SACE_2158; 2-phosphoglycerate dehydratase, SACE_0838; phosphoglycerate mutase, SACE_6967) were detected only in the HP strain while glyceraldehyde 3-phosphate dehydrogenase (SACE_2143) was overexpressed in the HP...”
- Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains
Li, BMC genomics 2013 - “...eno in glycolysis was moderately elevated in strain E3. Most genes of TCA cycle, including SACE_1638 ( sucB ), SACE_3674 ( mdh ), SACE_3811 ( acn ), SACE_3926/SACE_3927 ( korA ), SACE_3952 ( pdhA2 ), SACE_3953 ( pdhB1 ), SACE_3954 ( bkdC2 ), SACE_4581 ( citE3...”
- Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain
Peano, Microbial cell factories 2012 - “...286 ccdA Missense (G38S) Cytochrome c biogenesis protein SACE_0633 221 citA IPM Citrate synthase (N-terminal) SACE_1638 609 sucB Missense (V574A) 2-oxoglutarate dehydrogenase complex E2 component (dihydrolipoamide succinyltransferase) SACE_3073 375 hypD Nonsense (Y30*) Hydrogenase expression/formation protein HypD SACE_5291 335 dhaK Frameshift (-C 717) Dihydroxyacetone kinase N-terminal containing...”
SSO1529 Dihydrolipoamide S-acetyltransferase, amino-end (pdhC) from Sulfolobus solfataricus P2
39% identity, 19% coverage
IT767_RS02465 alpha/beta fold hydrolase from Klebsiella pneumoniae subsp. pneumoniae ATCC 43816
29% identity, 68% coverage
- Gallium Nitrate Enhances Antimicrobial Activity of Colistin against Klebsiella pneumoniae by Inducing Reactive Oxygen Species Accumulation
Guo, Microbiology spectrum 2023 - “...including sodB , sodC , katE , katG , pcaC , IT767_RS09590 , IT767_RS13980 , IT767_RS02465 , and IT767_RS06360 were downregulated by GaNt. These data suggest that GaNt is an oxidative stress-inducing compound. When GaNt was added to M9CA medium containing colistin, sodB , sodC ,...”
MAB_4366c Putative hydrolase, alpha/beta fold from Mycobacterium abscessus ATCC 19977
26% identity, 65% coverage
- The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus
Crowe, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...each encoding proteins with 40% amino acid sequence identity to HsaD Mtb : Mab_3810 and Mab_4366c. The former, identified henceforth as hsaD , occurs in a predicted single gene operon, 1.8 Mb from the hsaACB operon. Interestingly, a mycobacterial KstR-binding site as defined by Kendall etal....”
- “...hsaD start codon, with 15 nucleotides of the 18-nucleotide sequence being conserved. For its part, mab_4366c occurs within a putative six-gene operon predicted to encode enzymes involved in the degradation of an aromatic compound ( SI Appendix , Table S1 ). Similarly organized genes in R....”
BHE75_04577 alpha/beta fold hydrolase from Sphingomonas haloaromaticamans
27% identity, 66% coverage
HD73_4462 dihydrolipoamide acetyltransferase family protein from Bacillus thuringiensis serovar kurstaki str. HD73
33% identity, 27% coverage
- Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis
Peng, Frontiers in microbiology 2015 - “...kinase 2.728 HD73_4465 Dihydrolipoamide dehydrogenase - HD73_4464 BfmBAa - HD73_4463 2-oxoisovalerate dehydrogenase subunit beta - HD73_4462 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex - HD73_5327 NADPH dehydrogenase, quinone - HD73_5613 PTS system cellobiose-specific IIC component 0.460 HD73_5614 PTS system cellobiose-specific IIC component 0.460 HD73_0179...”
SCO6339 3-oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylase from Streptomyces coelicolor A3(2)
28% identity, 55% coverage
PP1064 hydrolase, alpha/beta fold family from Pseudomonas putida KT2440
30% identity, 68% coverage
carC / Q9AQM4 2-hydroxy-6-oxo-6-(2'-aminophenyl)-hexa-2,4dienoate hydrolase monomer (EC 3.7.1.13) from Pseudomonas resinovorans (see paper)
CARC_METRE / Q9AQM4 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase; HOPDA; EC 3.7.1.13 from Metapseudomonas resinovorans (Pseudomonas resinovorans) (see 3 papers)
Q9AQM4 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase (EC 3.7.1.13) from Pseudomonas resinovorans (see paper)
carC / BAC41548.1 meta cleavage compound hydrolase from Pseudomonas resinovorans (see 9 papers)
27% identity, 72% coverage
- function: Involved in the degradation of carbazole, a toxic N- heterocyclic aromatic compound containing dibenzopyrrole system. Catalyzes the hydrolytic cleavage of a carbon-carbon bond of 2-hydroxy- 6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid (HOPDA) to yield anthranilate. CarC is specific for 2-hydroxy-6-oxo-6-phenylhexa-2,4- dienoic acid (6-phenyl-HODA), and has little activity toward 2-hydroxy- 6-oxohepta-2,4-dienoic acid and 2-hydroxymuconic semialdehyde. The effect of the presence of an amino group or hydroxyl group at the 2'- position of phenyl moiety of 6-phenyl-HODA on the enzyme activity is found to be small.
catalytic activity: (2E,4E)-6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = (2E)-2-hydroxypenta-2,4-dienoate + anthranilate + H(+) (RHEA:27870)
subunit: Homodimer. - SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana, Nucleic acids research 2019 - “...O93523 3.5.4.45 Melamine deaminase Q9EYU0 98% 4v1x 4v1y 3.8.1.8 Atrazine chlorohydrolase P72156 3.7.1.13 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase Q9AQM4 98% 1j1i 3.7.1.8 2,6-dioxo-6-phenylhexa-3-enoate hydrolase Q84II3 4.1.2.9 Phosphoketolase Q9AEM9 95% 3ahc 3ahd 3ahe 3ahf 3ahg 3ahh 3ahi 3ahj 4.1.2.22 Fructose-6-phosphate phosphoketolase D6PAH1 4.2.3.32 Levopimaradiene synthase H8ZM70 99% 3s9v 4.2.3.18 4.2.3.132...”
BC4157 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex from Bacillus cereus ATCC 14579
32% identity, 27% coverage
BCAS0079 non-heme chloroperoxidase from Burkholderia cenocepacia J2315
28% identity, 68% coverage
RALTA_A0090 B-KETOADIPATE ENOL-LACTONE HYDROLASE (putative) from Cupriavidus taiwanensis
26% identity, 69% coverage
PA0231 beta-ketoadipate enol-lactone hydrolase from Pseudomonas aeruginosa PAO1
30% identity, 67% coverage
- Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions
Yan, Journal of applied genetics 2017 - “...), 46 PAH degradation genes were analyzed in this study as follows: PA0153, PA0154, PA0230, PA0231, PA0232, PA0247, PA0480, PA0817, PA0865, PA0880, PA1205, PA1210, PA1253, PA1966, PA2009, PA2024, PA2083, PA2085, PA2217, PA2418, PA2507, PA2508, PA2509, PA2512, PA2513, PA2514, PA2515, PA2516, PA2517, PA2518, PA2546, PA3240, PA3389, PA3629,...”
- “...gene PA0230, PA3008 encoding cell division inhibitor SulA was associated with the PAH degradation gene PA0231, PA5479 encoding glutamate/aspartate:proton symporter was associated with the PAH degradation gene PA2508. Notably, PAH degradation gene PA4124 was associated with R2/F2 pyocin gene locus (PA0612-PA0648) because ten genes (PA0615, PA0616,...”
- Evidence for the involvement of the anthranilate degradation pathway in Pseudomonas aeruginosa biofilm formation
Costaglioli, MicrobiologyOpen 2012 - “...acid transporter PcaT PA0230 pcaB 48 5.5.1.2 2.7 0.8 3-Carboxy- cis , cis -muconate cycloisomerase PA0231 pcaD 48 3.1.1.24 3.3 1.4 -Ketoadipate enol-lactone hydrolase PA0232 pcaC 48 4.1.1.44 4.8 2.2 -Carboxymuconolactone decarboxylase PA2507 catA 527 1.13.11.1 3.3 1.0 Catechol 1,2-dioxygenase PA2508 catC 527 5.3.3.4 2.4 0.4...”
- “...of 3-oxoadipate-enol-lactone into 3-oxoadipate. The enzyme responsible for this reaction, EC 3.1.1.24, is encoded by PA0231 ( pcaD ) in P. aeruginosa, which belongs to an operon that also contains the PA0229 ( pcaT ), PA0230 ( pcaB ), and PA0232 ( pcaC ) genes. The...”
Q6DCH2 Ephx2-prov protein from Xenopus laevis
NP_001087143 epoxide hydrolase 2, cytoplasmic L homeolog from Xenopus laevis
30% identity, 32% coverage
LPAAT_ARATH / O22975 1-acylglycerol-3-phosphate O-acyltransferase; Lipid droplet-binding protein CGI-58 homolog; EC 2.3.1.51 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
O22975 1-acylglycerol-3-phosphate O-acyltransferase (EC 2.3.1.51) from Arabidopsis thaliana (see paper)
AT4G24160 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
NP_194147 alpha/beta-Hydrolases superfamily protein from Arabidopsis thaliana
26% identity, 55% coverage
- function: Lysophosphatidic acid acyltransferase which functions in phosphatidic acid biosynthesis. Is highly specific for lysophosphatidic acid and able to use different acyl-CoA donors. May regulate neutral lipid accumulation and participate in the regulation of lipid turnover in vegetative cells. Possesses additional triacylglycerol lipase and phospholipase A2 activities in vitro. Is not active as esterase or lysophospholipase.
catalytic activity: a 1-acyl-sn-glycero-3-phosphate + an acyl-CoA = a 1,2-diacyl- sn-glycero-3-phosphate + CoA (RHEA:19709)
disruption phenotype: Accumulation of neutral lipid droplets with marked increase in absolute triacylglycerol levels in leaf mesophyll cells. - Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae
Liu, Plant communications 2024 - “...AT1G16630 AT1G19840 AT1G16650 AT1G19840 B1 AT1G19850 AT1G24256 AT1G19850 AT1G24140 B2 AT1G24260 AT1G27280 AT1G24310 AT1G27210 U2 AT4G24160 AT4G27730 AT4G24740 AT4G27540 B3 AT1G27290 AT1G30755 AT1G27320 AT1G30755 B4 AT1G30757 AT1G32750 AT1G30760 AT1G32750 CBK2 D2 AT1G61210 AT1G56210 AT1G61210 AT1G56230 D1 AT1G64670 AT1G61215 AT1G64670 AT1G61240 E1 AT1G64960 AT1G67270 AT1G65020 AT1G67260 E2...”
- Molecular Machinery of Lipid Droplet Degradation and Turnover in Plants
, International journal of molecular sciences 2023 - “...1326 1345 10.1104/pp.19.01255 31826923 74. Ghosh A. Chauhan N. Rajakumari S. Daum G. Rajasekharan R. At4g24160, a Soluble Acyl-Coenzyme A-Dependent Lysophosphatidic Acid Acyltransferase Plant Physiol. 2009 151 869 881 10.1104/pp.109.144261 19700561 75. Lass A. Zimmermann R. Haemmerle G. Riederer M. Schoiswohl G. Schweiger M. Kienesberger P....”
- “...with the LD surface and catalyzes MAG hydrolysis during seed germination [ 107 ] CGI-58 AT4G24160 Peroxisome Soluble acyltransferase, with lipase and phospholipase functions; participates in the regulation of lipid turnover [ 77 ] PXA1 AT4G39850 Peroxisome Imports polyunsaturated FAs into peroxisomes for -oxidation [ 78...”
- The Phytotoxin Myrigalone A Triggers a Phased Detoxification Programme and Inhibits Lepidium sativum Seed Germination via Multiple Mechanisms including Interference with Auxin Homeostasis
Nakabayashi, International journal of molecular sciences 2022 - “...GSTU25 , GSTU1 , CYP81D8 , UGT75B1 , UGT73B2 , UGT73B5 , OPR1/2 , /-hydrolase (AT4G24160), PMAT1 , SAT1 , tolB and NAC102 ( Table 4 , Figure S17 ). Of these, PMAT1 is a malonyltransferase important in phenolic-xenobiotic metabolism [ 110 ], SAT1 is a...”
- “...and tolB is also up-regulated in TNT-treated seedlings [ 8 ]. In contrast to /-hydrolase (AT4G24160), which was up-regulated by all phytotoxins, up-regulation of the /-hydrolase BDG1 was MyA-specific ( Figure S17B , Table 4 ). BDG1 is involved in cutin production required for the endosperm-associated...”
- Dissection of Resistance Genes to Pseudomonas syringae pv. phaseolicola in UI3 Common Bean Cultivar
González, International journal of molecular sciences 2017 - “...it has been demonstrated for other lysophospholipid acyltransferases in Arabidopsis, as is the case of AT4G24160 up-regulated during Pseudomonas syringae infection [ 97 ]. 4. Material and Methods 4.1. Plant Material and Phenotypic Assay Two populations of ~500 F 2 lines from two crosses of the...”
- “...1453 1456 10.4161/psb.5.11.13462 21051954 97. Ghosh A.K. Neha C. Rajakumari S. Daum G. Rajasekharan R. AT4G24160 , a soluble acyl-coenzyme A-dependent lysophosphatidic acid acyltransferase Plant Physiol. 2009 151 869 881 10.1104/pp.109.144261 19700561 98. Garcia R.A.V. Rangel P.N. Brondani C. Martins W.S. Melo L.C. Carneiro M.S. Borba...”
- Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots
Rodríguez-Celma, Scientific reports 2016 - “...1.25 AT5G13750 ZIFL1 Zinc induced facilitator-like 1 29.66 AT1G78660 GGH1 Gamma-glutamyl hydrolase 1 26.72 1.13 AT4G24160 Alpha/beta-Hydrolases superfamily protein 23.28 1.23 AT4G16760 ACX1 Acyl-CoA oxidase 1 19.87 1.25 AT4G12390 PME1 Pectin methylesterase inhibitor 1 19.3 1.08 AT1G34370 STOP1 C2H2 and C2HC zinc fingers superfamily protein 18.68...”
- Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure
Dumas, BMC genomics 2016 - “...transcriptional regulator family protein 0.15 1. 00E+00 0.62 1.00E+00 0.86 1.00E+00 1.56 0.00E+00 1.37 0.00E+00 AT4G24160 alpha/beta-Hydrolases superfamily protein 0.01 1.00E+00 0.40 1.00E+00 0.59 1.00E+00 1.52 0.00E+00 1.25 0.00E+00 AT3G10500 anac053_NAC053__NAC domain containing protein 53 0.12 1.00E+00 0.77 1.19E-01 0.66 1.00E+00 1.48 0.00E+00 1.16 0.00E+00 AT2G01180...”
- Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola
Wan, Frontiers in plant science 2016 - “...LPA to phosphatidic acid (PA), are catalyzed by glycerol-3-phosphate acyltransferase (ATS1) and lysophosphatidic acid acyltransferase (AT4G24160), respectively. Lipid phosphate phosphatases (LPPs) catalyze the dephosphorylation of PA to produce sn-1,2-diacylglycerol (DAG) prior to the final acylation catalyzed by diacylglycerol acyltransferase (DGAT). In addition, DAG can also be...”
- Reassessing the Potential Activities of Plant CGI-58 Protein
Khatib, PloS one 2016 - “...performed with BioEdit software and the shading threshold was set to 75% identity. Arabidopsis thaliana At4g24160 was retrieved from a sequenced RAFL19-16-I19 clone and the Physcomitrella patens sequence was reconstructed from a sequencing of ESTs BY990945.1 and BJ940330.1. All the aforementioned clones were obtained from the...”
- “..., Chauhan N , Rajakumari S , Daum G , Rajasekharan R ( 2009 ) At4g24160, a soluble acyl-coenzyme A-dependent lysophosphatidic acid acyltransferase . Plant Physiol 151 : 869 881 . 10.1104/pp.109.144261 19700561 13 Schweiger M , Lass A , Zimmermann R , Eichmann TO ,...”
- More
- CGI-58, a key regulator of lipid homeostasis and signaling in plants, also regulates polyamine metabolism.
Park, Plant signaling & behavior 2014 - GeneRIF: CGI-58 and PXA1 contribute to the regulation of polyamine metabolism at the transcriptional level.[CGI-58]
- The α/β hydrolase CGI-58 and peroxisomal transport protein PXA1 coregulate lipid homeostasis and signaling in Arabidopsis.
Park, The Plant cell 2013 - GeneRIF: Data indicate that CGI-58 (At4g24160) interacts with PXA1 into peroxisomes for their subsequent metabolism by beta-oxidation, including fatty acids and lipophilic hormone precursors of the jasmonate and auxin biosynthetic pathways.
- Disruption of the Arabidopsis CGI-58 homologue produces Chanarin-Dorfman-like lipid droplet accumulation in plants.
James, Proceedings of the National Academy of Sciences of the United States of America 2010 - GeneRIF: Disruption of the Arabidopsis CGI-58 homologue produces Chanarin-Dorfman-like lipid droplet accumulation in plants.
- At4g24160, a soluble acyl-coenzyme A-dependent lysophosphatidic acid acyltransferase.
Ghosh, Plant physiology 2009 - GeneRIF: These data establish At4g24160, a protein with a previously unknown function, as an enzyme that might play a pivotal role in maintaining the lipid homeostasis in plants by regulating both phospholipid and neutral lipid levels.
BA3187 hydrolase, alpha/beta fold family from Bacillus anthracis str. Ames
30% identity, 35% coverage
A9CGA0 Hydrolase from Agrobacterium fabrum (strain C58 / ATCC 33970)
28% identity, 69% coverage
Q84II3 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase (EC 3.7.1.13) from Janthinobacterium sp. J3 (see paper)
28% identity, 69% coverage
GYO_3335 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase from Bacillus spizizenii TU-B-10
28% identity, 65% coverage
- Disparate Effects of Two Clerodane Diterpenes of Giant Goldenrod (Solidago gigantea Ait.) on Bacillus spizizenii
Bozsó, International journal of molecular sciences 2024 - “...[ 47 ]. Moreover, up-regulation of other common genes of menaquinone synthesis (GYO_1191, yhcB ; GYO_3335, ytxM ; GYO_3490, dhbC ) supports the importance of menaquinone dependent respiratory electron transport during diterpene-induced stress response. Finally, a putative glycosyltransferase (GYO_2344, yojK ) was activated in all samples....”
- “...GYO_2953 1.1 1.0 2.1 1.7 B. subtilis (BSU_27160) yrhJ , cytochrome P450, fatty acid metabolism GYO_3335 1.1 2.1 1.0 1.7 B. subtilis (BSU_30810) ytxM , ubiquinone and menaquinone biosynthesis GYO_3455 1.2 1.4 2.3 1.1 B. subtilis (BSU_31650) mrpF , Na+/H+ antiporter subunit, sodium export GYO_3490 2.3...”
CBL13_02882 alpha/beta fold hydrolase from Pseudomonas putida
29% identity, 73% coverage
ODP2_MYCTU / P9WIS7 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex; Component of peroxynitrite reductase/peroxidase complex; Component of PNR/P; Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex; Pyruvate dehydrogenase complex component E2; PDH component E2; EC 2.3.1.12 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 5 papers)
Mb2238 Probable pyruvate dehydrogenase (E2 component) SucB from Mycobacterium bovis AF2122/97
NP_216731 pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase from Mycobacterium tuberculosis H37Rv
P9WIS6 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Rv2215 dihydrolipoamide acyltransferase from Mycobacterium tuberculosis H37Rv
41% identity, 14% coverage
- function: Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2)
function: Together with AhpC, AhpD and Lpd, constitutes an NADH- dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system
function: Appears to be essential for Mtb pathogenesis
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CoA (RHEA:17017)
cofactor: (R)-lipoate Note=Binds 2 lipoyl cofactors covalently
subunit: Forms a 24-polypeptide structural core with octahedral symmetry (By similarity). Identified in a complex with AhpC, AhpD and Lpd. Part of the PDH complex, consisting of multiple copies of AceE (E1), DlaT (E2) and Lpd (E3).
disruption phenotype: Cells lacking this gene show severely retarded growth in vitro, and display no PDH activity. They are also more sensitive to nitrosative stress caused by NaNO(2), and to macrophage- induced killing in vitro. They also show at least 20-fold reduction in survival in a mouse tuberculosis model, and are unable to cause disease in a guinea pig model of tuberculosis infection. Disruption of dlaT leads to high up-regulation of the expression of the bkdABC operon. - The Microbiome of Leonardo da Vinci's Drawings: A Bio-Archive of Their History
Piñar, Frontiers in microbiology 2020 - “...Pore size = 0.45 m) connected to an oil-free diaphragm vacuum pump (DA14 Charles Austen MB2238. Appleton Woods Ltd., United Kingdom). The total number of membranes used for sampling varied between the drawings, ranging from 10 to 36 membranes per drawing (depending on the size of...”
- Dihydrolipoamide acyltransferase is critical for Mycobacterium tuberculosis pathogenesis.
Shi, Infection and immunity 2006 - GeneRIF: Inactivation of dlaT in the chromosome of H37Rv results in a mutant (H37RvDeltadlaT) that displays phenotypes associated with DlaT's role in metabolism and in defense against nitrosative stress.
- Mycobacterium tuberculosis appears to lack alpha-ketoglutarate dehydrogenase and encodes pyruvate dehydrogenase in widely separated genes.
Tian, Molecular microbiology 2005 (PubMed)- GeneRIF: E2 component of pyruvate dehydrogenase complex
- GeneRIF: DlaT (dihydrolipoamide acyltransferase) and Lpd (lipoamide dehydrogenase) join with AceE to constitute pyruvate dehyrogenase[DlaT]
- AoP-LSE: Antioxidant Proteins Classification Using Deep Latent Space Encoding of Sequence Features.
Usman, Current issues in molecular biology 2021 - “...P0CU34 Peroxiredoxin TSA1 Q5ACV9 Cell surface superoxide dismutase P9WHH8 Dihydrolipoyl dehydrogenase P9WIE1 Putative peroxiredoxin Rv2521 P9WIS6 Dihydrolipoyllysine-residue P9WQB6 Alkyl hydroperoxide reductase P9WID9 Putative peroxiredoxin Rv1608c O17433 Cys peroxiredoxin P9WIE0 Putative peroxiredoxin MT2597 P9WID8 Putative peroxiredoxin MT1643 P9WGE8 Superoxide dismutase [Cu-Zn] C0HK70 Superoxide dismutase P9WQB4 Alkyl hydroperoxide...”
- Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex
Bruch, Proceedings of the National Academy of Sciences of the United States of America 2021 (secret) - AoP-LSE: Antioxidant Proteins Classification Using Deep Latent Space Encoding of Sequence Features.
Usman, Current issues in molecular biology 2021 - “...UniProtKB ACC NCBI Definition AODPred Vote9 AoP-LSE P9WQB7 Alkyl hydroperoxide reductase C P9WHH9 Dihydrolipoyl dehydrogenase P9WIS7 Dihydrolipoyllysine-residue P9WG35 Thiol peroxidase P9WGE9 Superoxide dismutase P9WQB5 Alkyl hydroperoxide reductase P9WIE3 Alkyl hydroperoxide reductase P0CU34 Peroxiredoxin TSA1 Q5ACV9 Cell surface superoxide dismutase P9WHH8 Dihydrolipoyl dehydrogenase P9WIE1 Putative peroxiredoxin Rv2521...”
- The unfoldase ClpC1 of Mycobacterium tuberculosis regulates the expression of a distinct subset of proteins having intrinsically disordered termini
Lunge, The Journal of biological chemistry 2020 (secret) - Evaluation of the cross-immunity between Mycobacterium tuberculosis and Mycobacterium abscessus in vitro
Xu, BMC microbiology 2025 - “...and belonged to the cell composition cluster (GO:0044464). The second cluster contained 4 proteins (Rv0952, Rv2215, Rv2195, and Rv0951) and belonged to the growth gene ontology term cluster (GO: 0040007). The third cluster contained 3 proteins (Rv0440, Rv0350, and Rv0006) and belonged to the response to...”
- Role of dormancy survival regulator and resuscitation-promoting factors antigens in differentiating between active and latent tuberculosis: a systematic review and meta-analysis
Wu, BMC pulmonary medicine 2024 - “...Rv1737c [ 27 ]. Higher levels of antibodies are found against Rv0440, Rv0867c, Rv1737c, Rv2029c, Rv2215, Rv2389c, and Rv3616c in active TB patients compared to healthy individuals [ 43 ]. Inconsistencies in the immunoreactivity outcomes of different studies may be due to different host immune responses,...”
- Gene Regulatory Mechanism of Mycobacterium Tuberculosis during Dormancy
Liu, Current issues in molecular biology 2024 - “...A mycolic acid cyclopropane synthetase, associated with persistence and virulence of Mtb [ 43 ]. Rv2215 (dlaT) Participates in the constitution of pyruvate dehydrogenase [ 32 ]. Rv0534c (menA) Involved in the synthesis of menaquinone which is critical for maintaining mycobacterial viability [ 33 ]. Rv1620c...”
- Antigen identification strategies and preclinical evaluation models for advancing tuberculosis vaccine development
Chugh, NPJ vaccines 2024 - “...from M. tuberculosis exposed individuals, and nine of these antigens (Rv3615, Rv2029, Rv3353, Rv1733, Rv0826, Rv2215, Rv1791, Rv2873, and Rv2626c) triggered the secretion of cytokine response (IP-10, TNF-, and IL-17) without induction of IFN- response 153 . Another study was performed in three different mice strains,...”
- The role of Mycobacterium tuberculosis acetyltransferase and protein acetylation modifications in tuberculosis
Huang, Frontiers in cellular and infection microbiology 2023 - “...source and energy metabolism regulation, isoniazid acetylation modification Lee etal. (2017) ; Arun etal. (2020) Rv2215 DlaT dihydrothioctylamine virulence factor, metabolism and nitrosation stress regulation Shi and Ehrt (2006) Rv2335 CysE serine regulate the growth rate of mycobacterium Qiu etal. (2014) Rv2416c Rv2669 Rv2704 Eis Rv2669...”
- Role of MHC class I pathways in Mycobacterium tuberculosis antigen presentation
Witt, Frontiers in cellular and infection microbiology 2023 - “...stimulates the secretion of IL-10 and MCP-1 via TLR2 activation Autophagosome Tiwari etal. (2014) DlaT (Rv2215) 553aa Function with Lpd as NADH-dependent peroxidase and peroxynitrite reductase that provides protection against nitrosative stress Phagosome, autophagolysosome Shi and Ehrt (2006) Mce2D (Rv0592) 508aa Less TNF- and IL-6; all...”
- 1,3-Diarylpyrazolyl-acylsulfonamides Target HadAB/BC Complex in Mycobacterium tuberculosis
Singh, ACS infectious diseases 2022 - “...M was generated for 1 and BCG_2231 (dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, DlaT, Rv2215, it was also competed by 2 , with a K d app value of 6.6 M). The K d app value for 1 and BCG_0628c (probable conserved lipoprotein lpqN, Rv0583c)...”
- Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches
Balamurugan, Frontiers in genetics 2022 - “...involved in cellular metabolism Arg247Arg a Rv3236c/kefB Growth attenuation Arg325His L6.2 Rv3236c/kefB Growth attenuation Val106Ala Rv2215 Involved in tricarboxylic acid cycle and antioxidant defense Ala338Val Rv1121/zwf1 Involved in the pentose phosphate pathway Gln277* L6.3 Rv1180/pks3 Potentially involved in intermediate steps for the synthesis of polyketide Pro401Thr...”
- More
SGRAN_1584 alpha/beta fold hydrolase from Sphingopyxis granuli
28% identity, 69% coverage
BCG_2231 DlaT, dihydrolipoamide acyltransferase, E2 component of pyruvate dehydrogenase from Mycobacterium bovis BCG str. Pasteur 1173P2
41% identity, 14% coverage
BCAM0061 putative 3-oxoadipate enol-lactonase I from Burkholderia cenocepacia J2315
28% identity, 68% coverage
SCO7123 acyltransferase from Streptomyces coelicolor A3(2)
44% identity, 18% coverage
Avin_02370 non-heme chloroperoxidase (abhydrolase_1 family) from Azotobacter vinelandii AvOP
28% identity, 67% coverage
LOC103329206 pheophytinase, chloroplastic-like from Prunus mume
27% identity, 71% coverage
- Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening
García-Gómez, Frontiers in plant science 2020 - “...PARG01655m01 ) and flavonoid biosynthesis LOC103339178 (EC:1.14.14.91; unknown PARG ID). Other genes of interest are LOC103329206 ( PARG00063m07 ) predicted as a pheophytinase, and LOC103328016 (PARG00063m07) as ABC transporter pleiotropic drug resistance (PDR). ME brown showed a positive correlation with blush color while a negative correlation...”
- “...2 ), we found differential expression in genes related with chlorophyll dephytylation in ME blue LOC103329206 ( PARG00063m07 ) as a pheophytinase, and ME yellow LOC103324364 ( PARG00058m01 ) as a pheophorbide A oxygenase ( Guyer etal., 2014 ) ( Figure 7 and Supplementary Data Sheet...”
FRAAL5152 dihydrolipoamide succinyltransferase, component of 2-oxoglutarate dehydrogenase complex (E2) from Frankia alni ACN14a
45% identity, 14% coverage
Bphyt_6134 alpha/beta hydrolase fold from Burkholderia phytofirmans PsJN
27% identity, 68% coverage
cmtE / Q51980 HOMODA hydrolase from Pseudomonas putida (see 2 papers)
cmtE / AAB62292.1 HOMODA hydrolase from Pseudomonas putida (see 3 papers)
28% identity, 67% coverage
Synpcc7942_0774 esterase from Synechococcus elongatus PCC 7942
32% identity, 57% coverage
- Transcriptomic and Phenomic Investigations Reveal Elements in Biofilm Repression and Formation in the Cyanobacterium Synechococcus elongatus PCC 7942
Simkovsky, Frontiers in microbiology 2022 - “...via PCR using primers listed in Supplementary Table S10 . An inactivation vector for gene Synpcc7942_0774 was constructed through blunt-end cloning of a PCR-amplified gene fragment, generated using the K273 and K274 primers listed in Supplementary Table S10 , into the pJet1.2 vector (Thermo Fisher Scientific)....”
- “...Supplementary Table S9 , Supplementary File S3 Sheet 15) or a pimeloyl-ACP methyl ester carboxylesterase (Synpcc7942_0774) decreased the reliability or strength of biofilm formation. Transcriptomics and Phenomics Reveal Novel Information on the Biofilm State and the Quality of the Genome Model The RNA-Seq time course data...”
- Biodegradation of Dimethyl Phthalate by Freshwater Unicellular Cyanobacteria
Zhang, BioMed research international 2016 - “...for the defined esterase, four genes encoding probable esterases with the lotus tags synpcc7942_0451, synpcc7942_0458, synpcc7942_0774, and synpcc7942_2527 were detected in Synechococcus sp. PCC7942 as well as 3 genes with lotus tags Cyan7822_1061, Cyan7822_2840, and Cyan7822_3463 in Cyanothece sp. PCC7822. However, the expression and the functional...”
MSMEG_1897 3-oxoadipate enol-lactonase from Mycobacterium smegmatis str. MC2 155
A0QTM5 3-oxoadipate enol-lactonase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_1897, MSMEI_1857 3-oxoadipate enol-lactonase from Mycolicibacterium smegmatis MC2 155
29% identity, 65% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...protein S5 0.075 12.333 A0R1B5 MSMEG_4692, MSMEI_4575 Uncharacterized protein MSMEG_4692/MSMEI_4575 0.082 4.500 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.102 4.500 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.030 3.000 A0QS62 rplJ , MSMEG_1364, MSMEI_1325 50S ribosomal protein L10 0.078 8.500 A0QX20 acnA , can...”
- “...hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.1 0.05 A0R617 pks13 , MSMEG_6392, MSMEI_6224 Polyketide synthase 0.16 0.14 A0QTE1 accA3 , MSMEG_1807, MSMEI_1762 Acetyl/propionyl-coenzyme A carboxylase alpha chain 0.13 0.17 A0QV28 glnB...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...MSMEI_1436 30S ribosomal protein S5 0.075 12.333 A0R1B5 MSMEG_4692, MSMEI_4575 Uncharacterized protein MSMEG_4692/MSMEI_4575 0.082 4.500 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.102 4.500 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.030 3.000 A0QS62 rplJ , MSMEG_1364, MSMEI_1325 50S ribosomal protein L10 0.078 8.500 A0QX20...”
- “...MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.1 0.05 A0R617 pks13 , MSMEG_6392, MSMEI_6224 Polyketide synthase 0.16 0.14 A0QTE1 accA3 , MSMEG_1807, MSMEI_1762 Acetyl/propionyl-coenzyme A carboxylase alpha chain 0.13...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...S5 0.075 12.333 A0R1B5 MSMEG_4692, MSMEI_4575 Uncharacterized protein MSMEG_4692/MSMEI_4575 0.082 4.500 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.102 4.500 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.030 3.000 A0QS62 rplJ , MSMEG_1364, MSMEI_1325 50S ribosomal protein L10 0.078 8.500 A0QX20 acnA , can ,...”
- “...(EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.1 0.05 A0R617 pks13 , MSMEG_6392, MSMEI_6224 Polyketide synthase 0.16 0.14 A0QTE1 accA3 , MSMEG_1807, MSMEI_1762 Acetyl/propionyl-coenzyme A carboxylase alpha chain 0.13 0.17 A0QV28 glnB ,...”
SCO2181 dihydrolipoamide succinyltransferase from Streptomyces coelicolor A3(2)
45% identity, 13% coverage
- A Proteomic Analysis Indicates That Oxidative Stress Is the Common Feature Triggering Antibiotic Production in Streptomyces coelicolor and in the pptA Mutant of Streptomyces lividans
Lejeune, Frontiers in microbiology 2021 - “...as well as the malate dehydrogenase SCO5261, the -ketoglutarate dehydrogenase SCO4595, and the dihydrolipoamide succinyltransferase SCO2181 that generates NADH. The malate synthase SCO6243 of the glyoxylate cycle also belongs to this cluster and is the only enzyme showing a clear upregulation in Pi limitation in the...”
- Expression of genes of the Pho regulon is altered in Streptomyces coelicolor
Millan-Oropeza, Scientific reports 2020 - “...72h (Fig. 5 ). These include, the NAD+-dependent isocitrate dehydrogenase SCO7000, as well as SCO2180, SCO2181 and SCO4919 putatively constituting the NAD+ dependent -ketoglutarate dehydrogenase complex converting -ketoglutarate into succinate; SCO0923 thought to be part of the FAD+-dependent succinate dehydrogenase complex converting succinate into fumarate that...”
- Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST
Tong, Proceedings of the National Academy of Sciences of the United States of America 2019 - “...strand of SCO5087 and the other targeting the noncoding strand of an intergenic region between SCO2181 and SCO2182. Both of the sgRNAs contain adenosines within a hypothetic editing window of 6 nt. We observed that the targeted adenosines were indeed converted to guanosines, albeit with a...”
- Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2)
Wentzel, BMC systems biology 2012 - “...encoding potential pyruvate dehydrogenase components are: SCO2183 aceE1 pyruvate dehydrogenase (PDH) E1 component (EC 1.2.4.1); SCO2181 aceF1 dihydrolipoyllysine-residue acetyltransferase PDH E2 component (EC 2.3.1.12); SCO2180 lpd1 dihydrolipoamide dehydrogenase PDH E3 component (EC 1.8.1.4); SCO7124 aceE3 PDH E1 component (EC 1.2.4.1); SCO7123 aceF3 PDH E2 component (EC...”
- Rapid functional screening of Streptomyces coelicolor regulators by use of a pH indicator and application to the MarR-like regulator AbsC
Yang, Applied and environmental microbiology 2010 - “...and TCA SCO1945 SCO1947 SCO2180 SCO2181 SCO4808 SCO4827 SCO7511 Triosephosphate isomerase, TpiA Glyceraldehyde-3-phosphate dehydrogenase, Gap1 Dihydrolipoamide...”
Q92Q67 Hydrolase from Rhizobium meliloti (strain 1021)
40% identity, 35% coverage
BMEI0733 NON-HEME CHLOROPEROXIDASE from Brucella melitensis 16M
40% identity, 32% coverage
YP_825272 alpha/beta hydrolase fold from Solibacter usitatus Ellin6076
35% identity, 30% coverage
- The combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method
Narihiro, Microbes and environments 2014 - “...Pirellula staleyi DSM 6068 YP_003372868 / hydrolase 39.9 V Acidobacteria NSm05 Candidatus Solibacter usitatus Ellin6076 YP_825272 / hydrolase 77.8 V Unidentified groups NSm06 uncultured bacterium clone pUlp286 ABQ11270 Lipase/esterase 53.8 V NSm07 uncultured bacterium clone pUlp286 ABQ11270 Lipase/esterase 50.5 V OS (oil-enriched soil) Alphaproteobacteria OSm01 Tistrella...”
- “...VIII OSm24 Candidatus Koribacter versatilis Ellin345 YP_589716 -lactamase 51.0 VIII OSm25 Candidatus Solibacter usitatus Ellin6076 YP_825272 / hydrolase 80.1 V Unidentified groups OSm26 uncultured bacterium ACD_17C00118G0001 EKE08525 Hypothetical lipase 50.0 NC OSm27 uncultured bacterium pELP141 AAS77238 Lipase/esterase 77.2 IV OSm28 uncultured organism EstC23 AFC77925 Lipase/esterase 74.8...”
SE37_03105 dihydrolipoamide acetyltransferase family protein from Geobacter soli
32% identity, 45% coverage
- Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T)
Yang, Standards in genomic sciences 2015 - “...soli possesses two sets of genes encoding pyruvate dehydrogenase complexes (SE37_03080, SE37_02045, SE37_02040, and SE37_03100; SE37_03105 and SE37_02035) to irreversibly convert pyruvate to acetyl-CoA. The reverse reaction in G. soli from acetyl-CoA is attributed to a homodimeric pyruvate-ferredoxin/flavodoxin oxidoreductase (SE37_14040). In addition to pyruvate, ethanol is...”
EQW00_01285, SERP_RS11420 dihydrolipoamide acetyltransferase family protein from Staphylococcus epidermidis RP62A
SERP2324 acetoin dehydrogenase, E2 component, dihydrolipoamide acetyltransferase from Staphylococcus epidermidis RP62A
38% identity, 20% coverage
- Unravelling staphylococcal small-colony variants in cardiac implantable electronic device infections: clinical characteristics, management, and genomic insights
Liu, Frontiers in cellular and infection microbiology 2023 - “...IS1182-like element ISSep1 family transposase cp8WT/cp8SCV2 cp10WT/cp10SCV2 cp10WT/cp10SCV3 EQW00_00140 IS6 family transposase cp6WT1/cp6SCV1 cp6WT1/cp6SCV2 cp8WT/cp8SCV2 EQW00_01285 2oxo acid dehydrogenase subunit E2 cp1WT/cp1SCV cp10WT/cp10SCV3 EQW00_00380 DUF1643 domaincontaining protein cp1WT/cp1SCV cp8WT/cp8SCV2 EQW00_00285 DUF1643 domaincontaining protein cp8WT/cp8SCV2 cp10WT/cp10SCV2 cp10WT/cp10SCV3 ebh hyperosmolarity resistance protein Ebh cp1WT/cp1SCV cp10WT/cp10SCV2 cp10WT/cp10SCV3 EQW00_07700 phage...”
- The Vancomycin Resistance-Associated Regulatory System VraSR Modulates Biofilm Formation of Staphylococcus epidermidis in an ica-Dependent Manner
Wu, mSphere 2021 - “...2-oxoglutarate dehydrogenase complex 0.21 ND SERP_RS04935 NC_002976.3 (10024851005289) 2-Oxoglutarate dehydrogenase subunit E1 component 0.28 ND SERP_RS11420 NC_002976.3 (23602692361546) Acetoin dehydrogenase subunit E2 0.38 0.110.08 SERP_RS11425 NC_002976.3 (23615602362600) Acetoin dehydrogenase, E1 component, beta subunit 0.16 ND SERP_RS11430 NC_002976.3 (23626712363624) Thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha 0.35...”
- Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis
Gonçalves, Frontiers in microbiology 2022 - “...formate lyase activating enzyme SERP2365 pflA Formate acetyltransferase SERP2366 pflB Dihydrolipoyl dehydrogenase SERP2327 Dihydrolipoamide acetyltransferase SERP2324 Oxidative Phosphorylation Cytochrome aa3-600 menaquinol oxidase subunit ii SERP0646 qoxB Cytochrome aa3-600 menaquinol oxidase subunit iii SERP0644 qoxC Succinate dehydrogenase / fumarate reductase, cytochrome b subunit SERP0730 sdhC NADH:flavin oxidoreductase/fumarate...”
- The Vancomycin Resistance-Associated Regulatory System VraSR Modulates Biofilm Formation of Staphylococcus epidermidis in an ica-Dependent Manner
Wu, mSphere 2021 - “...; pentose phosphate pathway-related genes sucCD (succinyl coenzyme A [succinyl-CoA] ligase subunits beta and alpha), serp2324 (acetoin dehydrogenase), serp0731 (succinate dehydrogenase), sdhAB ( l -serine dehydratase), etc.; carbohydrate metabolic process-related genes manA2 (mannose-6-phosphate isomerase), malA (alpha-glucosidase), rbsKD (ribokinase), etc.; and phosphate transport-related genes such as serp2114...”
- “...). The expression of genes related to glycolysis ( gntPKR , glpFKD ), PPP ( serp2324 , serp2325 , sucCD , serp0731 , serp0732 ), the phosphate transport system ( serp2114 , serp2343 , serp2344 , lacFD ), and the carbohydrate metabolic process ( rbsKDU ,...”
- Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Sivaranjani, Frontiers in microbiology 2019 - “...1.40 1.44 10 -10 SERP1990 nirB Nitrite reductase [NAD(P)H], large subunit 2.17 1.56 10 -10 SERP2324 Acetoin dehydrogenase, E2 component, dihydrolipoamide acetyltransferase 1.34 3.30 10 -10 SEA0017 yadH ABC transporter, permease protein 1.98 5.79 10 -10 SERP2325 acoB Acetoin dehydrogenase, E1 component, beta subunit 1.47 1.68...”
- PhoU2 but Not PhoU1 as an Important Regulator of Biofilm Formation and Tolerance to Multiple Stresses by Participating in Various Fundamental Metabolic Processes in Staphylococcus epidermidis
Wang, Journal of bacteriology 2017 - “...ND acnA NC_002976.3 (932350935056) Aconitate hydratase 0.64 ND icd NC_002976.3 (12961941297463) Isocitrate dehydrogenase 0.46 ND serp2324 NC_002976.3 (23602682361546) Branched-chain alpha-keto acid dehydrogenase subunit E2 0.24 ND sucC NC_002976.3 (815833817000) Succinyl coenzyme A synthetase subunit beta 1.78 ND sdhB NC_002976.3 (730805733414) Succinate dehydrogenase iron-sulfur subunit 0.20 ND...”
- “...alpha subunit 10 acnA Aconitate hydratase 11 acnA Aconitate hydratase 12 icd Isocitrate dehydrogenase 13 serp2324 Branched-chain alpha-keto acid dehydrogenase subunit E2 14 sucC Succinyl coenzyme A synthetase subunit beta 15 sdhA , sdhB Succinate dehydrogenase iron-sulfur subunit, succinate dehydrogenase flavoprotein subunit 16 fumC Fumarate hydratase...”
- Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis
Broach, Microbial genomics 2016 - “...< SERP1100 259.07 SERPs105 jaeL-105 2192309..2192465 SERP2163 > SERP2164 17.68 SERPs106 jaeL-106 2360082..2360248 SERP2323 < SERP2324 9.97 SERPs107 jaeL-107 54838..54966 SERP0066 > xpt 210.87 SERPs108 jaeL-108 617908..618225 SERP0626 > menA 80.31 SERPs109 jaeL-109 485246..485535 SERP0495 > sufC 45.94 SERPs110 jaeL-110 1263896..1264162 valS < SERP1229 380.5 SERPs111...”
- Staphylococcus epidermidis SrrAB regulates bacterial growth and biofilm formation differently under oxic and microaerobic conditions
Wu, Journal of bacteriology 2015 - “...and energy metabolism-related genes, including srrA, serp2324 (branched-chain alpha-keto acid dehydrogenase subunit E2), serp2327 (acetoin dehydrogenase, E3...”
- “...2.96 3.10 2.95 ND ND ND SERP2379 SERP2324 SERP2365 SERP2170 SERP2182 SERP2183 SERP1795 SERP1873 SERP2192 a WT, wild type; UD, under...”
MAP1956 SucB from Mycobacterium avium subsp. paratuberculosis str. k10
41% identity, 12% coverage
- A rhodanine agent active against non-replicating intracellular Mycobacterium avium subspecies paratuberculosis
Bull, Gut pathogens 2009 - “...system involving an oxidation/reduction cascade with three other genes called ahp D (MAP1588c), dla T (MAP1956) and lpd A (MAP3424). Previous work has shown that this cascade can be irreversibly inhibited by the binding of a group of rhodanine derivatives to the DlaT component found in...”
- “...Other genes in the AhpC oxidation/reduction cascade including lpdA (MAP3424) and the MAP homologue dlaT (MAP1956) of the proposed substrate for D157070 in MTB, were similarly unaffected. Table 1 Differentially regulated MAP genes after D157070 treatment Fold Change Gene Name p-value Day 1 Day 3 Putative...”
SMa1727 putative hydrolase from Sinorhizobium meliloti 1021
25% identity, 70% coverage
- Directed construction and analysis of a Sinorhizobium meliloti pSymA deletion mutant library
Yurgel, Applied and environmental microbiology 2013 - “...transcriptional repressor of bet operon; and lipase, SMa1727. Osmoadaptation was not affected in the Rm1021::pRG1SMa1696pD2SMa1740 strain, which lacks SMa1726,...”
- The LuxR homolog ExpR, in combination with the Sin quorum sensing system, plays a central role in Sinorhizobium meliloti gene expression
Hoang, Journal of bacteriology 2004 - “...periplasmic signal peptide protein SMa0089 SMc02111 SMa1727 SMa1262 SMc00777 SMa0091 SMb21097 SMc00670 (hisV) SMc01843 SMb20836 SMc02087 (gltA) SMa0645...”
- 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 - “...of betaine synthesis, BetI (SMA1726), and a lipase (SMA1727; Fig. 1). The S. meliloti chromosome also encodes a betaine aldehyde dehydrogenase, as well as...”
MSMEG_3289 gp61 protein from Mycobacterium smegmatis str. MC2 155
27% identity, 61% coverage
MOV58_10435 alpha/beta fold hydrolase from Staphylococcus hominis
26% identity, 69% coverage
8agsAAA / A0A1U9WZ52 8agsAAA
26% identity, 62% coverage
AT5G21950 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
26% identity, 64% coverage
lmo2109 similar to hydrolase from Listeria monocytogenes EGD-e
34% identity, 32% coverage
- N-acetylglucosamine-6-phosphate deacetylase (NagA) of Listeria monocytogenes EGD, an essential enzyme for the metabolism and recycling of amino sugars
Popowska, Archives of microbiology 2012 - “...with fructose metabolism can be found. This region, consisting of three genes: lmo2107, lmo2108, and lmo2109, was identified as operon 384 (Toledo-Arana et al. 2009 ). Gene lmo2109 encodes an alpha/beta hydrolase fold and is located upstream of gene lmo2110, which codes an enzyme similar to...”
- “...generated from EGD. The formation of visibly smaller amount of transcript from genes lmo0957 and lmo2109 located downstream of mutated genes lmo0956 and lmo2108 from cDNA matrix from the log phase of growth was observed . In the case of cDNA isolated from the stationary phase...”
- Glycerol metabolism and PrfA activity in Listeria monocytogenes
Joseph, Journal of bacteriology 2008 - “...California, Berkeley ileS lmo2067 lmo2085b lmo2098 lmo2108 lmo2109 lmo2115 lmo2121a,b lmo2122 lmo2123 lmo2124 lmo2125b lmo2134 lmo2135 lmo2136 lmo2143 lmo2159b...”
BC1G_05874 hypothetical protein from Botrytis cinerea B05.10
29% identity, 52% coverage
- Interkingdom gene transfer may contribute to the evolution of phytopathogenicity in botrytis cinerea
Zhu, Evolutionary bioinformatics online 2012 - “...lipophilic substrates. 33 The second and third HGT are two putative alpha/beta hydrolase fold proteins (BC1G_05874, PF00561, e-value 4.4e 11 and BC1G_15488, PF00561, e-value 5.1e 5 ). The fourth HGT candidate showed sequence similarity to a lipoprotein (BC1G_10872, PF12006, 2.06e 74 ), which is a biochemical...”
- “...plant species to B. cinerea ( Fig. 2 ). Two putative alpha/beta hydrolase fold proteins (BC1G_05874 and BC1G_15488) were encoded by an HGT candidate from Burkholderia species ( Supplementary Fig. 3 ) and Nakamurella multipartite ( Supplementary Fig. 4 ) to B. cinerea , respectively. The...”
bioH / BAB39459.1 BioH from Kurthia sp. 538-KA26 (see paper)
27% identity, 68% coverage
slr0314 bromoperoxidase from Synechocystis sp. PCC 6803
27% identity, 66% coverage
- Deep Proteogenomics of a Photosynthetic Cyanobacterium
Spät, Journal of proteome research 2023 - “...genes encoding hidden proteins, one with six genes ( ssr0511 , slr0311 , slr0313 , slr0314 , slr0316 , ssr0515 ), of which only one ( slr0316 ) was previously detected at the transcriptome level (TU3202). Interestingly, a significant proportion of the hidden proteins are encoded...”
Ent638_1149 alpha/beta hydrolase fold from Enterobacter sp. 638
27% identity, 68% coverage
- Transcriptional responses to sucrose mimic the plant-associated life style of the plant growth promoting endophyte Enterobacter sp. 638
Taghavi, PloS one 2015 - “...additional hydroperoxide reductases (a putative ahpC Ent638_3391 and Ent638_0498 having an AhpD domain), a chloroperoxidase (Ent638_1149), two thiol peroxidases (Ent638_2151 and Ent638_2976) and three glutathione S-transferase (GST) genes (Ent638_0139, Ent638_0268 and Ent638_1329), remained similar or decreased. Only expression of arcA , belonging to the arcAB (Ent638_09430944)...”
- Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638
Taghavi, PLoS genetics 2010 - “...additional hydroperoxide reductases (a putative ahpC Ent638_3391 and Ent638_0498 having an AhpD domain), a chloroperoxidase (Ent638_1149), and two thiol peroxidases (Ent638_2151 and Ent638_2976). We also identified a putative organic peroxide resistance protein, ohr (Ent638_0518) located next to its organic peroxide sensor/regulator ( ohrR , Ent638_0519). Enterobacter...”
AGH13448.1 hybrid C-C meta-cleavage hydrolase-carboxylesterase from Cycloclasticus zancles (see paper)
28% identity, 57% coverage
Q6IE26 Epoxide hydrolase 4 from Mus musculus
NP_001001804 epoxide hydrolase 4 isoform 1 from Mus musculus
25% identity, 69% coverage
RM25_RS07455 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Propionibacterium freudenreichii subsp. freudenreichii
43% identity, 12% coverage
LOC18044409 dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic from Citrus x clementina
40% identity, 17% coverage
SNA_09035 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Streptomyces natalensis ATCC 27448
42% identity, 13% coverage
- Streptomyces natalensis programmed cell death and morphological differentiation are dependent on oxidative stress
Beites, Scientific reports 2015 - “...a less extent, we have also identified over-expressed proteins in catR related with energy metabolism (SNA_09035, SNA_09040 and SNA_33550). The set of proteins identified in the wild-type strain that were down-regulated or even not detected in the katA1 and catR protein extracts included the molecular chaperon...”
- “...Down (0.2) Energy metabolism, carbon SNA_07865 (33) pyruvate dehydrogenase E1 Up ( * ) Absent SNA_09035 (35) dihydrolipoamide acyltransferase Absent Up ( * ) SNA_09040 (27) dihydrolipoamide dehydrogenase Up ( * ) Up ( * ) SNA_10650 (22) glucose 6-phosphate dehydrogenase Up ( * ) Absent...”
Daci_1886 alpha/beta hydrolase fold from Delftia acidovorans SPH-1
32% identity, 66% coverage
- Interference of Quorum Sensing by Delftia sp. VM4 Depends on the Activity of a Novel N-Acylhomoserine Lactone-Acylase
Maisuria, PloS one 2015 - “...with different Ntn-hydrolases. Inspection of genome database of Delftia acidovorans SPH-1, revealed /-hydrolase fold homologue (Daci_1886) that was also similar to reported /-hydrolase type AHL acylase of Ochrobactrum sp. A44 [ 41 ] and other homologues. The similarity of hypo_Daci4366 to the carboxylic ester hydrolases implies...”
- “...Rhodococcus erythropolis SK121 (AbH-Rerythro, gi|229491600), Parvibaculum lavamentivorans DS-1 (AbH_Plavament, gi|154156608) and D . acidovorans SPH-1 (Daci_1886, gi| 5747443, indicated as abHf_Daci1886). White letters on a black background depict identical residues, and similar residues are depicted by black letters on a gray background and gaps are represented...”
FRAAL3408 putative hydrolase from Frankia alni ACN14a
34% identity, 32% coverage
- The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules
Pujic, Microorganisms 2022 - “...- A 0.001 WP_050997247.1 FRAAL5736 ftsK Cell division protein FtsK 6.43 D A 0.000 WP_011604554.1 FRAAL3408 Alpha/beta hydrolase 6.37 R f 0.001 WP_041938863.1 FRAAL1156 sucC Succinyl-CoA synthetase subunit beta SucC 6.14 C A 0.012 WP_011605559.1 FRAAL4438 Sugar-phosphate dehydrogenase 6.08 C A 0.002 WP_041939760.1 FRAAL5796 smc Chromosome...”
slr1916 esterase from Synechocystis sp. PCC 6803
34% identity, 29% coverage
- Photosynthesis in Synechocystis sp. PCC 6803 is not optimally regulated under very high CO<sub>2</sub>
Carrasquer-Alvarez, Applied microbiology and biotechnology 2025 - “...3.18 0.05 2.21 slr1660 Hypothetical protein 4.72 1.57 2.23 slr0195 Hypothetical protein 3.03 0.17 2.26 slr1916 Probable esterase 2.77 0.50 2.31 sll0828 nylA Putative amidase 3.68 0.25 2.78 sll1968 pmgA Photomixotrophic growth-related protein 4.54 0.64 3.66 Gene set enrichment analyses (GSEA) were performed using pathways from...”
- “...al. 1998 ; Muramatsu et al. 2009 ). We also note that the pmgA and slr1916 mutants behaved very similarly in our system (Table 3 ) in agreement with previous findings that deletion mutants lacking these genes had both an increased PSI/PSII ratio and an increased...”
- The genome sequence of Synechocystis sp. PCC 6803 substrain GT-T and its implications for the evolution of PCC 6803 substrains
Koskinen, FEBS open bio 2023 - “...Function 157961 C T Val219Met sll0223 ndhB NAD(P)Hquinone oxidoreductase subunit 2 619782 T frameshift S56 slr1916 Esterase 938475 T C Gln589Arg sll1732 ndhF3 NAD(P)Hquinone oxidoreductase subunit F 1290831 G A Silent slr1813 Hypothetical protein 1840410 G A Silent sll1374 melB 1864740 A T Glu89Val slr1274 pilM...”
- “...phenotype, but two other insertions cause frameshift mutations. The first one is located in the slr1916 gene that encodes a putative esterase (Table 1 ). This esterase has been shown to have chlorophyll dephytylase activity invitro and slr1916 was found to have higher chlorophyll content than...”
- Adaptive Laboratory Evolution of Microorganisms: Methodology and Application for Bioproduction
Hirasawa, Microorganisms 2022 - “...II was maintained. Genome resequencing analysis revealed two mutations in slr0484 ( hik26 ) and slr1916 , which encode a histidine kinase of a two-component signal transduction system and possible esterase, respectively. 8. Improvement of Production of Target Compounds by Microorganisms with ALE Integrated with Other...”
- “...K. Ogawa K. Toya Y. Akimoto S. Matsuda F. Shimizu H. Mutations in hik26 and slr1916 lead to high-light stress tolerance in Synechocystis sp. PCC6803 Commun. Biol. 2021 4 343 10.1038/s42003-021-01875-y 33727624 81. Moser J.W. Prielhofer R. Gerner S.M. Graf A.B. Wilson I.B. Mattanovich D. Dragosits...”
- Evolution of Ycf54-independent chlorophyll biosynthesis in cyanobacteria
Chen, Proceedings of the National Academy of Sciences of the United States of America 2021 - “...Sequencing ycf54 revertants identified a single D219G amino acid substitution in CycI and frameshifts in slr1916, which encodes a putative esterase. Introduction of these mutations to the original ycf54 mutant validated the suppressor effect, especially in combination. However, comprehensive analysis of the ycf54 suppressor strains revealed...”
- “...suggesting that Ycf54 controls both the level and activity of CycI. We also show that Slr1916 has Chl dephytylase activity in vitro and its inactivation up-regulates the entire Chl biosynthetic pathway, resulting in improved cyclase activity. Finally, large-scale bioinformatic analysis indicates that our laboratory evolution of...”
- Mutations in hik26 and slr1916 lead to high-light stress tolerance in Synechocystis sp. PCC6803
Yoshikawa, Communications biology 2021 - “...Biology 2399-3642 Nature Publishing Group UK London 7966805 1875 10.1038/s42003-021-01875-y Article Mutations in hik26 and slr1916 lead to high-light stress tolerance in Synechocystis sp. PCC6803 Yoshikawa Katsunori 1 Ogawa Kenichi 1 Toya Yoshihiro 1 http://orcid.org/0000-0002-8951-8978 Akimoto Seiji 2 Matsuda Fumio 1 http://orcid.org/0000-0002-8986-0861 Shimizu Hiroshi shimizu@ist.osaka-u.ac.jp 1...”
- “...light conditions. Whole genome sequence analysis and reverse engineering revealed two mutations in hik26 and slr1916 involved in high light stress tolerance in the Tol strain. In this paper, the authors investigated the high light stress response in Synechocystis sp. PCC6803 and revealed two key mutations...”
- Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis
Shahbazi, 3 Biotech 2021 - “...ssl3769 fdx II, sll1382 probable esterase, slr1916 sigB2, sll0306 rimI, slr0853 hypothetical protein, slr0852 hypothetical protein, ssr3188 hypothetical...”
- Chlorophyllides: Preparation, Purification, and Application
Wang, Biomolecules 2021 - “...a , and chlorophyll b and chlorophyll a were especially preferred. Recently, a putative esterase, Slr1916, was found in the mutant of the cyanobacterium Synechocystis sp. PCC 6803. This study showed that Slr1916 functioned as chlorophyllase activity in vitro [ 103 ]. Therefore, recombinant chlorophyllase could...”
- Over Expression of the Cyanobacterial Pgr5-Homologue Leads to Pseudoreversion in a Gene Coding for a Putative Esterase in Synechocystis 6803
Margulis, Life (Basel, Switzerland) 2020 - “...survive. DNA sequencing of a pgr5 OE strain revealed a second site suppression mutation in slr1916 , a putative esterase associated with redox regulation. The phenotype of the slr1916 knockout is very similar to that of the strain reported here and to that of the pmgA...”
- “...mutation is a single codon substitution resulting in a phenylalanine to a serine mutation in slr1916 ( Figure 6 ), a protein that was previously identified as part of the redox regulatory pathway, with a similar phenotype to that of the pmgA mutant [ 60 ]....”
- More
BPSS0899 putative hydrolase from Burkholderia pseudomallei K96243
28% identity, 65% coverage
- Predicting toxins found in toxin-antitoxin systems with a role in host-induced Burkholderia pseudomallei persistence
Ross, Scientific reports 2020 - “...while toxins that were constitutively expressed were highly conserved. Further examination of highly conserved toxins BPSS0899, BPSS1321, and BPSL1494 showed that they were functional, and their mutation led to reduce survival within macrophages and reduced in vivo persistence-associated pathology (abscesses) during treatment, but did not affect...”
- “...in the next section and not previously investigated. Of the toxins BPSL0034, BPSL1494, BPSL2775, BPSL2851, BPSS0899, BPSS0698, BPSS0899, BPSS1321, and BPSS2196 that were tested, 75% of the over-expressed genes led to a reduction in growth, indicating their functionality (Supplemental Figure S2 ). Figure 1 Putative toxins...”
Ngar_c32780 alpha/beta fold hydrolase from Candidatus Nitrososphaera gargensis Ga9.2
26% identity, 66% coverage
- The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1
Chow, Scientific reports 2018 - “...( i . e . estN1 ), Ngar_c30910 ( i . e . estN2 ), Ngar_c32780 and Ngar_c35080, which could possibly encode a BioH analogue, were amplified with specific primers, cloned into pDrive (PCR Cloning Kit, Qiagen, Hilden, Germany) and transformed into competent E . coli...”
- “...[Ngar_c14400 ( i . e . EstN1), Ngar_c30910 ( i . e . EstN2) and Ngar_c32780; e-values between 4.2e 41 and 2.0e 20 ]. Hydrolytic activity of carboxylesterases from N . gargensis after expression in E . coli The six different putative /-hydrolase genes Ngar_c21820, Ngar_c24650,...”
YP_700747 probable poly(3-hydroxyalkanoate) depolymerase from Rhodococcus sp. RHA1
28% identity, 80% coverage
cpoF / PDB|1A8S non-heme chloroperoxidase; EC 1.11.1.10 from Pseudomonas fluorescens (see 2 papers)
O31158 Non-heme chloroperoxidase from Pseudomonas fluorescens
28% identity, 68% coverage
- CharProtDB strain BL914
- Crystal Structure and Functional Characterization of an Esterase (EaEST) from Exiguobacterium antarcticum
Lee, PloS one 2017 - “...code P22862), bromoperoxidase (PDB code 3FOB; UniProtKB code Q81NM3), haloperoxidase (PDB code 1A8S; UniProtKB code O31158), chloroperoxidase (PDB code 4DGQ; UniProtKB code B4EA96), and esterase (PDB code 1ZOI; UniProtKB code Q3HWU8). Secondary structural elements in the crystal structure of Ea EST are represented above the multiple...”
- Cloning and Characterization of a Novel Esterase from Rhodococcus sp. for Highly Enantioselective Synthesis of a Chiral Cilastatin Precursor
Zhang, Applied and environmental microbiology 2014 - “...L7ZQX6), CPO-F (Pseudomonas fluorescens; accession no. O31158), CPO-P (Pseudomonas pyrrocinia; accession no. P25026), CPO-L (Streptomyces lividans; accession...”
- Maspardin is mutated in mast syndrome, a complicated form of hereditary spastic paraplegia associated with dementia
Simpson, American journal of human genetics 2003 - “...maspardin with pseudomonas fluorescens chloroperoxidase (SwissProt: O31158 PRXC_PSEFL, PDB:1A8S). Line 1 shows the predicted secondary structure ( C3 ...”
EPOXH_BOSS2 / A0A126P745 Epoxide hydrolase; BoEH; EC 3.3.2.10 from Bosea sp. (strain PAMC 26642) (see paper)
27% identity, 69% coverage
- function: Catalyzes the hydrolysis of various epoxides into diols. In vitro, shows the strongest activity toward the linear aliphatic epoxide compounds, since it shows strong activity toward (R)-epichlorohydrin, (S)-epichlorohydrin, and 1,2-epoxy-9-decene, but very weak activity toward (R)-styrene oxide, (S)-styrene oxide, and 3,4-epoxy-1- cyclohexene.
catalytic activity: an epoxide + H2O = an ethanediol (RHEA:19037)
catalytic activity: (R)-epichlorohydrin + H2O = (R)-3-chloro-1,2-propanediol (RHEA:80783)
catalytic activity: (S)-epichlorohydrin + H2O = (S)-3-chloro-1,2-propanediol (RHEA:80779)
catalytic activity: 1,2-epoxy-9-decene + H2O = dec-9-ene-1,2-diol (RHEA:80787)
subunit: Homodimer.
YPTB1128 hypothetical protein from Yersinia pseudotuberculosis IP 32953
30% identity, 63% coverage
Swit_3055 alpha/beta hydrolase fold from Sphingomonas wittichii RW1
25% identity, 69% coverage
- Proteomic profiling of the dioxin-degrading bacterium Sphingomonas wittichii RW1
Colquhoun, Journal of biomedicine & biotechnology 2012 - “...[ 21 ]. The one identified in the present study is the product of the Swit_3055 locus, a gene also known as DxnB2 [ 21 ]. Its identification in this study corroborates previous findings [ 21 ]. Unlike the dioxin dioxygenase, this gene is found on...”
- “...148555586 Swit_2674 Adenosylhomocysteinase 1.97 0.062 418 148553385 Swit_0461 Elongation factor Ts 2.10 0.05 934 115279619 Swit_3055 Meta -cleavage pathway hydrolase 2.54 0.055 603 148555952 Swit_3046 Glyoxalase/bleomycin resistance protein/ dioxygenase 3.88 0.031 a Arbitrary identifier for spot location (see Figure 2 ). b NCBI gi number. c...”
- Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1
Coronado, Frontiers in microbiology 2012 - “...were characterized (Happe et al., 1993 ), and two hydrolases, DxnB and DxnB2 (Swit_4895 and Swit_3055), were described (Bnz et al., 1993 ; Seah et al., 2007 ). Several of the genes for the above-mentioned enzymes were cloned and characterized, such as fdx1 (Swit_5088, Armengaud and...”
slr1917 unknown protein from Synechocystis sp. PCC 6803
27% identity, 67% coverage
GM298_09990 alpha/beta fold hydrolase from Enterobacter sp. HSTU-ASh6
27% identity, 68% coverage
- Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses
Haque, Frontiers in microbiology 2022 - “...(3D-1D score), with their score recorded as 80.0597.97%. Among these, alpha/beta fold hydrolase family protein (GM298_09990) had the maximum ERRAT quality score of 97.35 ( Table 6 ). The individual protein average TM score, RMSD, IDEN, and Cov were 0.95, 0.75, 0.51, and 0.97, respectively, based...”
An09g00820 uncharacterized protein from Aspergillus niger
26% identity, 68% coverage
- Insights into the Underlying Mechanism of Ochratoxin A Production in Aspergillus niger CBS 513.88 Using Different Carbon Sources
Wei, Toxins 2022 - “...POD. In this study, the expression levels of An08g08920 and An14g00690 that encode CAT and An09g00820 and An16g00630 that encode POD, were all significantly down-regulated in three OTA-inducing conditions, when compared to non-inducing conditions ( Figure 4 A) ( Table 1 ). Correspondingly, the activities of...”
- “...*** 2.15 *** An14g00690 Catalase activity ( cat ) 2.65 *** 2.04 *** 3.21 *** An09g00820 Predicted peroxidase activity ( pod ) 2.04 *** 2.40 *** 2.75 *** An16g00630 Predicted peroxidase activity ( pod ) 2.16 ** 3.67 *** 1.59 * All data are the mean...”
Q2KTB5 triacylglycerol lipase (EC 3.1.1.3) from Psychrobacter sp. (see paper)
29% identity, 65% coverage
llmg_1737 non-heme chloride peroxidase from Lactococcus lactis subsp. cremoris MG1363
26% identity, 64% coverage
PUV_07140 alpha/beta fold hydrolase from Parachlamydia acanthamoebae UV-7
30% identity, 57% coverage
Atu2497 hydrolase from Agrobacterium tumefaciens str. C58 (Cereon)
26% identity, 59% coverage
SERP0273 hydrolase, alpha/beta hydrolase fold family from Staphylococcus epidermidis RP62A
26% identity, 69% coverage
- Toxin Mediates Sepsis Caused by Methicillin-Resistant Staphylococcus epidermidis
Qin, PLoS pathogens 2017 - “...ATP-binding protein -3.46 -8.38 2.42 czrA SERP1755 CzrA family transcriptional regulator -3.30 -2.32 -1.42 - SERP0273 alpha/beta hydrolase -3.08 -1.73 -1.78 - SERP0507 CBS domain-containing protein -3.06 -1.48 -2.07 - SERP2091 hypothetical protein -2.94 -1.32 -2.22 - SE0735 -2.91 -1.12 -2.60 - SERP1476 hypothetical protein -2.91...”
GSU2435 dehydrogenase complex E2 component, dihydrolipamide acetyltransferase from Geobacter sulfurreducens PCA
44% identity, 17% coverage
1hl7A / Q8GJP7 Gamma lactamase from an aureobacterium species in complex with 3a,4,7, 7a-tetrahydro-benzo [1,3] dioxol-2-one (see paper)
27% identity, 67% coverage
- Ligand: 3a,4,7,7a-tetrahydro-benzo [1,3] dioxol-2-one (1hl7A)
PA0480 probable hydrolase from Pseudomonas aeruginosa PAO1
30% identity, 67% coverage
- Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions
Yan, Journal of applied genetics 2017 - “...degradation genes were analyzed in this study as follows: PA0153, PA0154, PA0230, PA0231, PA0232, PA0247, PA0480, PA0817, PA0865, PA0880, PA1205, PA1210, PA1253, PA1966, PA2009, PA2024, PA2083, PA2085, PA2217, PA2418, PA2507, PA2508, PA2509, PA2512, PA2513, PA2514, PA2515, PA2516, PA2517, PA2518, PA2546, PA3240, PA3389, PA3629, PA3935, PA4091, PA4092,...”
- “...In ciprofloxacin treatment (left-hand panel in Fig. 7 ), 18 PAH degradation genes (PA0231, PA0232, PA0480, PA0865,PA0880, PA1210, PA1966, PA2024, PA2507, PA2513, PA2514, PA2518, PA3240, PA3935, PA4091, PA4092, PA4122, and PA4125) are only associated with upregulated genes, whereas five PAH degradation genes (PA0247, PA1205, PA2516, PA2546,...”
- Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa
Dettman, Genome biology and evolution 2014 - “...inner-membrane protein PA0133 PALES_01341 bauR , LysR-family transcriptional regulator, beta-alanine/polyamine metabolism PA0349 PALES_03461 Hypothetical protein PA0480 PALES_04761 Hydrolase, 3-oxoadipate enol-lactonase PA0556 PALES_05541 Hypothetical protein PA0588 PALES_05851 PrkA-family serine protein kinase ( yeaG ) PA4136 PALES_08351 Major facilitator superfamily (MFS) transporter, multidrug efflux PA4082 PALES_08941 cupB5 ,...”
- Degradation of aromatics and chloroaromatics by Pseudomonas sp. strain B13: cloning, characterization, and analysis of sequences encoding 3-oxoadipate:succinyl-coenzyme A (CoA) transferase and 3-oxoadipyl-CoA thiolase
Göbel, Journal of bacteriology 2002 - “...enol-lactone hydrolase, CatD1 Probable hydrolase, PA0480 3-Oxoadipate enol-lactone hydrolase Probable 3-oxoadipate enol-lactone hydrolase 3-Oxoadipate...”
bphD / Q75WN8 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.8) from Rhodococcus jostii (strain RHA1) (see 2 papers)
etbD / BAA18939.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Rhodococcus sp (see 2 papers)
26% identity, 64% coverage
Cbei_3932 alpha/beta hydrolase fold from Clostridium beijerincki NCIMB 8052
24% identity, 65% coverage
- Transcriptomic characterization of recombinant <i>Clostridium beijerinckii</i> NCIMB 8052 expressing methylglyoxal synthase and glyoxal reductase from <i>Clostridium pasteurianum</i> ATCC 6013
Kumar, Applied and environmental microbiology 2024 - “...hand, the mRNAs of genes that take part in fatty acid metabolism [alpha/beta fold hydrolases (Cbei_3932 and Cbei_3997), 3-oxoacid CoA-transferase subunits (Cbei_2654 and Cbei_2653), and acetyl-CoA acetyltransferase (Cbei_3630)] were less abundant in C. beijerinckii _mgsA+mgR relative to C. beijerinckii _p459. Quantitative RT-PCR A total of 11...”
- Multiplex genome engineering in Clostridium beijerinckii NCIMB 8052 using CRISPR-Cas12a
Patinios, Scientific reports 2023 - “...study https://benchling.com/s/seq-51mieTUESpOi1YjGlySN?m=slm-LklOYAluMlSUJB9Vs7P8 C. beijerinckii NCIMB 8052, Cbei_3238 Cbei_3238 This study https://benchling.com/s/seq-J8n9JPZdYYAFZWkztce4?m=slm-Qe2GaA2L75nmhpdaXVGn C. beijerinckii NCIMB 8052, Cbei_3932 Cbei_3932 This study https://benchling.com/s/seq-N60RTFAV4KA28JkzX1Aj?m=slm-IDRoJQUoZQknBmZeZBhF spo0A C. beijerinckii NCIMB 8052 shows retarded growth, elimination of solvent production and increased production of acids As previously described 27 29 , spo0A C. beijerinckii...”
- “...genes at different genomic loci: Cbei_0408 ( upp ; 630bp), Cbei_1291 (987bp), Cbei_3238 (888bp) and Cbei_3932 (813bp). An identical protocol as the one described for spo0A deletion was followed and obtained colonies were screened for mutants through colony PCR and Sanger sequencing (Table 1 and Table...”
sll1129 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase from Synechocystis sp. PCC 6803
28% identity, 68% coverage
- Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
Zhang, BMC genomics 2008 - “...genes 1 slr1933( rfbC ), sll0398( dgt ), slr1224( malK ) 2 sll0336( accD ), sll1129( todF ), sll0535( clpX ) 4 Phycobilisome degradation protein NblA (ssl0452 and ssl0453), sll1869( cbaB ), Sulfate transport system (slr1452( sbpA ), slr1453( cysT ), slr1454( cysW ), slr1455( cysA...”
ABHDB_BOVIN / Q3SZ73 sn-1-specific diacylglycerol lipase ABHD11; Alpha/beta hydrolase domain-containing protein 11; Abhydrolase domain-containing protein 11; EC 3.1.1.116 from Bos taurus (Bovine) (see paper)
28% identity, 72% coverage
- function: Catalyzes the hydrolysis of diacylglycerol in vitro and may function as a key regulator in lipid metabolism, namely by regulating the intracellular levels of diacylglycerol (PubMed:17393225). 1,2- diacyl-sn-glycerols are the preferred substrate over 1,3-diacyl-sn- glycerols (PubMed:17393225). The enzyme hydrolyzes stearate in preference to palmitate from the sn-1 position of 1,2-diacyl-sn- glycerols (PubMed:17393225). Maintains the functional lipoylation of the 2-oxoglutarate dehydrogenase complex (OGDHc) through its interaction with the OGDHc by preventing the formation of lipoyl adducts (By similarity). In addition, is also required for the expansion and differentiation of embryonic stem cells (ESCs) (By similarity).
catalytic activity: a 1,3-diacyl-sn-glycerol + H2O = a 1-acyl-sn-glycerol + a fatty acid + H(+) (RHEA:38503)
catalytic activity: 1-octadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol + H2O = 2-(9Z- octadecenoyl)-glycerol + octadecanoate + H(+) (RHEA:77103)
catalytic activity: 1-octadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn- glycerol + H2O = 2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-glycerol + octadecanoate + H(+) (RHEA:77107)
catalytic activity: a 1,2-diacyl-sn-glycerol + H2O = a 2-acylglycerol + a fatty acid + H(+) (RHEA:33275)
catalytic activity: 1,2-didecanoylglycerol + H2O = decanoylglycerol + decanoate + H(+) (RHEA:48596)
catalytic activity: 1-octadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycerol + H2O = 2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + octadecanoate + H(+) (RHEA:38507)
subunit: Interacts with OGDH and DLST; this interaction maintains the functional lipoylation of the 2-oxoglutarate dehydrogenase complex. - TNAP and EHD1 are over-expressed in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties.
Deracinois, PloS one 2012 - “...40 804 5,91 191,1 6,57 2 2 Lim. BBB Abhydrolase domain-containing protein 11 ABHDB_BOVIN ABHD11 Q3SZ73 33 527 9,55 46,7 6 1 3 Lim. BBB Serum albumin ALBU_BOVIN ALB P02769 69 248 5,82 105,9 5,1 2 3 Lim. BBB Beta-2-microglobulin B2MG_BOVIN B2M P01888 13 668 7,79...”
SSA_1140 Dihydrolipoamide acetyl transferase, E2 component, putative from Streptococcus sanguinis SK36
31% identity, 25% coverage
BJN34_33845 3-oxoadipate enol-lactonase from Cupriavidus necator
28% identity, 63% coverage
ABH52_CAEEL / H2KZ86 Abhydrolase domain-containing protein abhd-5.2 from Caenorhabditis elegans (see paper)
36% identity, 23% coverage
- function: Acts coordinately with phospholipase atgl-1 within the lipolytic cascade to distribute stored energy to tissues to maintain energy levels during the dauer phase. Localizes atgl-1 to lipid droplets, possibly to facilitate triglyceride hydrolysis. Regulates lipid droplet size, lipid content, the exchange of lipids between lipid droplets and fusion of lipid droplets during the dauer phase.
subunit: Interacts with atgl-1; the interaction tethers atgl-1 to lipid droplets.
disruption phenotype: Increased survival of dauer larvae and reduced lipase activity in a daf-2 constitutive dauer phase mutant background. - ABHD4-dependent developmental anoikis safeguards the embryonic brain.
László, Nature communications 2020 - “...( https://www.ncbi.nlm.nih.gov/ ) (accession numbers: Q8TB40, H2Q7Z0, Q8VD66, D3ZAW4, G1T725, Q5EA59, NP_001017287.1, NP_001017613.1, Q8WTS1, Q7JQU9, H2KZ86, A7S6S7). Sequence similarities were determined using protein alignment by Mega7 software 68 . The evolutionary history was inferred by the Maximum Parsimony method. The tree was obtained using the Subtree-Pruning-Regrafting...”
A0A0H2WW38 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20) from Staphylococcus aureus (see paper)
SAUSA300_0947 hydrolase, alpha/beta hydrolase fold family from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_0914 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
SACOL1053 hydrolase, alpha/beta hydrolase fold family from Staphylococcus aureus subsp. aureus COL
25% identity, 65% coverage
- Identification of novel genetic factors that regulate c-di-AMP production in <i>Staphylococcus aureus</i> using a riboswitch-based biosensor
Kviatkovski, mSphere 2024 - “...( pepS ), SAUSA300_1859 1S1E11 SAUSA300_0945 menD (menaquinone synthase) 1034224 SAUSA300_0945, SAUSA300_0946 ( mend ), SAUSA300_0947, SAUSA300_0947 ( menB ) 1S2D4 SAUSA300_0014 gdpP (phosphodiesterase) 18539 1S2E4 SAUSA300_1662 Aminotransferase/cysteine desulfurase 1827975 SAUSA300_1662, SAUSA300_1661, SAUSA300_1660, SAUSA300_1659, SAUSA300_1658, SAUSA300_1657 ( ackA ) 1S2F4 SAUSA300_0160 capI (capsular polysaccharide biosynthesis protein)...”
- Genome-Wide Identification of Resveratrol Intrinsic Resistance Determinants in Staphylococcus aureus
Liu, Antibiotics (Basel, Switzerland) 2021 - “...256 ++ SAUSA300_2079 fba Fructose bisphosphate aldolase 256 ++ SAUSA300_1791 cbf1 Cmp-binding-factor 1 256 + SAUSA300_0947 Hydrolase, alpha/beta hydrolase fold family 256 + SAUSA300_1558 mtnN 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase 256 + SAUSA300_1359 Polyprenyl synthetase 256 + SAUSA300_1902 Conserved hypothetical protein 256 +++ SAUSA300_1322 Hypothetical protein 256 ++ Exponentially...”
- cydA, spdC, and mroQ are novel genes involved in the plasma coagulation of Staphylococcus aureus
Luo, Microbiology and immunology 2021 - “...12 gene mutants (such as NWMN_0674, NWMN_0166, NWMN_0952, NWMN_2236, NWMN_1939, NWMN_0928, NWMN_1946, NWMN_1319, NWMN_1155, NWMN_1110, NWMN_0914, and NWMN_0757) agglutination ability disappeared. The detailed results are presented in Figure 1 . All wellknown genes involved in plasma agglutination, such as coa , vwbp , and clfA ,...”
- “...IS1272 6 Disappeared NWMN_1155 SuccinylCoA synthetase, sucC 6 Disappeared NWMN_1110 Uracil permease, pyrP 8 Disappeared NWMN_0914 Hydrolase fold family, menH 4 Decreased NWMN_0756 Clumping factor A, clfA 1 Disappeared NWMN_0757 von Willebrand factorbinding protein ( vwbp ) John Wiley & Sons, Ltd. 3.2 Importance of cydA...”
- Serine/threonine phosphatase Stp1 contributes to reduced susceptibility to vancomycin and virulence in Staphylococcus aureus
Cameron, The Journal of infectious diseases 2012 - “...wall metabolism SA1103 SA1898 Other cellular function SACOL1053 uppS Undecaprenyl pyrophosphate synthetase 1.77 sceD Transglycosylase 1.86 2.37 yfbB Acyl-CoA...”
- Identification of the genetic basis for clinical menadione-auxotrophic small-colony variant isolates of Staphylococcus aureus
Lannergård, Antimicrobial agents and chemotherapy 2008 - “...menD, SACOL1052; (orf encoding putative hydrolase), SACOL1053; menB, SACOL1054; gerC, SACOL1510; ubiE (menG), SACOL1511; (menC), SACOL1843; and (menE),...”
SAR0624 putative esterase from Staphylococcus aureus subsp. aureus MRSA252
36% identity, 32% coverage
4lxhA Crystal structure of the s105a mutant of a carbon-carbon bond hydrolase, dxnb2 from sphingomonas wittichii rw1, in complex with 3- cl hopda (see paper)
25% identity, 69% coverage
- Ligand: (2z,4e)-3-chloro-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (4lxhA)
5aljA / P34913 Ligand complex structure of soluble epoxide hydrolase (see paper)
24% identity, 47% coverage
- Ligand: 2-(3-fluoro-4-methyl-anilino)-4-methyl-quinolin-5-ol (5aljA)
PHAZ_ECTOL / P26495 Poly(3-hydroxyalkanoate) depolymerase; PHA depolymerase; ORF2; PHB depolymerase; EC 3.1.1.- from Ectopseudomonas oleovorans (Pseudomonas oleovorans) (see paper)
phaB / AAA25933.1 PHA-depolymerase from Pseudomonas oleovorans (see paper)
29% identity, 69% coverage
JJQ59_09740 3-oxoadipate enol-lactonase from Cupriavidus necator
29% identity, 69% coverage
SA0897 hypothetical protein from Staphylococcus aureus subsp. aureus N315
26% identity, 66% coverage
- Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model
Lasek-Nesselquist, Frontiers in microbiology 2019 - “...C 6, 10, 14 906481 Coding G170D SA0802 NADH dehydrogenase C 14 1018829 Coding A223G SA0897 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase C 6, 10, 14 1364621 Coding S337L SA1193/mprF phosphatidylglycerol lysyltransferase C b 14 1493152 Coding D857G SA1288 ATP-dependent helicase DinG C b 14 1510280 Coding M25I SA_RS07380 hypothetical...”
- “...of SA0454 and SA0613; SA0325 + 1 represents the similar mutation profiles of SA0325 and SA0897; SA0610 + 6 represents the similar mutation profiles of SA0610, SA2134, SA1228, SA_RS07380, SA2023, and SA2062. Colonies Confirm Presence of Low Frequency Variants The three colonies sequenced from population A...”
- Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria
Cui, Proceedings of the National Academy of Sciences of the United States of America 2012 - “...isochorismate synthase SA0896 mend Menaquinone biosynthesis protein SA0897 -- Similar to prolyl aminopeptidase (EC 3.4.11.5) SA0898 menB Naphthoate synthase...”
- An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2010 - “...menaquinone (vitamin K2) metabolism SA0898 SA1303 SA0895 SA1616 SA0897 SA0896 SA1615 SA1614 menD menE menC Citrate cycle (TCA cycle) SA0944 SA0945 phdB pdhC...”
Q6Q2C2 Bifunctional epoxide hydrolase 2 from Sus scrofa
32% identity, 22% coverage
BHE75_04587 alpha/beta fold hydrolase from Sphingomonas haloaromaticamans
39% identity, 31% coverage
XP_005210358 bifunctional epoxide hydrolase 2 isoform X1 from Bos taurus
29% identity, 29% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory