PaperBLAST
PaperBLAST Hits for VIMSS6630293 lipase 2 (587 a.a., MGTTLSPFRY...)
Show query sequence
>VIMSS6630293 lipase 2
MGTTLSPFRYIQLVRYAVNRWIDIIPAVKGKGKAHLDNLHARAGDYLLKSETASNAPPPP
ANAGQAEAGPSRLAGVNENRPHQHRHYENQQKEHHQHYRHPPRYPKLAPDPKWPPGPKEI
YNLMNDERLFVPGSIKPPREVVVLCHGLYGFSTATPIPLFPSLKLHYWASVLEVLRDKMG
VKVVVVGVKGTGSIKERAEQMHEFLKKTLPRGTGVNFVAHSMGGLDCRHLISTIKPTSYT
PLSLTTIGTPHRGSPFMDWCAANIGVGSAAAVAASLTAEKLKALPYSLKSPLLARPPPTQ
TKPDTITSIAAGLTSYLLSIFDSPAYSNLTTAYLRDHFNPATPDDPFVKYTSVAGRISKM
SVLHPLWFPKLVLDAAAENGYAEDTSNMVYGPEGKPRYEGNDGLVSVSSAKWGEYIGAVD
ECHHWDLRGEGGLFPSNVSSISLGDDNKKGEDKHGGGWELDKESAPGAGGVHEHLGLAAK
ERDMVELKKKGKDSGAEASPKSSESSIVTPSSWDIAQVGQVVDWVTDFLPGGKTTEAGKR
QLEEARMEKEGQVELEKEKEREKKRKDKFDLERFYGGLMIKLRDDGF
Running BLASTp...
Found 43 similar proteins in the literature:
CNE02710 lipase 2 from Cryptococcus neoformans var. neoformans JEC21
100% identity, 100% coverage
- Brain inositol is a novel stimulator for promoting Cryptococcus penetration of the blood-brain barrier
Liu, PLoS pathogens 2013 - “...2.59 CNL04840 CNAG_05138 Exo-beta-1,3-glucanase 2.54 CNC02410 CNAG_01737 Methyl sterol oxidase 2.54 CNB00990 CNAG_03596 2-Oxoglutarate_dehydrogenase_complex 2.53 CNE02710 CNAG_07639 Triacylglycerol lipase 2.50 Signal transduction CNA01180 CNAG_00130 Serine/threonine protein kinase 5.11 CNB05690 CNAG_04090 bZip transcription factor 3.13 CNB01230 CNAG_03621 Cyclophilin A 2.96 CNH00140 CNAG_05348 Small_GTPase_CDC42 2.88 CNH00970 CNAG_05431 Transcription...”
CNAG_07639 triacylglycerol lipase from Cryptococcus neoformans var. grubii H99
93% identity, 100% coverage
- Brain inositol is a novel stimulator for promoting Cryptococcus penetration of the blood-brain barrier
Liu, PLoS pathogens 2013 - “...CNL04840 CNAG_05138 Exo-beta-1,3-glucanase 2.54 CNC02410 CNAG_01737 Methyl sterol oxidase 2.54 CNB00990 CNAG_03596 2-Oxoglutarate_dehydrogenase_complex 2.53 CNE02710 CNAG_07639 Triacylglycerol lipase 2.50 Signal transduction CNA01180 CNAG_00130 Serine/threonine protein kinase 5.11 CNB05690 CNAG_04090 bZip transcription factor 3.13 CNB01230 CNAG_03621 Cyclophilin A 2.96 CNH00140 CNAG_05348 Small_GTPase_CDC42 2.88 CNH00970 CNAG_05431 Transcription factor...”
MGL_4063 uncharacterized protein from Malassezia globosa CBS 7966
39% identity, 70% coverage
- Skin Commensal Fungus Malassezia and Its Lipases
Park, Journal of microbiology and biotechnology 2021 - “...region (PF04083) MGL_1975 [ 11 ] MGL_2531 [ 11 ] Putative serine esterase, Lipase-like (PF05057) MGL_4063 [ 11 ] GDSL-like Lipase/Acylhydrolase (PF00657) MGL_1366 O [ 11 ] M. sympodialis ATCC 42132 Class 3 (PF01764) MSYG_1326 O [ 81 ] MSYG_2002 [ 81 ] MSYG_2462 O [...”
MRET_3765 triacylglycerol lipase from Malassezia restricta
45% identity, 57% coverage
- Skin Commensal Fungus Malassezia and Its Lipases
Park, Journal of microbiology and biotechnology 2021 - “...12 , 71 ] MRET_4144 [ 12 , 71 ] Putative serine esterase, Lipase-like (PF05057) MRET_3765 [ 12 , 71 ] GDSL-like Lipase/Acylhydrolase (PF00657) MRET_3994 O [ 12 , 71 ] M. globosa CBS 7966 Class 3 (PF01764) MGL_0279 [ 11 ] MGL_0797 ( MgLIP1 )...”
TGL2_YEAST / P54857 Triacylglycerol lipase 2; Lipase 2; Neutral lipid hydrolase; EC 3.1.1.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
NP_010343, YDR058C Protein with lipolytic activity towards triacylglycerols and diacylglycerols when expressed in E. coli; role in yeast lipid degradation is unclear from Saccharomyces cerevisiae
NP_010343 triglyceride lipase from Saccharomyces cerevisiae S288C
31% identity, 51% coverage
- function: Mitochondrial triacylglycerol (TAG) lipase with activity toward long-chain diacylglycerols (DAGs) and triacylglycerols (TAGs) (PubMed:19959834, PubMed:9544243). Involved in mitochondrial lipid metabolism (PubMed:31483742).
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
catalytic activity: 1,2,3-tri-(9Z-octadecenoyl)-glycerol + H2O = di-(9Z)- octadecenoylglycerol + (9Z)-octadecenoate + H(+) (RHEA:38575)
catalytic activity: 1,2,3-tributanoylglycerol + H2O = dibutanoylglycerol + butanoate + H(+) (RHEA:40475)
catalytic activity: 1,2,3-trioctanoylglycerol + H2O = dioctanoylglycerol + octanoate + H(+) (RHEA:47864)
catalytic activity: di-(9Z)-octadecenoylglycerol + H2O = (9Z-octadecenoyl)- glycerol + (9Z)-octadecenoate + H(+) (RHEA:47868)
catalytic activity: dioctanoylglycerol + H2O = octanoylglycerol + octanoate + H(+) (RHEA:47880)
subunit: Interacts with MIA40; forms mixed disulfide intermediates with MIA40. - High-throughput biochemical fingerprinting of Saccharomyces cerevisiae by Fourier transform infrared spectroscopy
Kohler, PloS one 2015 - “...RSB1 44 WT WT BY4743 5 YOR100C CRC1 45 YJR019C TES1 6 YOR171C LCB4 46 YDR058C TGL2 7 YOR196C LIP5 47 1 YJL196C ELO1 8 YOR245C DGA1 48 1 , 2 YKR053C YSR3 9 YOR377W ATF1 49 1 YCR048W ARE1 10 1 , 2 YOL002C IZH2...”
- “...GC. ORF Gene sample # YHR067W HTD2 1 a , b WT WT BY4743 4 YDR058C TGL2 7 YKR067W GPT2 12 YLR450W HMG2 13 YJR073C OPI3 19 a , b YJR103W URA8 20 YKL140W TGL1 22 YLL012W YEH1 24 YML008C ERG6 31 a , b YMR205C...”
- Identification of genes affecting vacuole membrane fragmentation in Saccharomyces cerevisiae
Michaillat, PloS one 2013 - “...1.8 YOL011W PLB3 Phospholipase B 1.5 YOR081C TGL5 Triacylglycerol lipase preferring VLCFAs; acyltransferase activity 1.8 YDR058C TGL2 Acylglycerol lipase 1.5 YIL040W APQ12 Unknown; mutant accumulates triglycerides 2.0 YOR084W LPX1 Putative lipase 1.5 YDR503C LPP1 Lipid phosphate phosphatase 1.0 YDL052C SLC1 Lyso-PA acyl transferase 1.3 YNR008W LRO1...”
- Gene cloning and characterization of a novel esterase from activated sludge metagenome
Zhang, Microbial cell factories 2009 - “...the putative lipase/esterase from Magnaporthe grisea 70-15 and Saccharomyces cerevisiase Tg12p (XP_368471, 31% identity; and NP_010343, 29% identity, respectively), members of the family of fungal hydrolases. And also, the EstAS contained a catalytic triad (Ser92, His125, and Asp249) and a LHYFRG conserved motif (starting from His36),...”
- “...Server http://www.ch.embnet.org/software/BOX_form.html . XP_504639, esterase/lipase from Yarrowia lipolytica CLIB122; XP_368471, LipA from Magnaporthe grisea 70-15; NP_010343, esterase/lipase from Saccharomyces cerevisiae Tg12p; ZP_02733109, lipase from Gemmata obscuriglobus UQM 2246. Figure 2 Phylogenetic analysis of EstAS and closely related proteins . Phylogenetic analysis was performed using the program...”
- The yeast protein kinase C cell integrity pathway mediates tolerance to the antifungal drug caspofungin through activation of Slt2p mitogen-activated protein kinase signaling
Reinoso-Martín, Eukaryotic cell 2003 - “...c YLR017w YDR444w YDR461w YHR096c YAL042w YAR071w YDR058c YBR145w YCL009c YGL009c YDL182w YBR272c YBR014c YBR153w YJR024c Function ER-associated protein...”
- The mitochondrial intermembrane space-facing proteins Mcp2 and Tgl2 are involved in yeast lipid metabolism.
Odendall, Molecular biology of the cell 2019 - GeneRIF: Data show that mitochondrial protein MCP2 (MCP2) has a negative genetic interaction with the gene triglyceride lipase TGL2 (TGL2) encoding a neutral lipid hydrolase.
- The TGL2 gene of Saccharomyces cerevisiae encodes an active acylglycerol lipase located in the mitochondria.
Ham, The Journal of biological chemistry 2010 - GeneRIF: mitochondrial Tgl2p-dependent lipolysis is crucial for the survival of cells under antimitotic drug treatment
XP_504639 YALI0E31515p from Yarrowia lipolytica CLIB122
31% identity, 49% coverage
- Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment
Jeon, Evidence-based complementary and alternative medicine : eCAM 2011 - “...ACJ13070, a lipase from uncultured bacterium; (ACJ13070); XP_390196, a hypothetical protein from Gibberella zeae PH-1; XP_504639, a YALI0E31515p from Yarrowia lipolytica . Triangles and squares represent the residues involved in the formation of the catalytic triad and the oxyanion hole, respectively, and the conserved pentapeptide motifs...”
- Gene cloning and characterization of a novel esterase from activated sludge metagenome
Zhang, Microbial cell factories 2009 - “...amino acid identity to esterase/lipase from Gemmata obscuriglobus UQM 2246 (ZP_02733109) and Yarrowia lipolytica CLIB122 (XP_504639), respectively; and several conserved regions were identified, including the putative active site, HSMGG, a catalytic triad (Ser92, His125 and Asp216) and a LHYFRG conserved motif. The EstAS was overexpressed, purified...”
- “...Gemmata obscuriglobus UQM 2246 (ZP_02733109, 33% identity), followed by the lipase from Yarrowia lipolytica CLIB122 (XP_504639, 31% identity), the putative lipase/esterase from Magnaporthe grisea 70-15 and Saccharomyces cerevisiase Tg12p (XP_368471, 31% identity; and NP_010343, 29% identity, respectively), members of the family of fungal hydrolases. And also,...”
PADG_04319 V-type ATPase, G subunit from Paracoccidioides brasiliensis Pb18
28% identity, 71% coverage
- Proteomic Analysis of Paracoccidioides brasiliensis During Infection of Alveolar Macrophages Primed or Not by Interferon-Gamma
Chaves, Frontiers in microbiology 2019 - “...flavoprotein beta-subunit; PADG_11981, V-type proton ATPase catalytic subunit A; PADG_03175, V-type proton ATPase subunit F; PADG_04319, V-type ATPase, G subunit; PADG_00688, F-type H+-transporting ATPase subunit H; PADG_08391, plasma membrane ATPase; PADG_08394, cytochrome bc1 complex subunit 2; PADG_07042, ATP synthase F1, delta subunit; PADG_04729, ATP synthase subunit...”
- “...flavoprotein subunit alpha; PADG_11468, electron transfer flavoprotein beta-subunit; PADG_11981, V-type proton ATPase catalytic subunit A; PADG_04319, V-type ATPase, G subunit; PADG_03175, V-type proton ATPase subunit F; PADG_00688, F-type H+-transporting ATPase subunit H; PADG_08391, plasma membrane ATPase; PADG_08394, cytochrome bc1 complex subunit 2; PADG_06221, formate dehydrogenase; PADG_01551,...”
MGG_00773 triacylglycerol lipase from Pyricularia oryzae 70-15
30% identity, 49% coverage
- Dysfunctional Pro1 leads to female sterility in rice blast fungi
Uchida, iScience 2023 - “...examine whether the DNA sequences were consistent with the phenotype. SNPs within MGG_00779, MGG_00693, and MGG_00773 genes were selected as targets for genotyping because these genes were close to the FS1L, FS1C, and FS1R loci, respectively ( Figures2 A and 2B). Among 37 F 4 progenies,...”
ZP_02733109 Esterase/lipase/thioesterase family active site from Gemmata obscuriglobus UQM 2246
29% identity, 48% coverage
- Gene cloning and characterization of a novel esterase from activated sludge metagenome
Zhang, Microbial cell factories 2009 - “...it showed 33% and 31% amino acid identity to esterase/lipase from Gemmata obscuriglobus UQM 2246 (ZP_02733109) and Yarrowia lipolytica CLIB122 (XP_504639), respectively; and several conserved regions were identified, including the putative active site, HSMGG, a catalytic triad (Ser92, His125 and Asp216) and a LHYFRG conserved motif....”
- “...quite low identity with other esterase/lipases, highest with the esterase/lipase from Gemmata obscuriglobus UQM 2246 (ZP_02733109, 33% identity), followed by the lipase from Yarrowia lipolytica CLIB122 (XP_504639, 31% identity), the putative lipase/esterase from Magnaporthe grisea 70-15 and Saccharomyces cerevisiase Tg12p (XP_368471, 31% identity; and NP_010343, 29%...”
LIC_12988 alpha/beta fold hydrolase from Leptospira interrogans serovar Copenhageni str. Fiocruz LV130
LIC12988 lipase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
28% identity, 47% coverage
- A comprehensive in silico analysis of putative outer membrane and secretory hydrolases from the pathogenic Leptospira: Possible implications in pathogenesis
Shankar, Biotechnology and applied biochemistry 2024 (PubMed)- “...generate a deeper understanding. Our analysis yielded four putative outer/secretory hydrolases, LIC_10995, LIC_11183, LIC_11463, and LIC_12988, containing / hydrolase fold and displayed similarity with lipase motif. Moreover, their conservation analysis of the predicted hydrolases across the spectrum of different Leptospira species showed high clustering with the...”
- Extracellular Proteome Analysis Shows the Abundance of Histidine Kinase Sensor Protein, DNA Helicase, Putative Lipoprotein Containing Peptidase M75 Domain and Peptidase C39 Domain Protein in Leptospira interrogans Grown in EMJH Medium
Sarma, Pathogens (Basel, Switzerland) 2021 - “...Ex. S 8 WP_000416054.1 LIC_11345 TonB-dependent siderophore receptor - - 0.04 Ex. S 9 WP_000738678.1 LIC_12988 lipase - - 14.3 Ex. S 10 WP_000812418.1 LIC_10645 hypothetical protein - - 1.4 Ex. S 11 WP_000844347.1 LIC_10346 SGNH/GDSL hydrolase family protein - - 1.2 Ex. S 12 WP_000899352.1...”
- Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches
Viratyosin, BMC genomics 2008 - “...the consensus vote Lai Locus Copen Locus Protein annotation LA3731 LIC10497 Fmh-like protein/hypothetical protein LA0587 LIC12988 Lactonizing lipase/lipase LA0872 LIC12760 Microbial collagenase LA1450 LIC12302 Probable O-sialoglycoprotein endopeptidase LA2448 LIC10830 Putative outermembrane protein/putative lipoprotein LA1765 LIC12047 Rhs family protein/cytoplasmic membrane protein LA4161 LIC13320 Thermolysin/thermolysin precursor LA4164 LIC13321...”
7cofA / A0A1Y1BQV9 Cholesterol esterase from burkholderia stabilis (orthorhombic crystal form)
36% identity, 21% coverage
- Ligand: calcium ion (7cofA)
PA14_63620 lipase LipC from Pseudomonas aeruginosa UCBPP-PA14
33% identity, 20% coverage
PA4813 lipase LipC from Pseudomonas aeruginosa PAO1
NP_253500 lipase LipC from Pseudomonas aeruginosa PAO1
33% identity, 20% coverage
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits in Pseudomonas aeruginosa
Tortuel, Microbiology spectrum 2022 - “...precursor 8.68 PA3910 eddA Extracelullar DNA degradation protein, EddA 3.91 PA4175 piv* Protease IV 29.41 PA4813 lipC Lipase LipC 6.38 Type 3 secretion system PA1690 pscU Translocation protein in type III secretion ExsA 7.95 PA1691 pscT Translocation protein in type III secretion ExsA 13.76 PA1692 pscS...”
- New Mouse Model for Chronic Infections by Gram-Negative Bacteria Enabling the Study of Anti-Infective Efficacy and Host-Microbe Interactions
Pletzer, mBio 2017 - “...length regulator Surface LPS 24.4 fimT (PA4549) Type 4 pilus biogenesis protein Adherence 17.9 lipC (PA4813) Lipase type II secretion system substrate Lipase C 13.2 lipA (PA2862) Major lipase type II secretion system substrate Lipase A 10.4 chpE (PA0417) Probable chemotaxis protein Chemotaxis 8.2 pchB (PA4230)...”
- The Pseudomonas aeruginosa PhoP-PhoQ two-component regulatory system is induced upon interaction with epithelial cells and controls cytotoxicity and inflammation
Gellatly, Infection and immunity 2012 - “...PA no. Gene Description PA3724 PA4175 PA1249 PA2862 PA2863 PA4813 PA0026 PA1092 PA4526 PA1178 lasB piv aprA lipA lipH lipC plcB fliC pilB oprH PA1179 PA3552...”
- Mucin promotes rapid surface motility in Pseudomonas aeruginosa
Yeung, mBio 2012 - “...1.4 2.2 0.8 PA3104 xcpP 7.1 1.3 8.9 2.5 PA3724 lasB 72.6 2.5 13.8 3.3 PA4813 lipC 5.1 1.5 3.6 1.4 Pyoverdine biosynthesis PA2385 pvdQ 5.1 1.3 7.7 2.4 PA2399 pvdD 3.3 1.1 6.2 2.1 PA2426 pvdS 6.1 1.6 5.7 2.1 Pyochelin biosynthesis PA4221 fptA 4.3...”
- The lipase LipA (PA2862) but not LipC (PA4813) from Pseudomonas aeruginosa influences regulation of pyoverdine production and expression of the sigma factor PvdS
Funken, Journal of bacteriology 2011 - “...20 The Lipase LipA (PA2862) but Not LipC (PA4813) from Pseudomonas aeruginosa Influences Regulation of Pyoverdine Production and Expression of the Sigma Factor...”
- “...33). Among those enzymes is the lipase LipC (PA4813), which was found to affect motility, biofilm formation, and rhamnolipid production (19), whereas the second...”
- Protein Secretion Systems in Pseudomonas aeruginosa: An Essay on Diversity, Evolution, and Function
Filloux, Frontiers in microbiology 2011 - “...et al. ( 1998 ) LipA (PA2862) Lipase Jaeger et al. ( 1994 ) LipC (PA4813) Lipase Martinez et al. ( 1999 ) LoxA (PA1169) Lipoxygenase Vance et al. ( 2004 ) PaAP (PA2939) Aminopeptidase Braun et al. ( 1998 ) PhoA (PA3296) Alkaline phosphatase Filloux...”
- Multiple roles of Pseudomonas aeruginosa TBCF10839 PilY1 in motility, transport and infection
Bohn, Molecular microbiology 2009 - “...to be involved in the control of the expression of the P. aeruginosa lipase LipC (PA4813) ( Martnez et al ., 1999 ). The PilY1 protein carries a prepilin peptidase export signal and is transported across the inner membrane ( Lewenza et al ., 2005 )....”
- Pseudomonas aeruginosa twitching motility-mediated chemotaxis towards phospholipids and fatty acids: specificity and metabolic requirements
Miller, Journal of bacteriology 2008 - “...PAO1 lipA (PA2862) extracellular lipase PAO1 lipC (PA4813) extracellular lipase PAO1 estA (PA5112) extracellular esterase/lipase PAO1 estA pBBX estA PAO1 fadL1...”
- “...PA3581 PA3582 PA3994 PA4148 PA4152 PA4198 PA4338 PA4589 PA4733 PA4813 PA5112 Genea 4042 MILLER ET AL. J. BACTERIOL. TABLE 2--Continued PA no. or function tar...”
- More
- Pressure-induced conformational switch of an interfacial protein.
Johnson, Proteins 2016 (PubMed)- GeneRIF: By monitoring the width of the access channel, this study found that the protein undergoes a conformational transition and opens the access channel at high hydrostatic pressures (>100 MPa).
- The lipase LipA (PA2862) but not LipC (PA4813) from Pseudomonas aeruginosa influences regulation of pyoverdine production and expression of the sigma factor PvdS.
Funken, Journal of bacteriology 2011 - GeneRIF: The LipA (PA2862) but not LipC (PA4813) influences regulation of pyoverdine production and expression of the sigma factor PvdS.
- Lipase LipC affects motility, biofilm formation and rhamnolipid production in Pseudomonas aeruginosa.
Rosenau, FEMS microbiology letters 2010 (PubMed)- GeneRIF: LipC is required for motility, biofilm formation and rhamnolipid production.
LIP_BURCE / P22088 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Burkholderia cepacia (Pseudomonas cepacia) (see 8 papers)
lipA / GI|557867 triacylglycerol lipase; EC 3.1.1.3 from Burkholderia cepacia (see 5 papers)
35% identity, 20% coverage
- function: Catalyzes the hydrolysis of triacylglycerol. It shows a preference for triacylglycerols with a chain length between 6 and 12 carbons.
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
subunit: Monomer. - A Novel Lipase from Streptomyces exfoliatus DSMZ 41693 for Biotechnological Applications
Rodríguez-Alonso, International journal of molecular sciences 2023 - “...tool of the BioEdit program and the amino acid sequence of Burkholderia cepacia lipase (UniProt P22088) as reference. Hypothetical genes encoding lipases from S. exfoliatus DSMZ 41693, including their signal peptide coding sequence ( lipA , lipB , lipC , and lipD ), were amplified by...”
- Comparative Structural Analysis of Different Mycobacteriophage-Derived Mycolylarabinogalactan Esterases (Lysin B).
Korany, Biomolecules 2019 - “...pancreatic lipase HuPL 1LPB P16233 8.6 2.8 147 465 15 Pseudomonas cepacia lipase PCL 1YS1 P22088 9.1 3.1 143 364 16 Candida rugosa lipase CRL 1Lpo P20261 7.3 3.4 100 549 12 1 Length according to UniprotKB. Note: Crystal structures were retrieved from Dali server. biomolecules-10-00045-t002_Table...”
GB|BAA00960.1 triacylglycerol lipase; EC 3.1.1.3 from Pseudomonas sp. KWI-56 (see paper)
35% identity, 20% coverage
BCAM0949 exported lipase LipA from Burkholderia cenocepacia J2315
I35_RS20825 triacylglycerol lipase from Burkholderia cenocepacia H111
35% identity, 21% coverage
- Identification by Reverse Vaccinology of Three Virulence Factors in Burkholderia cenocepacia That May Represent Ideal Vaccine Antigens
Irudal, Vaccines 2023 - “...24 proteins. The localization and different aspects of virulence were investigated for three of themBCAL1524, BCAM0949, and BCAS0335. The three antigens were localized in the outer membrane vesicles confirming that they are surface exposed. We showed that BCAL1524, a collagen-like protein, promotes bacteria auto-aggregation and plays...”
- “...was obtained by growth in LB medium. To complement each deleted strain, BCAL1524 (1674 bp), BCAM0949 (1099 bp) and BCAS0335 (3595 bp) genes were amplified using B. cenocepacia K56-2 DNA as template and the primers pairs are listed in Table S3 . Fragments were cloned into...”
- Various Evolutionary Trajectories Lead to Loss of the Tobramycin-Potentiating Activity of the Quorum-Sensing Inhibitor Baicalin Hydrate in Burkholderia cenocepacia Biofilms
Sass, Antimicrobial agents and chemotherapy 2019 - “...same location (e.g., changes in BCAL1315, BCAL1664, and BCAM0949); we speculate that these mutations were already present in the starting population at low...”
- “...chemotaxis protein SNP in CDS (907087 G to T, A369C) 52 BCAM0949 Exported lipase LipA SNP in CDS (1051105 C to G, S180W) 47 100 100 100 100 100 100 100 100...”
- Phenotypic and genotypic characterisation of Burkholderia cenocepacia J2315 mutants affected in homoserine lactone and diffusible signal factor-based quorum sensing systems suggests interplay between both types of systems
Udine, PloS one 2013 - “...measured the expression of cepI (BCAM1870), cepR (BCAM1868), cciI (BCAM0239a), cciR (BCAM0240), zmpA (BCAS0409), lipA (BCAM0949), lipB (BCAM0950) and orbI (BCAL1696) by qPCR. Gene expression was measured in planktonic cells in the presence or absence of added signalling molecules. Although no difference in cepR gene expression...”
- Differential modulation of Burkholderia cenocepacia virulence and energy metabolism by the quorum-sensing signal BDSF and its synthase
Deng, Journal of bacteriology 2009 - “...zmpA (Bcas0409) encoding a metalloprotease (8, 20), lipA (Bcam0949) and lipB (Bcam0950) encoding a lipase and a lipase chaperone (14), respectively, and the...”
- “...increased the transcript levels of zmpA (Bcas0409), lipA (Bcam0949), lipB (Bcam0950), and orbI (Bcal1696) (Fig. 4A). We then tested whether BDSF can further...”
- Reciprocal regulation by the CepIR and CciIR quorum sensing systems in Burkholderia cenocepacia
O'Grady, BMC genomics 2009 - “...CciI NC 52.1 NC BCAM0240 N -acylhomoserine lactone dependent regulatory protein CciR NC 4.0 -23.5 BCAM0949 Exported lipase LipA -3.1 NC NC BCAM0950 Lipase chaperone LipB -2.5 NC NC BCAM1869 Conserved hypothetical protein -5.9 NC NC BCAM1871 Conserved hypothetical protein -37.6 NC -20.2 BCAM2307 Zinc metalloprotease...”
- “...medium and phase of growth influence regulation by CciR. Genes encoding the exported lipase LipA (BCAM0949) and the lipase chaperone LipB (BCAM0950, previously called limA ) are required for lipase production [ 32 ]. Expression of both lipA and lipB was decreased in the cepR mutant...”
- Transcriptional Response of Burkholderia cenocepacia H111 to Severe Zinc Starvation
Barnett, British journal of biomedical science 2023 - “...I35_RS10860 Imidazolonepropionase 2.326828435 0.022280782 I35_RS06165 Phenol degradation protein 2.320499563 2.27E28 I35_RS22340 Hypothetical protein 2.300982216 0.00000167 I35_RS20825 Alpha/beta hydrolase 2.246852811 0.035832439 I35_RS13380 ABC transporter permease 2.238628283 5.97E30 I35_RS10865 Hypothetical protein 2.099694274 0.022469745 I35_RS16595 DNA-binding protein 2.091617711 0.000362322 I35_RS29435 Hypothetical protein 2.072176035 0.022280782 I35_RS27035 2,2-Dialkylglycine decarboxylase 2.047152459 0.00024177...”
LIP_PSEPS / P0DUB9 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudarthrobacter phenanthrenivorans (Arthrobacter phenanthrenivorans) (see 2 papers)
35% identity, 20% coverage
- function: Catalyzes the hydrolysis of triacylglycerol.
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit. {ECO:0000269|PubMed:8683577, ECO:0000305|Ref.)3}
subunit: Monomer (Probable). Interacts with lipase-specific foldase Lif (By similarity).
MXAN_5522 lactonizing lipase from Myxococcus xanthus DK 1622
32% identity, 22% coverage
- Neutral and Phospholipids of the Myxococcus xanthus Lipodome during Fruiting Body Formation and Germination
Ahrendt, Applied and environmental microbiology 2015 - “...throughout the first 24 h of development. Similarly, MXAN_5522, encoding a lipase homolog involved in DAG and TAG degradation, was also downregulated. This...”
- “...development. In TAG metabolism, the downregulation of MXAN_5522, encoding a triacylglycerol lipase, might prevent the degradation of already formed TAGs....”
- Lipolytic enzymes in Myxococcus xanthus
Moraleda-Muñoz, Journal of bacteriology 2007 - “...encoded by MXAN_3852 contains motifs characteristic of patatins. MXAN_5522 encodes a protein with the G-X-S-X-G motif characteristic of the lipase subfamily of...”
- “...of lipolytic enzymes. Strains with deletions of MXAN_5522 and MXAN_4569 undergo faster development and earlier myxospore formation than the wild-type strain....”
1tahB / P0DUB8 The crystal structure of triacylglycerol lipase from pseudomonas glumae reveals a partially redundant catalytic aspartate (see paper)
35% identity, 20% coverage
- Ligand: calcium ion (1tahB)
LIP_BURPL / P0DUB8 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Burkholderia plantarii (see 6 papers)
lipA / GB|CAA49812.1 Triacylglycerol lipase; EC 3.1.1.3 from Burkholderia glumae (see 4 papers)
35% identity, 20% coverage
- function: Catalyzes the hydrolysis of triacylglycerol.
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
subunit: Monomer (Probable). Interacts with lipase-specific foldase Lif (PubMed:16518399).
disruption phenotype: Loss of extracellular active lipase. Not required for growth on oleic acid as a carbon source.
Q75NT4 sterol esterase (EC 3.1.1.13) from Burkholderia cepacia (see paper)
36% identity, 21% coverage
- Efficient Preparation of High-Purity Fucoxanthinol by SpyTag-Tailored Active Cholesterol Esterase Aggregates.
Jin, Marine drugs 2022 - “...90.79%. 2.3. Preparation of Active Cholesterol Esterase Aggregates by SpyTag Tailoring We designed cholesterol esterase (Q75NT4) containing SpyTag. The fusion gene Pet-Q75NT4-SpyTag was transformed and induced, and SpyTag was terminally fused to Q75NT4. Figure 3 shows the diagrammatic sketch of the Pet-Q75NT4-SpyTag chimera design. Pet-Q75NT4-SpyTag was...”
- “...hydrolysis of cholesterol oleate ester and had cholesterol esterase activity, indicating that the target enzyme Q75NT4 was expressed in the form of active cholesterol esterase aggregates in Escherichia coli . Induction conditions were optimized on the basis of the yield of active cholesterol esterase aggregates. As...”
BPSS1741 Lipase precursor from Burkholderia pseudomallei K96243
34% identity, 20% coverage
- Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence
Chin, BMC genomics 2015 - “...BPSS0486, BPSS0712, BPSS1285 and BPSS2328 ), seven phospholipases and lipase-related genes ( BPSL1064, BPSS0016, BPSS1740, BPSS1741, BPSS1937, BPSS2279 and BPSS2319 ) as well as seven cell envelope biogenesis-related genes ( BPSL0607, BPSL1872, BPSL3094, BPSL3312, BPSS1840, BPSS1932 and BPSS2016 ) were up-regulated in the high biofilm producer...”
A9QXC9 triacylglycerol lipase (EC 3.1.1.3) from Burkholderia cepacia (see paper)
35% identity, 20% coverage
H16_A1322 triacylglycerol lipase from Cupriavidus necator H16
H16_A1322 triacylglycerol lipase from Ralstonia eutropha H16
34% identity, 21% coverage
- Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates
Sharma, AMB Express 2016 - “...chains from glycerol before they may be metabolized via the -oxidation pathway. Two lipase genes (H16_A1322 and H16_A3742) were identified previously in C. necator H16 transcriptomes from cells grown on palm oil (Brigham et al. 2010 ). However, neither of these proteins was present in the...”
- “...Most of the triglycerides were hydrolyzed in REG-GB and REG-FFA, therefore no induction of lipases (H16_A1322, H16_A1323) was observed. The -oxidation pathway provided the precursor for PHB synthesis when cultivated on REG-GB and REG-FFA. It appears that activities of -oxidation enzymes were maximum and no further...”
- Characterization of an extracellular lipase and its chaperone from Ralstonia eutropha H16
Lu, Applied microbiology and biotechnology 2013 (PubMed)- “...lipase (encoded by the lipA gene, locus tag H16_A1322) and lipase-specific chaperone (encoded by the lipB gene, locus tag H16_A1323) produced by R. eutropha...”
- “...H16 revealed two putative lipase genes (locus tags H16_A1322 and H16_A3742) that were upregulated during trioleate growth. Deletion of lipase H16_A1322 (GeneID,...”
BTH_II0639 lipase from Burkholderia thailandensis E264
32% identity, 20% coverage
LEPBI_I0886 lactonizing lipase (triacylglycerol lipase) from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
26% identity, 47% coverage
LEPBI_I0777 putative triglyceride lipase; putative signal peptide from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
23% identity, 47% coverage
- Transcriptome Sequencing Reveals Wide Expression Reprogramming of Basal and Unknown Genes in Leptospira biflexa Biofilms
Iraola, mSphere 2016 - “...0.46 9e6 LEPBI_I0104 acdA1 Acyl-CoA dehydrogenase Down 0.33 1e3 LEPBI_I0052 Enoyl-CoA hydratase Down 0.36 4e4 LEPBI_I0777 Putative triglyceride lipase Up 0.69 1.5e6 LEPBI_II0198 fabG 3-Oxoacyl-ACP reductase Down 0.45 7e7 LEPBI_II0199 fabG 3-Oxoacyl-ACP reductase Down 0.39 4e3 LEPBI_II0211 fabG 3-Oxoacyl-ACP reductase Down 0.38 2e3 Iron metabolism LEPBI_I1883...”
- “...used for matrix composition in L.biflexa . This hypothesis is reinforced by the overexpression of LEPBI_I0777 , which codes for a triglyceride lipase (EC 3.1.1.3), allocated to glycerolipid metabolism and involved in degrading triglycerides to single fatty acids ( Table2 ). Furthermore, most enzymes belonging to...”
PL78_18430 triacylglycerol lipase from Yersinia entomophaga
32% identity, 20% coverage
BPSS2319 lipase precursor from Burkholderia pseudomallei K96243
34% identity, 21% coverage
- Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence
Chin, BMC genomics 2015 - “...BPSS2328 ), seven phospholipases and lipase-related genes ( BPSL1064, BPSS0016, BPSS1740, BPSS1741, BPSS1937, BPSS2279 and BPSS2319 ) as well as seven cell envelope biogenesis-related genes ( BPSL0607, BPSL1872, BPSL3094, BPSL3312, BPSS1840, BPSS1932 and BPSS2016 ) were up-regulated in the high biofilm producer (Figs. 2 and 3...”
U876_RS20585 triacylglycerol lipase from Aeromonas hydrophila NJ-35
28% identity, 49% coverage
- In Vitro Antibiofilm Activity of Resveratrol against Aeromonas hydrophila
Qin, Antibiotics (Basel, Switzerland) 2023 - “...Extracellular Proteases U876_RS04035 1.86 2.85 Protease U876_RS18875 2.76 4.74 Elastase U876_RS20565 2.94 3.58 Collagenase Lipase U876_RS20585 1.66 2.34 Lipase U876_RS20590 1.68 1.93 Lipase chaperone T6SS U876_RS21275 1.47 - Type II/IV secretion system protein U876_RS13095 1.72 - Type VI secretion system baseplate subunit TssK U876_RS13100 1.73 -...”
MUW98_RS20835 triacylglycerol lipase from Aeromonas hydrophila
28% identity, 49% coverage
- The antivirulence activity, transcriptomics of EGCG and its protective effects on zebrafish infected by Aeromonas hydrophila
Yin, Frontiers in cellular and infection microbiology 2023 - “...Log2 Fold Change Description Genes associated with bacterial virulence MUW98_RS02610 -2.462476078 SGNH/GDSL hydrolase family protein MUW98_RS20835 -1.537520536 triacylglycerol lipase MUW98_RS04750 -2.189222336 methyl-accepting chemotaxis protein MUW98_RS09395 -1.877322408 methyl-accepting chemotaxis protein MUW98_RS19490 -1.749066889 methyl-accepting chemotaxis protein MUW98_RS11305 -1.427660893 methyl-accepting chemotaxis protein MUW98_RS20975 -1.17387116 HlyD family efflux transporter periplasmic...”
VCA0221 lactonizing lipase from Vibrio cholerae O1 biovar eltor str. N16961
32% identity, 24% coverage
YE1842 lipase from Yersinia enterocolitica subsp. enterocolitica 8081
34% identity, 20% coverage
LIP_VIBCH / P15493 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see 2 papers)
32% identity, 24% coverage
- function: Catalyzes the hydrolysis of triacylglycerol.
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
subunit: Monomer.
disruption phenotype: Cells lacking this gene do not show lipase activity.
FUT48_16475 triacylglycerol lipase from Pseudomonas sp. JG-B
28% identity, 20% coverage
IV454_06595 triacylglycerol lipase from Massilia antarctica
30% identity, 21% coverage
1ex9A / P26876 Crystal structure of the pseudomonas aeruginosa lipase complexed with rc-(rp,sp)-1,2-dioctylcarbamoyl-glycero-3-o-octylphosphonate (see paper)
30% identity, 25% coverage
- Ligands: calcium ion; octyl-phosphinic acid 1,2-bis-octylcarbamoyloxy-ethyl ester (1ex9A)
FH974_07335 triacylglycerol lipase from Photobacterium ganghwense
30% identity, 24% coverage
WP_003239806 triacylglycerol lipase from Pseudomonas hydrolytica
30% identity, 20% coverage
- Insights into the biodegradation of polycaprolactone through genomic analysis of two plastic-degrading Rhodococcus bacteria
Zampolli, Frontiers in microbiology 2023 - “...al., 2015 ; Shi et al., 2020 ), BAI99230 (Hu et al., 2010 ), WP_004373894, WP_003239806 (Li et al., 2022 ), ADK73612 (Inglis et al., 2011 ), BAC67242 (Masaki et al., 2005 ), A0A0K8P6T7 (Yoshida et al., 2016 ), ADH43200 (Ribitsch et al., 2011 ), and...”
- “...2010 R3 WP_004373894 A0A8I0SEY2 JADMNJ010000005 MBF8162059 Hypothetical protein Pseudomonas mendocina Li et al., 2022 R4 WP_003239806 A0A8I0SFQ4 JADMNJ010000002 MBF8160636 Triacylglycerol lipase Pseudomonas mendocina Li et al., 2022 R5 ADK73612 E9KJL1 GU592443 ADK73612 Cutinase A precursor Pseudomonas oleovorans Inglis et al., 2011 R6 BAC67242 Q874E9 AB102945 BAC67242...”
LIP_PSEAE / P26876 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 3 papers)
P26876 triacylglycerol lipase (EC 3.1.1.3) from Pseudomonas aeruginosa (see 2 papers)
NP_251552 lactonizing lipase from Pseudomonas aeruginosa PAO1
PA14_27100 lactonizing lipase precursor from Pseudomonas aeruginosa UCBPP-PA14
PA2862 lactonizing lipase precursor from Pseudomonas aeruginosa PAO1
30% identity, 25% coverage
- function: Catalyzes the hydrolysis of triacylglycerol (PubMed:1748875). It also exhibits some esterase activity with p-nitrophenyl acetate and Tween 80 as substrates, however the lipase activity is approximately eight times the esterase activity (PubMed:1748875). It shows a marked specificity for the 1,3-oleyl residues of triolein (PubMed:1748875).
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
subunit: Monomer. - Genome Wide Analysis of the Potato Soft Rot Pathogen Pectobacterium carotovorum Strain ICMP 5702 to Predict Novel Insights into Its Genetic Features.
Mallick, The plant pathology journal 2022 - “..., PA0688 P35482 Alkaline phosphatase L. Peg.3112 167 cp1 C5J5F5 Haloprotease CP1 Peg.2990 141 lipA P26876 Triacylglycerol lipase Peg.2760 401 lasA P14789 Protease LasA Peg.651 165 VC_A0027 Q9KND8 Chitinase Peg.1830 192 chiA P13656 Probable bifunctional chitinase/lysozyme Table 3 Protein encoding genes associated with type III secreted...”
- Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves
Wang, Scientific reports 2019 - “...A: Diacylglycerol Acyltransferase 458 Q8GGG1 PF03007 PF06974 Pseudomonas aeruginosa B lip Lip Triacylglycerol lipase 311 P26876 PF00561 Wax Ester (WE) Acinetobacter baylyi B wax-dgaT WS/DGAT Wax Ester Synthase/Acyl Coenzyme A: Diacylglycerol Acyltransferase 458 Q8GGG1 PF03007PF06974 # D: three life domains: Archaea (A), Bacteria (B) and Eukaryote...”
- Evidence of a double-lid movement in Pseudomonas aeruginosa lipase: insights from molecular dynamics simulations
Cherukuvada, PLoS computational biology 2005 - “...http://www.rcsb.org/pdb/ ) accession number is 1EX9, and the Uniprot ( http://www.ebi.ac.uk/swissprot/access.html ) accession number is P26876. In appreciation of Prof. Varadachari Krishnan, JNCASR, Bangalore, India. We thank the Department of Biotechnology Government of India through the BioTechnology Information Services programme and the Department of Science and...”
- Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation.
Viegas, Scientific reports 2020 - GeneRIF: Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation.
- The Pseudomonas transcriptional regulator AlgR controls LipA expression via the noncoding RNA RsmZ in Pseudomonas protegens Pf-5.
Li, Biochemical and biophysical research communications 2017 (PubMed)- GeneRIF: In conclusion, this study for the first time indicates that AlgR directly binds to rsmZ to regulates the expression of lipA via regulating transcription of rsmZ, and mainly regulates the expression of lipA at transcriptional level in P. protegens Pf-5.
- The lipase LipA (PA2862) but not LipC (PA4813) from Pseudomonas aeruginosa influences regulation of pyoverdine production and expression of the sigma factor PvdS.
Funken, Journal of bacteriology 2011 - GeneRIF: The LipA (PA2862) but not LipC (PA4813) influences regulation of pyoverdine production and expression of the sigma factor PvdS.
- Mucin Glycans Signal through the Sensor Kinase RetS to Inhibit Virulence-Associated Traits in Pseudomonas aeruginosa
Wang, Current biology : CB 2021 - “...may upregulate the expression of genes associated with acute infections, including those that encode lipase (PA14_27100), rhamnolipids (PA14_1910019110), and the T3SS (PA14_4225042660). 21 , 36 However, unlike the H1-T6SS, the mechanism by which RetS controls these acute infection genes is unclear, because these transcripts are not...”
- Polysorbate 80 inhibition of Pseudomonas aeruginosa biofilm formation and its cleavage by the secreted lipase LipA
Toutain-Kidd, Antimicrobial agents and chemotherapy 2009 - “...The ligT gene is directly upstream of lipA (PA14_27100), which codes for an extracel- lular lipase. The lipases in bacteria have been extensively studied...”
- The periplasmic chaperone Skp prevents misfolding of the secretory lipase A from Pseudomonas aeruginosa
Papadopoulos, Frontiers in molecular biosciences 2022 - “...P. aeruginosa PAO1 strain were identified using Pseudomonas Genome database ( www.pseudomonas.com ). Those included PA2862 ( lipA ), PA2863 ( lipH ), PA3262 ( fkpA ), PA3801 ( yfgM ), PA 1805 ( ppiD ), PA0594 ( surA ) and PA3647 ( skp/ompH/hlpA ). The...”
- “...( Bernad et al., 2007 ; Tria et al., 2015 ). Lipase isolation The gene PA2862 encoding for the mature LipA was cloned into pET22b plasmid via NdeI/BamHI restriction sites ( Hausmann et al., 2008 ) and the protein was expressed in E. coli BL21(DE3). Briefly,...”
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits in Pseudomonas aeruginosa
Tortuel, Microbiology spectrum 2022 - “...4.81 PA0844 plcH Hemolytic phospholipase C precursor 2.94 PA0852 cbpD* Chitin-binding protein CbpD precursor 33.33 PA2862 lipA Lactonizing lipase precursor 2.02 PA2939 paaP* Probable aminopeptidase 50.00 PA3296 phoA Alkaline phosphatase 2.95 PA3319 plcN Nonhemolytic phospholipase C precursor 8.68 PA3910 eddA Extracelullar DNA degradation protein, EddA 3.91...”
- Putative RNA Ligase RtcB Affects the Switch between T6SS and T3SS in Pseudomonas aeruginosa
Dadashi, International journal of molecular sciences 2021 - “...6 4.76 10 5 1.2 PA1948 T2SS ToxA 5.76 10 6 4.91 10 5 1.1 PA2862 T2SS LipA 1.08 10 7 1.17 10 6 4.8 PA2939 T2SS PaAP 3.42 10 17 7.92 10 16 1.5 PA2676 T2SS HplS 0.010726 0.041385 1.8 PA2677 T2SS HplR 5.62 10...”
- A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen
Reales-Calderón, Journal of proteomics 2021 - “...included other virulence factors, such as AprA (PA1249) [ 80 ] and the lipase LipA (PA2862) [ 81 ]. Thus, the analysis of the proteome under T3SS induction conditions has provided important contributions to the P. aeruginosa PeptideAtlas. Proteins involved in T3SS regulation, such as MexT...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...hpcG 3.8 2-Oxo-hept3ene-1,7-dioate hydratase PA5351 rubA1 1.4 Rubredoxin 1 PA4670 prs 1.6 2.0 Ribose-phosphate pyrophosphokinase PA2862 lipA 1.8 2.7 Lactonizing lipase precursor PA3363 amiR 1.5 1.0 Aliphatic amidase regulator Central intermediary metabolism PA0654 speD 1.5 S -Adenosylmethionine decarboxylase proenzyme PA2393 1.6 Putative dipeptidase PA3182 pgl 1.8...”
- New Mouse Model for Chronic Infections by Gram-Negative Bacteria Enabling the Study of Anti-Infective Efficacy and Host-Microbe Interactions
Pletzer, mBio 2017 - “...protein Adherence 17.9 lipC (PA4813) Lipase type II secretion system substrate Lipase C 13.2 lipA (PA2862) Major lipase type II secretion system substrate Lipase A 10.4 chpE (PA0417) Probable chemotaxis protein Chemotaxis 8.2 pchB (PA4230) Pyochelin siderophore biosynthesis Iron uptake 8.2 exsA (PA1713) Type III secretion...”
- Characterization of the GbdR regulon in Pseudomonas aeruginosa
Hampel, Journal of bacteriology 2014 - “...(Table 3). We also noted that the lipA transcript (PA2862) was the only transcript whose abundance decreased under these conditions in a manner befitting a...”
- “...19.7 158.6 8.5 64.2 84.2 32.6 Transcript decreased in abundance PA2862 lipA 1.0 2.7 2.7 3.4 WT All changes are significant with P values of 0.00001. b PC,...”
- Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions
Tielen, PloS one 2013 - “...following primers were used: fur (PA4764) fur-fw `3-GAGGTGATCGAGTTCATGGATGC-5, fur-bw `3-GCACGTAGAGCACCAGATTGTGA-5, pvdS (PA2426) pvdS-fw`3-GATAACCGTACGATCCTGGTGAAGA-5, pvdS-bw`3-AGGTAGCTGAGCTGTGCCTTGAAC-5, lipA (PA2862) lipA-fw `3-CAGCACCTACACCCAGACCAAATAC -5, lipA-bw `3-GCTGACTTCGGTGACGTAGACCT-5, aprA (PA1249) aprA-fw `3-ATATCTACTCGCTGGGCAAGTTCAG-5, aprA-bw `3-GTCGACGAAGTGGATATTGGTGAC-5, lasB (PA3724) lasB-fw `3-GACCAACACCTACAAGCAGGTCAAC-5, lasB-bw `3-CTTCATGTACAGCTTGTGGGTCAG -5, narG (PA3875) narG-fw `3-TGAACGGCACCAGCTTCTTC-5, narG-bw `3-CGTTCGGCCTGGATGTTGTA-5. qRT-PCR was performed with SsoFast EvaGreen...”
- More
LIP_PSEU0 / P26877 Triacylglycerol lipase; Extracellular lipase; Lactonizing lipase; Lipase P; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudomonas sp. (strain 109) (see paper)
30% identity, 25% coverage
- function: Catalyzes the hydrolysis of triacylglycerol. Also able to catalyze, in anhydrous organic solvents, intramolecular transesterification of omega-hydroxyfatty acid esters to form macrocyclic lactones. This biosynthesis is dependent on the chain length of the substrates, and the formation of monomer lactone is maximum with methyl 18-hydroxyoctadecanoate. With shorter substrates, monomer lactone decreases and the formation of diolide (dimer lactone) increases.
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
subunit: Monomer.
A8QYB2 triacylglycerol lipase (EC 3.1.1.3) from Pseudomonas aeruginosa (see paper)
30% identity, 25% coverage
Q9L6C7 Triacylglycerol acylhydrolase from Pseudomonas aeruginosa
30% identity, 25% 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