PaperBLAST
PaperBLAST Hits for WP_016936851.1 triacylglycerol lipase (Bacillus siamensis) (214 a.a., MKQIKSKILA...)
Show query sequence
>WP_016936851.1 triacylglycerol lipase (Bacillus siamensis)
MKQIKSKILAILTVCMLSVISVFAFQPTVSKASSEHNPVVMVHGIGGASFNFAGIKTYLA
SQGWSRNEMYAIDFLDKTGNNRHNAPRLSNYVKKVLSETGAKKVDIVAHSMGGANTLYYI
KNLDGGDKIANVVTLGGANGLVTNRALPGTDPNQKILYTSIYSSADLIVMNPLSRLIGGK
NVQIHGVGHIGLLMNSQVNGLIKEGLNGGGQNTN
Running BLASTp...
Found 31 similar proteins in the literature:
JD965_RS01465 triacylglycerol lipase from Bacillus siamensis
100% identity, 100% coverage
ESTA_BACSU / P37957 Lipase EstA; Lipase A; Triacylglycerol lipase; EC 3.1.1.3 from Bacillus subtilis (strain 168) (see 5 papers)
NP_388152 secreted alkaliphilic lipase from Bacillus subtilis subsp. subtilis str. 168
BSU02700 secreted alkaliphilic lipase from Bacillus subtilis subsp. subtilis str. 168
78% identity, 100% coverage
- function: Active toward triacylglycerides with a preference for esters with C8:0 acyl groups; barely active on C18:1 or C18:4 substrates. Active against p-nitrophenylesters with fatty acid chain lengths from C6 to C18.
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)
subunit: Monomer. - Construction of Pseudomonas aeruginosa SDK-6 with synthetic lipase gene cassette and optimization of different parameters using response surface methodology for over-expression of recombinant lipase
Kaur, Folia microbiologica 2024 (PubMed)- “...An alkalophilic lipase gene (GenBank accession number: NP_388152) from Bacillus subtilis was synthetically designed and introduced in the pJN105 vector and...”
- “...an alkalophilic lipase (NCBI GenBank accession number: NP_388152) from Bacillus subtilis subsp. subtilis 168. The retrieved sequence was optimized for...”
- QSSR Modeling of Bacillus Subtilis Lipase A Peptide Collision Cross-Sections in Ion Mobility Spectrometry: Local Descriptor Versus Global Descriptor.
Ni, The protein journal 2021 (PubMed)- GeneRIF: QSSR Modeling of Bacillus Subtilis Lipase A Peptide Collision Cross-Sections in Ion Mobility Spectrometry: Local Descriptor Versus Global Descriptor.
- [Effect of non-classical secreted proteins on LipaseA secretion].
Cui, Wei sheng wu xue bao = Acta microbiologica Sinica 2015 (PubMed)- GeneRIF: LipaseA was secreted via non-classical secretion pathway.
- Purification and characterization of a mesophilic lipase from Bacillus subtilis FH5 stable at high temperature and pH.
Hasan, Acta biologica Hungarica 2007 (PubMed)- GeneRIF: Bacillus subtilis was isolated from tannery waste; therefore, its lipase is environmentally compatible for application in leather degreasing process.
- Implementation of Spore Display in Paenibacillus polymyxa with Different Hydrolytic Enzymes
Zander, Microorganisms 2024 - “...lipases known from B. subtilis in the P. polymyxa genome. No analog to lipase A (P37957) was found in the P. polymyxa genome. We thus used the lipA sequence from B. subtilis and used it for the spore display as a heterologous gene. The bioinformatic search...”
- Structure and Mechanism of a Cold-Adapted Bacterial Lipase
van, Biochemistry 2022 - “...B. subtilis LipA structures in the Protein Data Bank (identified by their UniProt accession number P37957) shows a highly conserved mainchain structure with an average root-mean-square deviation (RMSD) for the C-atoms of 0.3 aligned to the 1.3 resolution structure with PDB code 1ISP. 19 The atomic...”
- Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences
Verma, 3 Biotech 2019 - “...well-studied Bacillus subtilis alkaliphilic lipase sequence (Uniport IDs: P37957) was used as an input query to retrieve orthologs (lipase gene of common...”
- RankProt: A multi criteria-ranking platform to attain protein thermostabilizing mutations and its in vitro applications - Attribute based prediction method on the principles of Analytical Hierarchical Process
Chakravorty, PloS one 2018 - “...lipase of Bacillus subtilis 168 (1i6w) was collected from Uniprot Knowledgebase release 2010_06 (Uniprot ID: P37957). Mutations were predicted using RankProt. To validate the stability of mutations, they were also analyzed through I-Mutant2, Cupsat and ERIS web servers [ 21 23 ]. Biophysical characterization was performed...”
- A combination of mutational and computational scanning guides the design of an artificial ligand-binding controlled lipase
Kaschner, Scientific reports 2017 - “...analysis Evolutionary coupling analysis was carried out for lipases using the BsLA sequence (Uniprot ID: P37957) as input sequence for the EVcouplings webserver ( www.evfold.org ). For the generation of the alignment the JackHHMer software (5 interations) 52 , implemented as part of the EVcouplings webserver,...”
- Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
Morrison, NPJ microgravity 2019 - “...CcpA, PhoP, SigA BSU02310 ybfO 1.46 1.51 1.89 1.99 Similar to erythromycin esterase AbrB, SigW BSU02700 lipA 1.44 1.50 1.23 1.27 Extracellular lipase Unknown BSU02710 yczC 1.93 1.99 1.08 1.07 Unknown Unknown BSU03200 putB 3.16 3.67 1.02 1.02 Proline dehydrogenase CodY PutR, SigA, Spo0A BSU03480 srfAA...”
- Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis
Skoczinski, Microbial cell factories 2017 - “...expression vector pBSlipA, site saturation mutagenesis and library construction The lipA gene (KEGG Accession Number BSU02700) without its native signal sequence was amplified from the E. coli expression vector pET22lipA [ 18 ] using the oligonucleotides Eco RI_fw(5cgcggaattcgctgaacac3) and Hin dIII_rev (5agtgcggccgcaagcttgtcgacgtaatgttcattaattcgtatt3). The resulting 568bp Eco...”
- Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production
Wiegand, Microbial cell factories 2013 - “...strongly transcribed TatAyCy system. It has recently been shown that the extracellular B. subtilis lipase BSU02700, which is Sec-dependently secreted under standard conditions, is translocated by the B. subtilis Tat pathway in a hyper-secreting strain [ 80 ]. Hence, this phenomenon has been assumed to be...”
- Regulon of the N-acetylglucosamine utilization regulator NagR in Bacillus subtilis
Bertram, Journal of bacteriology 2011 - “...above). THE NagR REGULON IN B. SUBTILIS lip, estA ywjC BSU02700 BSU37210 cydC xpt ybgH, glnT ybbB, Btr albE albF feuA feuB feuC yusV fhuD yxeB ydbN yuiG, bioYB...”
W8FKE7 Lipase from Bacillus pumilus
75% identity, 98% coverage
- Structure and Mechanism of a Cold-Adapted Bacterial Lipase
van, Biochemistry 2022 - “...Methods Protein Production A synthetic Bacillus pumilus lipase gene construct corresponding to UniProt accession ID W8FKE7 was codon-optimized for expression in Escherichia coli and synthesized by GenScript. The mature peptide sequence, excluding the signal peptide, was subcloned into pET22b with cytosolic expression. The expression vector containing...”
- ThermoSlope: A Software for Determining Thermodynamic Parameters from Single Steady-State Experiments
Lund, Molecules (Basel, Switzerland) 2021 - “...Production The DNA sequence encoding residues 35215 of the mature Bacillus pumilus Lipase L5 (UniProtKB W8FKE7) was optimised for E. coli expression, synthesised and subcloned into pET-22b(+) within the NdeI/XhoI sites by GenScript Biotech (Leiden, The Netherlands). The plasmid was transformed into NiCo21(DE3) chemically competent E.coli...”
lip / CAB95850.2 lipase precursor from Bacillus licheniformis (see 2 papers)
73% identity, 100% coverage
5ct4A / P37957 Wild-type bacillus subtilis lipase a with 5% [bmim][cl] (see paper)
83% identity, 84% coverage
- Ligands: 1-butyl-3-methyl-1h-imidazol-3-ium; chloride ion (5ct4A)
7r1kA / W8FKE7 Phosphorylated bacillus pumilus lipase a
82% identity, 84% coverage
- Ligand: oxaloacetate ion (7r1kA)
ESTB_BACSU / Q79F14 Extracellular esterase EstB; Extracellular esterase LipB; Lipase B; Triacylglycerol lipase; EC 3.1.1.3 from Bacillus subtilis (strain 168) (see 2 papers)
Q79F14 acylglycerol lipase (EC 3.1.1.23) from Bacillus subtilis (see paper)
BSU08350 secreted esterase / lipase from Bacillus subtilis subsp. subtilis str. 168
70% identity, 97% coverage
- function: An esterase which preferentially hydrolyzes triacylglyceride substrates with short chain fatty acids (C3-C10) with the maximum activity towards tricaprylin (C8:0); essentially inactive on C18:1 or C18:4 substrates. Active against p-nitrophenylesters with fatty acid chain lengths from C6 to C18.
catalytic activity: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044) - Secondary structural entropy in RNA switch (Riboswitch) identification
Manzourolajdad, BMC bioinformatics 2015 - “...0.3376 79 ylaA BSU14710 0.816 77 909862 910018 forward BSU08330 yfiN -658 0.3503 79 estB BSU08350 0.816 78 4109617 4109773 reverse BSU40030 yxaB -1253 0.3885 79 yxaD BSU40010 0.813 79 3252983 3253139 forward BSU31660 mrpG -538 0.3949 4632 yuzC BSU31730 0.811 80 4066294 4066450 reverse BSU39600...”
WP_029418313 triacylglycerol lipase from Bacillus sonorensis
69% identity, 96% coverage
Q8RJP5 triacylglycerol lipase (EC 3.1.1.3) from Priestia megaterium (see paper)
69% identity, 97% coverage
WP_043054382 triacylglycerol lipase from Bacillus paralicheniformis
66% identity, 97% coverage
WP_003183220 triacylglycerol lipase from Bacillus licheniformis
66% identity, 97% coverage
WP_020452056 triacylglycerol lipase from Bacillus paralicheniformis
65% identity, 97% coverage
OOZ19_29350 triacylglycerol lipase from Saccharopolyspora sp. NFXS83
29% identity, 87% coverage
DR2078 lipase, putative from Deinococcus radiodurans R1
27% identity, 73% coverage
IV454_31865 triacylglycerol lipase from Massilia antarctica
25% identity, 87% coverage
5h6bA / H0B8D4 Crystal structure of a thermostable lipase from marine streptomyces (see paper)
36% identity, 44% coverage
H0B8D4 Putative secreted lipase from Streptomyces sp. W007
SPW_1544 triacylglycerol lipase from Streptomyces sp. W007
36% identity, 37% coverage
- The Meaning of Mas
Bader, Hypertension (Dallas, Tex. : 1979) 2018 - “...51 kDA Catalytic subunit of the mitochondrial processing protease Strepto-myces sp. W007 mas1 (SPW_1544) Mas1 H0B8D4 MArine Streptomyces 1 Uniprot: H0B8D4 31 kDa Putative secreted thermostable lipase...”
- The Meaning of Mas
Bader, Hypertension (Dallas, Tex. : 1979) 2018 - “...SGD: S000004153 51 kDA Catalytic subunit of the mitochondrial processing protease Strepto-myces sp. W007 mas1 (SPW_1544) Mas1 H0B8D4 MArine Streptomyces 1 Uniprot: H0B8D4 31 kDa Putative secreted thermostable lipase...”
C9Z1F6 Putative secreted lipase from Streptomyces scabiei (strain 87.22)
32% identity, 53% coverage
- Physical, Chemical and Proteomic Evidence of Potato Suberin Degradation by the Plant Pathogenic Bacterium Streptomyces scabiei
Beaulieu, Microbes and environments 2016 - “...). The abundance of most lipases and esterases detected in this study (Sub1, C9Z6Y6, C9YUN4, C9Z1F6, and C9YTK3) increased over time. The maximal production of these lipolytic enzymes in the late phase of the culture may reflect the bacterial growth phase. In some streptomycetes, esterases and...”
- “...Day 30 Day 60 C9Z6Y6 Cholesterol esterase 0.54 (39.42) 0.68 (34.17) 1.20 (34.19) 1.25 (33.42) C9Z1F6 Lipase 0.22 (16.06) 0.36 (18.09) 0.56 (15.95) 0.62 (16.58) C9YTK3 Lipase 0.11 (8.03) 0.28 (14.01) 0.44 (12.54) 0.36 (9.63) C9YUN4 Cholesterol esterase 0.03 (2.19) 0.10 (5.03) 0.14 (3.99) 0.15 (4.10)...”
SCO1735 secreted lipase from Streptomyces coelicolor A3(2)
31% identity, 53% coverage
sll1969 unknown protein from Synechocystis sp. PCC 6803
31% identity, 53% coverage
- Triple-Gene Overexpression of the AcrA-AcrB-TolC Transporter System in <i>Synechocystis</i> sp. PCC 6803 Contributes to a Higher Secretion of Free Fatty Acids in Response to Nitrogen Shortage and Salt Stress
Eungrasamee, International journal of molecular sciences 2024 - “...precursor to synthesizing membrane lipids ( Figure 1 ). The lipA gene, encoded by the sll1969 gene found on the membrane, can hydrolyze membrane lipids to free fatty acids (FFAs) [ 15 , 16 ]. Intracellular FFAs are generated as a result of this breakdown and...”
- Deacylation of galactolipids decomposes photosystem II dimers to enhance degradation of damaged D1 protein
Jimbo, Plant physiology 2023 (PubMed)- “...sp. PCC 6803. We identified a protein encoded by the sll1969 gene, previously named lipase A (lipA), in the Synechocystis sp. PCC 6803 genome as a candidate for...”
- “...| PLANT PHYSIOLOGY 2022: Page 2 of 9 Results Sll1969 cleaves C18 acyl-chains bound to galactolipids and TAG In the genome of Synechocystis, several genes are...”
- Incorporation, fate, and turnover of free fatty acids in cyanobacteria
Kahn, FEMS microbiology reviews 2023 - “...investigation of putative lipase genes and their protein products (Fig. 6A ). The candidate gene sll1969 , encoding LipA in Synechocystis 6803, was first suggested to be involved in membrane autolysis (Liu et al. 2011 ). Later, Synechocystis 6803 was engineered in an attempt to enhance...”
- Enhanced productivity of extracellular free fatty acids by gene disruptions of acyl-ACP synthetase and S-layer protein in Synechocystis sp. PCC 6803
Eungrasamee, Biotechnology for biofuels and bioproducts 2022 - “..., 16 ]. For membrane lipid hydrolysis, the lipase A enzyme, encoded by lipA ( sll1969 ), is capable of releasing free fatty acids inside the cells [ 3 , 8 , 9 , 17 ]. The FFAs recycling to fatty acyl-ACP occurs viaa fatty acyl-ACP...”
- High-Light-Induced Stress Activates Lipid Deacylation at the Sn-2 Position in the Cyanobacterium Synechocystis Sp. PCC 6803
Kojima, Plant & cell physiology 2022 - “...about cyanobacterial lipases. The Synechocystis sp. PCC 6803 genome database shows two ORFs, sll0482 and sll1969, as putative lipase genes, but with no genetic or biochemical evidence. Identification of the gene responsible for the HL-induced, sn -2-specific lipase activity and elucidation of the molecular mechanism of...”
- Overexpression of lipA or glpD_RuBisCO in the Synechocystis sp. PCC 6803 Mutant Lacking the Aas Gene Enhances Free Fatty-Acid Secretion and Intracellular Lipid Accumulation
Eungrasamee, International journal of molecular sciences 2021 - “...membrane lipid degradation or hydrolysis, are produced by lipase A catalysis encoded by lipA or sll1969 in Synechocystis 6803 [ 16 ]. In addition, the intracellular FFA level is regulated to lower its toxicity to the cells by both the FFAs recycling reaction catalyzed by fatty...”
- “...membrane lipids could be hydrolyzed into free fatty acids (FFAs) by lipase A encoded by sll1969 in Synechocystis PCC 6803 [ 16 ]. Those FFAs products are either partly secreted out of cells into the medium or are incorporated into membrane lipids biosynthesis via FFA recycling...”
- Specific Incorporation of Polyunsaturated Fatty Acids into the sn-2 Position of Phosphatidylglycerol Accelerates Photodamage to Photosystem II under Strong Light
Jimbo, International journal of molecular sciences 2021 - “...in the mutant lacking LPGAT has not been investigated. Synechocystis has a phospholipase encoded by sll1969 [ 43 ], which suggests that lysoPG is synthesized by the phospholipase in Synechocystis cells. Further biochemical analysis of the phospholipase is needed to investigate whether this phospholipase is involved...”
- Hydrocarbon Desaturation in Cyanobacterial Thylakoid Membranes Is Linked With Acclimation to Suboptimal Growth Temperatures
Vuorio, Frontiers in microbiology 2021 - “...acyl chains can be released by the action of the lipolytic enzyme (LipA encoded by sll1969 ) and re-attached to the ACP by acyl-ACP synthetase (Aas encoded by slr1609 ), which may again serve as a substrate for the AAR/ADO. Therefore, all the alkenes produced by...”
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SCO1265 lipase from Streptomyces coelicolor A3(2)
32% identity, 41% coverage
- Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters
Lee, Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2024 - “...). Interestingly, SigJ and SCO3450 seem to regulate catabolic genes clustered at specific genomic loci (SCO1265 SCO1288 and SCO3437 SCO3465, respectively), and their overexpression may promote phosphate consumption, resulting in actinorhodin production. Overall, each sigma factor affects antibiotic production differently, and ICA can be used to...”
- The Inhibition of Antibiotic Production in Streptomyces coelicolor Over-Expressing the TetR Regulator SCO3201 IS Correlated With Changes in the Lipidome of the Strain
Zhang, Frontiers in microbiology 2020 - “...putative siderophore encoded by sco5799 - sco5801 as well as the PKS encoding genes ( sco1265 - sco1273 ) and ( sco7670 - sco7671 ) was also down-regulated in M145/pWHM3- sco3201 ( Figure 3 ). The transcriptional activity of genes of the coelibactin cluster ( sco7681...”
- Cytosolic copper is a major modulator of germination, development and secondary metabolism in Streptomyces coelicolor
González-Quiñónez, Scientific reports 2019 - “...0.3 SCO0494 Coelichelin biosynthesis 0.5 0.5 0.7 1.4 SCO0495 Coelichelin biosynthesis 0.7 0.6 0.6 1.6 SCO1265 Aromatic polyketide biosynthesis 0.8 0.9 1.8 1.9 SCO1867 5-Hydroxyectoine biosynthesis 0.4 1.3 1.3 0.4 SCO2782 Desferrioxamine biosynthesis 0.6 1.4 0.7 2.7 SCO3218 CDA biosynthesis 1.8 1 3.6 0.5 SCO3221 CDA...”
TTE0555 predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold from Thermoanaerobacter tengcongensis MB4
33% identity, 26% coverage
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...of 1h at 100C 44.5 (1) Levisson et al. ( 2007 ) Thermoanaerobacter tengcongensis Esterase TTE0555 p NP-C3/C4 NR NR NR 70 9 Half-life of 1.5h at 70C 43 Zhang et al. ( 2003 ) Thermosyntropha lipolytica Lipase (LipA) NR p NP-C12 NR NR NR 96...”
cg0109 triacylglycerol lipase precursor from Corynebacterium glutamicum ATCC 13032
NCgl0079 triacylglycerol lipase from Corynebacterium glutamicum ATCC 13032
33% identity, 31% coverage
- Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
Zhang, Scientific reports 2018 - “...413.77 917.71 2.0 52 NCgl0647 cg0779 trpS Tryptophanyl-tRNA synthetase 5.11/37826.54 1378.57 0.00 NC 54 NCgl0079 cg0109 Triacylglycerol lipase precursor 5.11/35814.40 341.27 1637.98 NC 55 NCgl2156 cg2456 Zn-ribbon protein 5.19/26131.12 2802.33 0.00 2.7 56 NCgl0317 cg0391 rmlB2 dTDP-glucose 4,6-dehydratase 5.12/33536.53 717.37 2083.02 NC 57 NCgl2359 cg2686 TetR...”
- Metabolic engineering Corynebacterium glutamicum to produce triacylglycerols
Plassmeier, Metabolic engineering 2016 (PubMed)- “...precursor consumption by deleting four cellular lipases (cg0109, cg0110, cg1676 and cg1320) and the diacylglycerol kinase (cg2849), (iii) enhancement of fatty...”
- “...and precursor consumption by deleting four cellular lipases ( cg0109 , cg0110 , cg1676 and cg1320 ) and the diacylglycerol kinase ( cg2849 ), (iii) enhancement...”
- Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
Zhang, Scientific reports 2018 - “...9.89/18278.42 413.77 917.71 2.0 52 NCgl0647 cg0779 trpS Tryptophanyl-tRNA synthetase 5.11/37826.54 1378.57 0.00 NC 54 NCgl0079 cg0109 Triacylglycerol lipase precursor 5.11/35814.40 341.27 1637.98 NC 55 NCgl2156 cg2456 Zn-ribbon protein 5.19/26131.12 2802.33 0.00 2.7 56 NCgl0317 cg0391 rmlB2 dTDP-glucose 4,6-dehydratase 5.12/33536.53 717.37 2083.02 NC 57 NCgl2359 cg2686...”
O16380 Lipase from Caenorhabditis elegans
30% identity, 27% coverage
cg0110 triacylglycerol lipase precursor from Corynebacterium glutamicum ATCC 13032
28% identity, 34% coverage
WP_015793408 triacylglycerol lipase from Catenulispora acidiphila DSM 44928
27% identity, 52% coverage
- Cloning and characterization of an acidic lipase from a lipolytic bacterium in tempeh
Nur, Journal, genetic engineering & biotechnology 2023 - “...closer relationship with lipase from Streptomyces cinnamoneus and Propionibacterium acnes . Lipase from Catenulispora acidiphila (WP_015793408) and Williamsia sp. (WP_023956064) are some other members of subfamily I.6 [ 27 ]. Lipases from families I generally share a Gly-X-Ser-X-Gly consensus sequence [ 28 ]. Lipases categorized as...”
7v3kC / A3TMR7 Crystal structure of maj1
25% identity, 46% coverage
- Ligand: calcium ion (7v3kC)
A3TMR7 Putative lipase from Janibacter sp. HTCC2649
25% identity, 41% coverage
HMPREF0675_4855 triacylglycerol lipase from Cutibacterium acnes SK137
39% identity, 21% coverage
CAA67627.1 triacylglycerol lipase from Cutibacterium acnes (see paper)
PPA2105 triacylglycerol lipase from Cutibacterium acnes KPA171202
PPA2105 triacylglycerol lipase precursor from Propionibacterium acnes KPA171202
32% identity, 32% coverage
- Inhibition of Biofilm Formation in Cutibacterium acnes, Staphylococcus aureus, and Candida albicans by the Phytopigment Shikonin
Kim, International journal of molecular sciences 2024 - “...gene ( 16s rRNA ). Notably, the expression levels of adhesin/invasion (PPA0721), lipase (PPA1796 and PPA2105), hyaluronate lyase ( hly ), and virulence-related genes (PPA0149, btuR , cbiL , roxP , and PPA0349) were downregulated by shikonin at 5 g/mL, while the expression levels of hyaluronate...”
- “...observation that shikonin reduced the expression levels of adhesin (PPA0721) and lipase genes (PPA1796, and PPA2105). Furthermore, C. acnes is known to possess a hyaluronate lyase gene ( hly ), the protein product of which degrades hyaluronic acid, an extracellular matrix component of the epidermis [...”
- Phytopigment Alizarin Inhibits Multispecies Biofilm Development by Cutibacterium acnes, Staphylococcus aureus, and Candida albicans
Lee, Pharmaceutics 2022 - “...the housekeeping gene ( 16s rRNA ). Importantly, the expressions of lipase (PPA1761, PPA1796, and PPA2105), hyaluronate lyase ( hly ), adhesin/invasion- (PPA1715 and PPA1961) and virulence-related genes ( btuR , PPA0149, PPA0349, PPA1035, PPA1098, PPA1222, and PPA2139) were downregulated while the expressions of the antioxidant...”
- “...Our qRT-PCR study showed that alizarin suppressed the expressions of lipase genes (PPA1761, PPA1796, and PPA2105), hyaluronate lyase ( hly ), adhesion and invasion-related genes (PPA1715 and PPA1961), and virulence-related genes ( btuR , PPA0149, PPA0349, PPA1035, PPA1098, PPA1222, and PPA2139) genes but upregulated the expressions...”
- The Anticancer Agent 3,3'-Diindolylmethane Inhibits Multispecies Biofilm Formation by Acne-Causing Bacteria and Candida albicans
Kim, Microbiology spectrum 2022 - “...gene ( 16s rRNA ) was unchanged. Notably, the expressions of lipase genes (PPA1796 and PPA2105), the hyaluronate lyase gene ( hly ), and the precorrin-2 C(20)-methyltransferase ( cbiL ) gene were downregulated while the expression of hemolysin ( tly ) was upregulated 3-fold by DIM...”
- “...). Our qRT-PCR study showed that DIM downregulated the expressions of lipase genes (PPA1796 and PPA2105), the hyaluronate lyase ( hly ), and precorrin-2 C(20)-methyltransferase ( cbiL ) genes ( Fig.8 ). Previously, it was reported that extracellular lipases are associated with biofilm formation by C....”
- Circulating Antibodies to Skin Bacteria Detected by Serological Lateral Flow Immunoassays Differentially Correlated With Bacterial Abundance
Huang, Frontiers in microbiology 2021 - “...more abundantly expressed in acne lesions ( ONeill and Gallo, 2018 ). The gehA gene (PPA2105) encoding C. acnes lipase can increase sebum concentrations of free palmitate, which plays an important role in lipotoxic inflammasome activation of macrophages ( Legrand-Poels et al., 2014 ). The secretion...”
- Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies
McLaughlin, Microorganisms 2019 - “...genes during mid-log phase. These included genes for several putative virulence factors, including triacylglycerol lipase (PPA2105), endoglycoceramidase (PPA0644) and DsA1 (PPA2127), which were all upregulated in 266 (2.5-, 4- and 6-fold, respectively). A putative haemolysin (PPA0565) and the immunoreactive iron acquisition protein htaA (PPA0786) were also...”
- “...endo-glycoceramidases (PPA0644; PPA2106), lysozyme (PPA1612), a protease (PPA1310), peptidase/glycosyl hydrolyase (PPA2239), the triacylglycerol lipase GehA (PPA2105), which is believed to hydrolyse sebum triacylglycerides, and hypotheticals (PPA0533; PPA0533; PPA1939). Key phylogroup differences included reduced lysozyme and increased GehA secretion by type IA 1 (266) versus type IB...”
- Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro
Lanter, Infection and immunity 2015 - “...increased expression of mRNAs for the triacylglycerol lipases PPA2105 and PPA1796 and the hyaluronate lyase PPA380 compared to that in untreated biofilms. These...”
- “...for certain lipases (PPA1035, PPA1761, PPA1796, and PPA2105) and hyaluronate lyase (PPA380) were affected by iron-induced dispersion, 8-day-old P. acnes...”
- Linking diet to acne metabolomics, inflammation, and comedogenesis: an update
Melnik, Clinical, cosmetic and investigational dermatology 2015 - “...associated with moderate to severe acne and possesses particular virulence potential. 192 The gehA gene (PPA2105) encoding the secreted triacylglycerol lipase is a virulence factor that is upregulated in P. acnes strain 266 during exponential growth phases. 193 Recently, P. acnes biofilm formation has been confirmed...”
- Proteome analysis of human sebaceous follicle infundibula extracted from healthy and acne-affected skin
Bek-Thomsen, PloS one 2014 - “...(1) 8 (4) PPA0816 Glyceraldehyde 3-phosphate dehydrogenase 11 (2) 0 (0) 10 (2) 8 (4) PPA2105 GehA; triacylglycerol lipase 16 (3) 0 (0) 0 (0) 6 (3) PPA0687 CAMP factor 2 11 (2) 0 (0) 0 (0) 4 (2) PPA0545 Enolase 5 (1) 0 (0) 5...”
- “...major lipase found in vivo was not the characterized triacylglycerol lipase GehA (glycerol-ester hydrolase A, PPA2105). Instead, a so far not studied lipase of P. acnes (PPA1796; proposed gene name GehB) was found in 50% of all healthy individuals (nose-H1) and 10% of acne-affected skin samples...”
- Comparative genomics reveals distinct host-interacting traits of three major human-associated propionibacteria
Mak, BMC genomics 2013 - “...73.4 5-nucleotidase/2,3-cyclic phosphodiesterase or related esterase 547 7 PPA0687 28.6 CAMP factor 2 394 4 PPA2105 35.9 Triacylglycerol lipase precursor 353 4 PPA2239 41.0 Lipoprotein A-like protein 342 5 PPA1340 30.3 CAMP factor 1 230 3 Listed are all surface-exposed proteins that possess a typical N-terminal...”
- “...under the applied growth conditions, is a triacylglycerol lipase that is 48% similar to GehA (PPA2105), a characterized lipase of P. acnes . Furthermore, a homolog of CAMP factor 3 and several proteins of unknown function could be detected in the supernatant of P. avidum ATCC25577...”
- Comparative genomics and transcriptomics of Propionibacterium acnes
Brzuszkiewicz, PloS one 2011 - “...frameshifted in KPA; this lipase is 45% identical to the characterized glycerol-ester hydrolase A (GehA, PPA2105, PAZ_c21800) [24] . Substantial differences also exist in genes encoding putative adhesins such as proteins with thrombospondin type 3 repeats ( Table S1 ). Whole genome gene expression analysis of...”
- “...organic phosphate cosubstrates were omitted from the scheme. Regarding possible virulence factors, the gehA gene (PPA2105) encoding the secreted triacylglycerol lipase [24] is among the up-regulated genes in strain 266. In addition, the genes for the secreted factors endoglycoceramidase (PPA0644) and the adhesin PA-25957 (PPA2127) are...”
- Proteomic identification of secreted proteins of Propionibacterium acnes
Holland, BMC microbiology 2010 - “...5'-nucleotidase, metallo-phosphoesterase UshA (5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases); Jonesia denitrificans SP, TAT IB, II + PPA2105 triacylglycerol lipase lipase class 2, esterase/lipase superfamily; Rhodococcus SP IA, IB, II, III ++ PPA2106 putative endoglycoceramidase cellulase, glycoside hydrolase family 5; Nocardioides SP, (TAT) IA, IB, II, III +/42%...”
- “...in the secretory fraction, including the previously characterized triacylglycerol lipase, designated glycerol-ester hydrolase A (GehA; PPA2105). GehA is recognized as one of the virulence factors involved in the pathogenesis of acne [ 37 - 39 ], and is thought to be the main enzyme responsible for...”
- The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications
Falentin, PloS one 2010 - “...another lipase with 41% identity to GehA at the protein level, encoded by the genes PPA2105 and PPA1796, respectively [21] , [34] . Neither of these proteins has an ortholog in P. freudenreichii. P. freudenreichii was recently shown to produce a secreted lipase active on milk...”
A9QXC9 triacylglycerol lipase (EC 3.1.1.3) from Burkholderia cepacia (see paper)
27% 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