PaperBLAST
PaperBLAST Hits for VIMSS329899 carboxylesterase (249 a.a., MMLKQPEPFF...)
Show query sequence
>VIMSS329899 carboxylesterase
MMLKQPEPFFFEHGQHAVILLHAYAGSANDVRMLARALEREDYTVYGPQFSGHATDDPRD
ILAQTPAQWWQDTQQAISFMRQKGYTKISIFGLSLGGIFATAALERDPQLLGGGTFSSPL
FAGNRSDVAEMFITLSHHQLAHSQFSIAEREQILMTLPELVQRQLQAVNTFTTTEVTSHL
SAVTQPFFIGQGGQDELIDATVARQLRDQLPQVPVDFHWYADAGHVITVNSAHHQLEQDV
LTYLKTIYK
Running BLASTp...
Found 30 similar proteins in the literature:
F9UM18 feruloyl esterase (EC 3.1.1.73) from Lactiplantibacillus plantarum (see paper)
lp_0796 carboxylesterase from Lactobacillus plantarum WCFS1
lp_0796 carboxylesterase from Lactiplantibacillus plantarum WCFS1
100% identity, 100% coverage
- Role of Phenolic Acid Metabolism in Enhancing Bioactivity of Mentha Extract Fermented with Plant-Derived Lactobacillus plantarum SN13T
Shakya, Probiotics and antimicrobial proteins 2024 - “...hydrolase family enzyme, displaying no significant similarities with previously reported esterases Lj1228 , HceP , Lp_0796 , and Est_1092 from Lact. johnsonii N6.2, Lact. plantarum TMW1.46, Lact. plantarum WCFS1, and Lact. plantarum DSM 1055, respectively [ 39 ]. These findings reinforce that the characterization of the...”
- Characterization of isogenic mutants with single or double deletions of four phenolic acid esterases in Lactiplantibacillus plantarum TMW1.460
Gaur, International journal of food microbiology 2023 (PubMed)- “...Lp. plantarum TMW1.460, which encodes for four esterases: TanA, Lp_0796, Est_1092 and a homolog of Lj0536 and Lj1228 that was termed HceP. To determine which of...”
- “...responsible for esterase activity, mutants with deletions in lp_0796, est_1092, tanB, hceP, or hceP and est_1092 were constructed. The phenotype of wild type...”
- Feruloyl Esterase (LaFae) from Lactobacillus acidophilus: Structural Insights and Functional Characterization for Application in Ferulic Acid Production
Jeon, International journal of molecular sciences 2023 - “...has been observed in other FAEs, including FaeI from Cellulosilyticum ruminicola [ 21 ] and Lp_0796 from L. plantarum [ 14 ]. We discovered that the activity of La Fae is optimal within a temperature range of 25 and 37 C and shows approximately 75% of...”
- Conversion of (poly)phenolic compounds in food fermentations by lactic acid bacteria: Novel insights into metabolic pathways and functional metabolites
Gaur, Current research in food science 2023 - “...methyl ferulate Lp. plantarum TMW1.460 ( Gaur, 2022 , Gaur et al., in press ) Lp_0796; YP_004888771 Methyl ferulate, methyl caffeate, methyl p-coumarate, methyl sinapate Lp. plantarum WCFS1 ( Esteban-Torres et al., 2013 ) Est_1092; WP_015825406 Methyl ferulate, methyl caffeate, methyl p-coumarate, methyl sinapate Lp. plantarum...”
- Enhancing the Hydrolysis and Acyl Transfer Activity of Carboxylesterase DLFae4 by a Combinational Mutagenesis and In-Silico Method
Li, Foods (Basel, Switzerland) 2023 - “...Haowen Zhang et al. rationally increased 4- and 5-fold catalytic efficiency of a feruloyl esterase LP_0796 from Lactobacillus plantarum by mutation Asp with Ala23 and Ile198, respectively [ 35 ]. Eight mutants were generated based on the simulated structure to enhance the catalytic efficiency of a...”
- Isolation, characterization and comparative genomics of potentially probiotic Lactiplantibacillus plantarum strains from Indian foods
Surve, Scientific reports 2022 - “...Esterases characterized from L. plantarum , Lp_2945 (Gallate decarboxylase from WCFS1), Lp_2956 (Tannase from WCFS1, Lp_0796 (Esterase from WCFS1), EFK29314 (Tannase from ATCC14917) and JDM1_1092 (Esterase from JDM1). ( d ) Riboflavin and ( e ) folate biosynthesis proteins, adapted from 36 . Bile and acid...”
- A reverse catalytic triad Asp containing loop shaping a wide substrate binding pocket of a feruloyl esterase from Lactobacillus plantarum
Zhang, International journal of biological macromolecules 2021 (PubMed)- “...hemicellulose and ferulic acid in plant cell walls. LP_0796 from Lactobacillus plantarum was identified as a feruloyl esterase that may have potential...”
- “...and catalytic mechanisms limits its application. Here, LP_0796 showed the highest activity towards methyl caffeate at pH 6.6 and 40 C. The crystal...”
- New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni
Collombel, Frontiers in microbiology 2019 - “...ND ND ND https://www.ncbi.nlm. nih.gov/protein/329667314 Guinane et al., 2011 Lactobacillus plantarum WCFS1 Feruloyl esterase/carboxyl esterase Lp_0796 28 Methyl ferulate, methyl caffeate, methyl p -coumarate, and methyl sinapinate lp_0796 https://www.ncbi.nlm. nih.gov/protein/YP_004888771.1 Esteban-Torres et al., 2013 7 Lactobacillus plantarum Feruloyl esterase Est-1092 33.5 Methyl ferulate, methyl caffeate est-1092...”
- More
- Impact of Lactic Acid Bacteria Fermentation on Phenolic Compounds and Antioxidant Activity of Avocado Leaf Extracts
De, Antioxidants (Basel, Switzerland) 2023 - “...strains was related to the presence of two esterases with differences in their substrate range: Lp_0796 that hydrolyses esters of caffeic, p -coumaric, ferulic and sinapic acids, while Est_1092 was able to hydrolyse both hydroxycinnamoyl and hydroxybenzoyl esters [ 54 ]. This cinnamoyl esterase activity is...”
3dltA / B2CZF3 Snapshots of esterase d from lactobacillus rhamnosus: insights into a rotation driven catalytic mechanism
48% identity, 98% coverage
- Ligand: butanoic acid (3dltA)
WP_011232515 carboxylesterase from Geobacillus kaustophilus HTA426
GK3045 carboxylesterase from Geobacillus kaustophilus HTA426
32% identity, 99% coverage
EST_GEOSE / Q06174 Carboxylesterase; EC 3.1.1.1 from Geobacillus stearothermophilus (Bacillus stearothermophilus) (see 2 papers)
Q06174 carboxylesterase (EC 3.1.1.1) from Geobacillus stearothermophilus (see paper)
31% identity, 99% coverage
- function: Involved in the detoxification of xenobiotics. Shows maximal activity with C6 substrates, with gradually decreasing activity from C8 to C12 substrates. No activity for higher chain length substrates acids rather than long-chain ones
catalytic activity: a carboxylic ester + H2O = an alcohol + a carboxylate + H(+) (RHEA:21164)
subunit: Homodimer. - Structural and Biochemical Insights into Bis(2-hydroxyethyl) Terephthalate Degrading Carboxylesterase Isolated from Psychrotrophic Bacterium Exiguobacterium antarcticum
Hwang, International journal of molecular sciences 2023 - “...alignment of Ea Est2 and selected structural homologs including carboxylesterase from Geobacillus stearothermophilus (UniProtKB code Q06174; PDB code 1TQH), esterase from Bacillus licheniformis (UniProtKB code Q65EQ1; PDB code 6NKG), carboxylesterase from Bacillus subtilis, strain168 (UniProtKB code O32232), and thermostable monoacylglycerol lipase from Bacillus sp. (UniProtKB code...”
1tqhA / Q06174 Covalent reaction intermediate revealed in crystal structure of the geobacillus stearothermophilus carboxylesterase est30 (see paper)
31% identity, 97% coverage
- Ligand: propyl acetate (1tqhA)
lmo2450 similar to carboxylesterase from Listeria monocytogenes EGD-e
31% identity, 99% coverage
- Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response
Fellner, ACS infectious diseases 2023 - “...negatively regulated by SarS. 54 In addition, in L. monocytogenes , the FphH homologue Q8Y4I9 (Lmo2450) but no other member of the secG-yvaK-rnr-smpB cluster was repressed in 1,2-propanediol and ethanolamine induced stress conditions. 52 Two lines of evidence point toward a physiological role of FphH related...”
- Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
Pleitner, Applied and environmental microbiology 2014 - “...acyl-carrier proteins (lmo0970, lmo1806, lmo1807, lmo2202, and lmo2450) responsible for membrane lipid production (36), which suggests reduced availability of...”
- “...and phospholipid metabolism lmo0970 lmo1806 lmo1807 lmo2202 lmo2450 Protein synthesis lmo0177 lmo0244 lmo0695 lmo1294 lmo1658 lmo1755 lmo2047 lmo2597 lmo2633...”
- Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling
Schauer, BMC genomics 2010 - “...6.2 2.3 lmo1363 geranyltransferase no 5.0 2.8 lmo1739 amino acid ABC transporter rf 5.5 2 lmo2450 carboxylesterase possible 4.2 3.0 3,5,7,8 lmo1847 ABC transporter specific for metal cations no 5.8 2.3 metabolism of coenzymes and prosthetic groups lmo2124 maltodextrin ABC transport system, permease rf 3.4 0...”
SAOUHSC_00802 carboxylesterase precursor, putative from Staphylococcus aureus subsp. aureus NCTC 8325
Q2G025 Carboxylesterase, putative from Staphylococcus aureus (strain NCTC 8325 / PS 47)
NWMN_0748 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
SACOL0845 carboxylesterase from Staphylococcus aureus subsp. aureus COL
30% identity, 99% coverage
- Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response
Fellner, ACS infectious diseases 2023 - “...10 database lists 54 entries of 90% or higher sequence similarity to the fphH (Q2G025, SAOUHSC_00802) entry for S. aureus reference strain NCTC 8325/PS 47 ( Table S1 ), all from other Staphylococci strains (mostly S . aureus ), with one likely mis-annotated Escherichia coli entry....”
- Newly discovered Staphylococcus aureus serine hydrolase probe and drug targets
Fellner, ADMET & DMPK 2022 - “...pocket which appears to be designed for a specific substrate [ 6 ]. FphH - SAOUHSC_00802 The fphH transposon mutant was the only Fph S. aureus single knockout mutant that strongly suggested a functional link to the other Fph proteins, as a gel-based labelling assay suggested...”
- Inferring multilayer interactome networks shaping phenotypic plasticity and evolution
Yang, Nature communications 2021 - “...no contribution to phenotypic plasticity. However, a dramatically different pattern is observed for S784955 (at SAOUHSC_00802 encoding carboxylesterase). This SNP has a formidable independent effect, but because of striking down-regulation by SNP595377 (in a non-coding region) its observed effect almost can be neglected. In practice, the...”
- “...to deliver an impactful effect on S. aureus response to vancomycin. Similarly, S784955 located at SAOUHSC_00802 encoding carboxylesterase is observed to be insignificant for S. aureus reaction to E. coli, but it displays a large independent effect. Thus, if we silence the expression of its inhibitor,...”
- Low-level predation by lytic phage phiIPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus
Fernández, Scientific reports 2017 - “...2.07 SAOUHSC_00796 pgk Phosphoglycerate kinase 2.90 SAOUHSC_00797 tpiA Triosephosphate isomerase 3.32 SAOUHSC_00799 eno Enolase 4.31 SAOUHSC_00802 Carboxylesterase, putative 2.11 SAOUHSC_00818 nuc Thermonuclease 5.72 SAOUHSC_00933 trpS TryptophantRNA ligase 2.25 SAOUHSC_00994 atl Bifunctional autolysin 5.42 SAOUHSC_01002 qoxA Probable quinol oxidase subunit 2 2.54 SAOUHSC_01092 pheS PhenylalaninetRNA ligase alpha...”
- Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response
Fellner, ACS infectious diseases 2023 - “...Uniprot 10 database lists 54 entries of 90% or higher sequence similarity to the fphH (Q2G025, SAOUHSC_00802) entry for S. aureus reference strain NCTC 8325/PS 47 ( Table S1 ), all from other Staphylococci strains (mostly S . aureus ), with one likely mis-annotated Escherichia coli...”
- “...FphH Sequence Database Searches For all 90% identical sequences to Uniprot 10 entry of FphH Q2G025, a list with all gene identifiers and literature mentions of these identifiers in Google Scholar was compiled. Within the 50% identical sequences, the genes from the most well studied bacterial...”
- Identification of a S. aureus virulence factor by activity-based protein profiling (ABPP)
Lentz, Nature chemical biology 2018 - “.... In brief, transposon mutagenesis was used to generate insertion mutations in each NWMN_0169, NWMN_0262, NWMN_0748, NWMN_1210, NWMN_1683, NWMN_2092, NWMN_2350, NWMN_2379, NWMN_2434, NWMN_2480, NWMN_2528, and NWMN_2569. Homologs of the aforementioned genes were first identified through the Basic Local Alignment Search Tool (BLASTn) in S. aureus USA300...”
- Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions
McClary, Frontiers in microbiology 2018 - “...binding protein 0.19 9.1 metL Homoserine dehydrogenase 0.19 3.4 NWMN_0860 Conserved hypothetical protein 0.16 0.4 NWMN_0748 Conserved hypothetical protein 0.14 12.6 NWMN_1913 Conserved hypothetical protein 0.13 9.1 NWMN_1004 Conserved hypothetical protein 0.13 0.1 NWMN_1101 Conserved hypothetical protein 0.09 0.1 Functional classification of differentially expressed genes The...”
- Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
Tsuchiya, The Biochemical journal 2018 - “...protein 8.9913 ASLQVAC*ENGK 121.95 SAZ172_1861 Ribosomal large subunit pseudouridine synthase D-like protein 31.387 C*VSPTGQR 88.056 NWMN_0748 Uncharacterized protein 28.19 GIVTMC*APMGGK 138.55 SAZ172_0851 Pathogenicity island protein 15.839 IIC*DFSTEREEK 134.38 SAKOR_01965 RecT protein 16.895 NQC*YFIPYGNK 86.772 gtf1 Glycosyltransferase Gtf1 58.273 SSFVTC*YLQNEQK 187.56 fbp Fructose-1,6-bisphosphatase class 3 76.213 VC*LANLLR...”
- Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response
Fellner, ACS infectious diseases 2023 - “...in strain SH1000 demonstrated that expression of fph H (described as carboxyl esterase est , SACOL0845) was over 10-fold up-regulated in response to the antibiotic fusidic acid. 29 Fusidic acid is a protein biosynthesis inhibitor that blocks amino acid transfer from aminoacyl-tRNAs from the ribosome. 30...”
- “...of S. aureus SH1000 revealed a 16.8-fold upregulation of the fphH gene ( est , SACOL0845). 29 Our data clearly indicate that recombinant FphH can indeed deacetylate and thus inactivate fusidic acid in vitro . In the cellular system, however, we found that transposon-based inactivation of...”
- The fusidic acid stimulon of Staphylococcus aureus
Delgado, The Journal of antimicrobial chemotherapy 2008 - “...SACOL0674 SACOL2295 SACOL2291 SACOL2557 SACOL2348 SACOL0845 SACOL2138 SACOL1845 SACOL2088 SACOL1442 SACOL2137 SACOL2739 SACOL2731 SACOL0406 SACOL2546 SACOL1823...”
SE0564 carboxyesterase precursor-like protein from Staphylococcus epidermidis ATCC 12228
31% identity, 99% coverage
SA0734 hypothetical protein from Staphylococcus aureus subsp. aureus N315
31% identity, 99% coverage
SAR0835 putative carboxylesterase from Staphylococcus aureus subsp. aureus MRSA252
30% identity, 99% coverage
SAB0735 probable carboxylesterase precursor from Staphylococcus aureus RF122
30% identity, 99% coverage
8ftpA / A0A0H2XJL0 Fphh, staphylococcus aureus fluorophosphonate-binding serine hydrolases h, apo form (see paper)
30% identity, 98% coverage
- Ligand: calcium ion (8ftpA)
Q65EQ1 Esterase/lipase/thioesterase from Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)
28% identity, 99% coverage
Aflv_2499 Esterase/lipase from Anoxybacillus flavithermus WK1
28% identity, 99% coverage
EST_BACSU / O32232 Carboxylesterase; EC 3.1.1.1 from Bacillus subtilis (strain 168) (see paper)
26% identity, 99% coverage
- function: Involved in the detoxification of xenobiotics. Shows maximal activity with C6 substrates, with gradually decreasing activity from C8 to C12 substrates. No activity for higher chain length substrates acids rather than long-chain ones (By similarity).
catalytic activity: a carboxylic ester + H2O = an alcohol + a carboxylate + H(+) (RHEA:21164)
subunit: Homodimer.
disruption phenotype: No visible phenotype. - Structural and Biochemical Insights into Bis(2-hydroxyethyl) Terephthalate Degrading Carboxylesterase Isolated from Psychrotrophic Bacterium Exiguobacterium antarcticum
Hwang, International journal of molecular sciences 2023 - “...Bacillus licheniformis (UniProtKB code Q65EQ1; PDB code 6NKG), carboxylesterase from Bacillus subtilis, strain168 (UniProtKB code O32232), and thermostable monoacylglycerol lipase from Bacillus sp. (UniProtKB code P82597; PDB codes 3RM3 and 4KEA). The catalytic triad residues (Ser93, Asp190, and His220) are indicated by red triangles, and the...”
lmo2452 similar to carboxylesterase from Listeria monocytogenes EGD-e
32% identity, 96% coverage
SA0416 hypothetical protein from Staphylococcus aureus subsp. aureus N315
25% identity, 99% coverage
SAUSA300_0430 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAOUHSC_00417 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
25% identity, 99% coverage
- Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
Kulkarni, American journal of respiratory cell and molecular biology 2016 - “...SAUSA300_0853 SAUSA300_2409 SAUSA300_2266 SAUSA300_0945 SAUSA300_0074 SAUSA300_0073 SAUSA300_0430 SAUSA300_0429 1.4 1.4 1.4 1.4 1.4 1.4 1.4 1.4 1.3 1.3...”
- Newly discovered Staphylococcus aureus serine hydrolase probe and drug targets
Fellner, ADMET & DMPK 2022 - “...well-defined acyl binding pocket compared to the larger Fph proteins [ 6 ]. FphI - SAOUHSC_00417 FphI might be a distant homolog of FphH, as these two are the only Fph proteins that share more than 25 % sequence identity at 28 %, and they are...”
- Proteomic and Metabolomic Analyses of a Tea-Tree Oil-Selected Staphylococcus aureus Small Colony Variant
Torres, Antibiotics (Basel, Switzerland) 2019 - “...nucleotide metabolism 3.4 SAOUHSC_00362 208 aa protein uncharacterized 1.9 SAOUHSC_00369 prolipoprotein diacylglyceryl transferase uncharacterized 1.7 SAOUHSC_00417 esterase/lipase uncharacterized 2.2 SAOUHSC_00442 DnaX DNA polymerase III subunits gamma and tau DNA replication, recombination and repair 1.6 SAOUHSC_00461 MetG methionyl-tRNA synthetase protein synthesis 1.3 SAOUHSC_00474 RplY 50S ribosomal protein...”
- A multihost bacterial pathogen overcomes continuous population bottlenecks to adapt to new host species
Bacigalupe, Science advances 2019 - “...NCTC8325 SNP 393,634 Missense SAOUHSC_00390 Conserved hypothetical protein HP | P NCTC8325 SNP 420,058 Missense SAOUHSC_00417 Conserved hypothetical protein TM NCTC8325 SNP 464,931 Missense rnmV Ribonuclease M5 TM NCTC8325 SNP 541,242 Missense SAOUHSC_00535 Epimerase/dehydratase TM NCTC8325 SNP 546,984 Missense azo1 FMN-dependent NADPH-azoreductase TM NCTC8325 SNP 568,990...”
SAR0457 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
25% identity, 99% coverage
4ke8C / P82597 Crystal structure of monoglyceride lipase from bacillus sp. H257 in complex with monopalmitoyl glycerol analogue (see paper)
32% identity, 45% coverage
- Ligand: tetradecyl hydrogen (r)-(3-azidopropyl)phosphonate (4ke8C)
MGLP_BAC25 / P82597 Thermostable monoacylglycerol lipase; MGLP; bMGL; EC 3.1.1.23 from Bacillus sp. (strain H-257) (see 3 papers)
P82597 acylglycerol lipase (EC 3.1.1.23) from Bacillus sp. (in: Bacteria) (see 4 papers)
T260_16665 carboxylesterase from Geobacillus thermopakistaniensis
32% identity, 44% coverage
- function: Hydrolyzes monoacylglycerols, with the highest activity occurring with 1-monolauroylglycerol.
catalytic activity: Hydrolyzes glycerol monoesters of long-chain fatty acids.
subunit: Monomer. - Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1
Siddiqui, Genome announcements 2014 - “...five types of alcohol dehydrogenases (T260_01930, T260_06755, T260_07340, T260_09050, T260_12960) and lipases (T260_04645, T260_04700, T260_15915, T260_16665, T260_19075). According to the protein homology search analysis using the Basic Local Alignment Search Tool (BLAST) for five open reading frames annotated as glycoside hydrolases from G.thermopakistaniensis sp. MAS1, the...”
- Structural and Biochemical Insights into Bis(2-hydroxyethyl) Terephthalate Degrading Carboxylesterase Isolated from Psychrotrophic Bacterium Exiguobacterium antarcticum
Hwang, International journal of molecular sciences 2023 - “...Bacillus subtilis, strain168 (UniProtKB code O32232), and thermostable monoacylglycerol lipase from Bacillus sp. (UniProtKB code P82597; PDB codes 3RM3 and 4KEA). The catalytic triad residues (Ser93, Asp190, and His220) are indicated by red triangles, and the consensus motif is colored in blue. Secondary structures obtained from...”
- Characterization of a monoacylglycerol lipase in the medicinal leech, Hirudo verbana
Kabeiseman, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 2020 - “...As corny cota S. cerevisiae Magl sceMagL P28321 22.9% Firmicutes Bacillus sp. H-257 Magl bsuMagL P82597 18.2% Table 2. Primer Sequences used in this study. Primer Sequence Purpose 1 a 5-GGG CTCGAG AATGGATGACCAGCTAATGGG-3 Cloning HirMAGL into pRSET 2 5-CCCC AAGCTT TCACTTTGCATAGACTTC-3 vector 3 5-GGG GGTACC ATGCGGGGTTCTCATCATC-3...”
- The structure of monoacylglycerol lipase from Bacillus sp. H257 reveals unexpected conservation of the cap architecture between bacterial and human enzymes
Rengachari, Biochimica et biophysica acta 2012 - “...MGL ortholog from the moderately thermophilic Bacillus sp. H257 (also termed MGLP, UniProtKB accession code P82597 ) shares only 17% sequence identity with hMGL. bMGL is very specific for MG, especially 1-monolauroylglycerol, and does not show any activity towards di- and triacylglycerols [24] . The specificity...”
YP_003253705 BAAT/Acyl-CoA thioester hydrolase from Geobacillus sp. Y412MC61
32% identity, 44% coverage
G3JWZ2 carboxylesterase (EC 3.1.1.1) from Geobacillus thermodenitrificans (see paper)
32% identity, 45% coverage
TPANIC_0902 carboxylesterase from Treponema pallidum subsp. pallidum str. Nichols
TP0902 carboxylesterase (est) from Treponema pallidum subsp. pallidum str. Nichols
33% identity, 39% coverage
TM_1022 carboxylesterase from Thermotoga maritima MSB8
TM1022 esterase from Thermotoga maritima MSB8
31% identity, 39% coverage
- Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea
Zweerink, Nature communications 2017 - “...for analysis of heterologously expressed enzymes from their native promotors. We selected the serine hydrolase TM_1022 (MW 28.8kDa 41 ) from the hyperthermophilic bacterium Thermotoga maritima because (i) we had access to a full genome sample from this organism and thus wanted to test if the...”
- “...transcription machinery, (ii) its molecular weight should allow facile detection on the gel and (iii) TM_1022 features a S33 serine hydrolase domain that in principle can be robustly labelled 31 . Accordingly, we PCR-amplified the gene including a 500bp upstream region of the transcription start (...”
- Characterization of Thermotoga maritima Esterase Capable of Hydrolyzing Bis(2-hydroxyethyl) Terephthalate
Feng, Journal of agricultural and food chemistry 2024 (PubMed)- “...The gene-encoding carboxylesterase (TM1022) from the hyperthermophilic bacterium Thermotoga maritima (T. maritima) was cloned and expressed in Escherichia coli Top10 and BL21 (DE3). Recombinant TM1022 showed the best activity at pH 8.0 and 85...”
- “...53% activity after incubation at pH 10.0 and 37 C for 6 h. The esterase TM1022 exhibited the optimum thermo-alkali stability and kcat/Km (598.57 19.97 s-1mM-1) for pN-C4. TM1022 hydrolyzed poly(ethylene terephthalate) (PET) degradation intermediates, such as bis(2-hydroxyethyl) terephthalate (BHET) and mono(2-hydroxyethyl) terephthalate (MHET). The...”
- Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea
Zweerink, Nature communications 2017 - “...removed by overlap extension PCR introducing a silent mutation in the respective position. The gene tm1022 was cloned with its own promoter, that is, including an approximately 500bp region upstream of its start codon. The purified PCR products were restricted by the endonucleases depicted in Supplementary...”
- “...for this study: pSVA- saci_1116 , pSVAmZ- saci_1105 pSVAmZ_ lipS , pSVAmZ_ lipT and pSVA-p- tm1022 ( Supplementary Data 3 ). Successful cloning was confirmed by sequencing, and the plasmids were transformed in E. coli R1821 cells for methylation. Electrocompetent S. acidocaldarius cells (50l, theoretical OD...”
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...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 GHSLG Properties of characterized esterases The first carboxylic ester hydrolase isolated and characterized from a hyperthermophile...”
- Recombination in Thermotoga: implications for species concepts and biogeography
Nesbø, Genetics 2006 - “...sequenced for each strain, except for T. petrophila RKU1 TM1022 where only one clone from a cloned PCR product gave the right sequence. The sequences have been...”
- “...results). (E) Maximum-likelihood tree of TM0938. (F) Maximum-likelihood tree of TM1022. For the maximum-likelihood trees in A-C and E and F, a GTR 1 G 1 I model...”
YP_075874 esterase from Symbiobacterium thermophilum IAM 14863
29% identity, 40% coverage
Q6N0W4 Alpha/beta fold hydrolase from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
RPA4646 putative carboxylesterase from Rhodopseudomonas palustris CGA009
28% identity, 40% coverage
Rv3177 POSSIBLE PEROXIDASE (NON-HAEM PEROXIDASE) from Mycobacterium tuberculosis H37Rv
24% identity, 64% coverage
- Environmental fungi target thiol homeostasis to compete with Mycobacterium tuberculosis
Malhotra, PLoS biology 2024 - “...recently discovered mycothiol-dependent reductase mycoredoxin 2 ( Rv2466c ), several peroxidases, dehydrogenases ( katG , Rv3177 , Rv3178 , ahpC , ahpD ), ferric uptake transcriptional regulator ( furA ), several probable oxidoreductases ( Rv1726 , Rv2454 , Rv3463 ). In fact, a recent study reported...”
- Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis
Singh, 2023 - Aldehyde accumulation in Mycobacterium tuberculosis with defective proteasomal degradation results in copper sensitivity
Limón, mBio 2023 - “...or reductase 27.58 0 Rv3175 Possible amidase 2.31 1.11E-11 mesT Probable epoxide hydrolase 7.52 3.85E-80 Rv3177 Possible peroxidase 7.07 4.08E-86 Rv3178 Conserved hypothetical protein 5.48 1.41E-51 Rv0195-Rv0197 Rv0195 Possible two-component transcriptional regulatory protein (LuxR family) 2.46 2.17E-24 Rv0196 Possible transcriptional regulatory protein 15.86 2.99E-80 Rv0197 Possible...”
- Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis
Shee, eLife 2023 - “...), thiol buffering ( mshB, ino1, thiX, egtB, doxX ), antioxidant enzymes ( mymT, rv2633c, rv3177 ), Fe homeostasis ( mbtL, dppA ), sufR, redox-regulated chaperone ( rv0991c Becker et al., 2020 ), and respiration ( rv0247c, rv0248c, rv0249c, sdhA, sdhB, ctaC, ctaD, fixB ), were...”
- “...(The gradient of cyan to red colour indicates increasing log 2 fold change values). * rv3177 is 10.02 log 2 fold-change enriched. ( B ) The E MSH of Mtb mutants harboring transposon in the genes identified as part of Mtb redoxosome. The mutants were grown...”
- Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes
Comín, Scientific reports 2022 - “...2004 isolate. In CLS_93, the isolate from 2019 had an extra IS copy located in Rv3177 , absent in the isolate from 2008. In CLS_71, the isolate from 2020 had two extra IS copies located in Rv1371 and phoT that were not present in the isolate...”
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...dehydrogenase/reductase Bacon et al., 2004 1.80 4.70E-03 MT3264 Rv3175 Possible amidase (aminohydrolase) 1.44 5.28E-03 MT3266 Rv3177 Putative peroxidase Reyes et al., 2012 2.78 4.78E-08 MT3301 * Rv3206c moeZ Molybdenum cofactor biosynthesis and cysteine biosynthesis Voss et al., 2011 1.16 2.66E-06 MT3318 MT3318 Conserved hypothetical 1.25 2.00E-10...”
- Biochemical characterisation of pimelate biosynthetic genes of Mycobacterium tuberculosis
Gugu, 2019 - Unraveling the role of the transcriptional regulator VirS in low pH-induced responses of Mycobacterium tuberculosis and identification of VirS inhibitors
Singh, The Journal of biological chemistry 2019 (secret) - More
MT3266 hydrolase, alpha/beta hydrolase fold family from Mycobacterium tuberculosis CDC1551
24% identity, 61% coverage
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...Putative dehydrogenase/reductase Bacon et al., 2004 1.80 4.70E-03 MT3264 Rv3175 Possible amidase (aminohydrolase) 1.44 5.28E-03 MT3266 Rv3177 Putative peroxidase Reyes et al., 2012 2.78 4.78E-08 MT3301 * Rv3206c moeZ Molybdenum cofactor biosynthesis and cysteine biosynthesis Voss et al., 2011 1.16 2.66E-06 MT3318 MT3318 Conserved hypothetical 1.25...”
SCO2123 esterase/lipase from Streptomyces coelicolor A3(2)
30% identity, 37% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory