PaperBLAST
PaperBLAST Hits for BBR_RS19865 (82 a.a., MLLEQDPARK...)
Show query sequence
>BBR_RS19865
MLLEQDPARKLYATGHHNIVNVPGTDEWIIAYHRFAYNPAGRWAGGDGCHREVVFAPLDY
NPDGSLVPVRPQVGSYVRSLAF
Running BLASTp...
Found 16 similar proteins in the literature:
Blon_2411 glycoside hydrolase, family 43 from Bifidobacterium longum subsp. infantis ATCC 15697
95% identity, 25% coverage
DMZ48_07370 family 43 glycosylhydrolase from Robertkochia solimangrovi
38% identity, 12% coverage
SCAB_11431 putative hydrolase from Streptomyces scabiei 87.22
C9Z507 Putative secreted hydrolase from Streptomyces scabiei (strain 87.22)
45% identity, 4% coverage
- Suberin Regulates the Production of Cellulolytic Enzymes in Streptomyces scabiei, the Causal Agent of Potato Common Scab
Padilla-Reynaud, Microbes and environments 2015 - “...C9Z1T6 SCAB_9291 or SCAB_91051 Lactonase NF ND 0.26 C9Z1U5 SCAB_9381 Exo--sialidase NF ND 0.53 C9Z507 SCAB_11431 Glycosyl hydrolase GH43 0.22 1.11 C9Z878 SCAB_13491 Glucan endo-1,3--d-glucosidase GH64 ND 0.13 C9ZD59 SCAB_16521 Arabinofuranosidase GH43, CBM42 ND 1.81 C9ZD61 SCAB_16551 Mannosidase GH26, CBM23 ND 0.11 C9YT63 SCAB_19561 -fructofuranosidase GH43,...”
- Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
Komeil, Proteome science 2014 - “...0.050.02 0.080.05 nd 0.020.01 0.020.01 C9Z1T6 SCAB_9291 Lactonase nd 0.140.05 0.200.07 nd 0.020.03 nd C9Z507 SCAB_11431 Glycosyl hydrolase 0.390.10 0.880.30 0.640.17 nd 0.420.13 0.330.14 C9Z878 SCAB_13491 Glycosyl hydrolase nd 0.030.02 0.040.02 nd nd 0.010.01 C9ZD50 SCAB_16431 Cellulase 0.430.29 1.520.86 1.040.61 nd 0.930.72 0.390.04 C9ZD59 SCAB_16521 Arabinofuranosidase...”
- Suberin Regulates the Production of Cellulolytic Enzymes in Streptomyces scabiei, the Causal Agent of Potato Common Scab
Padilla-Reynaud, Microbes and environments 2015 - “...D C9Z1T6 SCAB_9291 or SCAB_91051 Lactonase NF ND 0.26 C9Z1U5 SCAB_9381 Exo--sialidase NF ND 0.53 C9Z507 SCAB_11431 Glycosyl hydrolase GH43 0.22 1.11 C9Z878 SCAB_13491 Glucan endo-1,3--d-glucosidase GH64 ND 0.13 C9ZD59 SCAB_16521 Arabinofuranosidase GH43, CBM42 ND 1.81 C9ZD61 SCAB_16551 Mannosidase GH26, CBM23 ND 0.11 C9YT63 SCAB_19561 -fructofuranosidase...”
- Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
Komeil, Proteome science 2014 - “...0.030.00 0.050.02 0.080.05 nd 0.020.01 0.020.01 C9Z1T6 SCAB_9291 Lactonase nd 0.140.05 0.200.07 nd 0.020.03 nd C9Z507 SCAB_11431 Glycosyl hydrolase 0.390.10 0.880.30 0.640.17 nd 0.420.13 0.330.14 C9Z878 SCAB_13491 Glycosyl hydrolase nd 0.030.02 0.040.02 nd nd 0.010.01 C9ZD50 SCAB_16431 Cellulase 0.430.29 1.520.86 1.040.61 nd 0.930.72 0.390.04 C9ZD59 SCAB_16521...”
BACCELL_00858 hypothetical protein from Bacteroides cellulosilyticus DSM 14838
38% identity, 11% coverage
JM81_RS16510 family 43 glycosylhydrolase from Maribacter sp. MAR_2009_72
38% identity, 10% coverage
- Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72
Kalenborn, FEMS microbiology ecology 2024 - “...proteins (JM81_RS16470 and JM81_RS16475) annotated as unsaturated rhamnogalacturonyl hydrolases were expressed similar in all proteomes. JM81_RS16510 includes two domains, GH43_19 and GH43_34. It was expressed in the arabinose, arabinogalactan, and galactose proteome, whereby the highest intensities were measured for arabinose. Another - l -arabinofuranosidase, a GH51...”
- “...chains of hemicelluloses, like arabinoxylan, arabinogalactan, and arabinan (Shallom et al. 2002a , b ). JM81_RS16510 encodes a protein that consists out of two GH43 domains, GH43_19 and GH43_34. Over 70% of subfamily GH43_34 proteins contain a second GH43 domain (Mewis et al. 2016 ). GH43_34...”
BT_3675 family 43 glycosylhydrolase from Bacteroides thetaiotaomicron VPI-5482
BT3675 endo-1,4-beta-xylanase D precursor from Bacteroides thetaiotaomicron VPI-5482
39% identity, 21% coverage
- Mechanism of Cooperative Degradation of Gum Arabic Arabinogalactan Protein by Bifidobacterium longum Surface Enzymes
Sasaki, Applied and environmental microbiology 2022 - “...30 ) and Paenibacillus sp. JDR-2 (Pjdr2_0435) ( 30 ) and two - l -arabinofuranosidases (BT_3675 and BT_3662) from B. thetaiotaomicron VPI-5482, based on the CAZy database. BT_3675 acts on the 1,3-Ara f linkage present in single 1,3-Ara f -substituted gum arabic AGP ( 7 ),...”
- Mechanism of Cooperative Degradation of Gum Arabic Arabinogalactan Protein by Bifidobacterium longum Surface Enzymes
Sasaki, Applied and environmental microbiology 2022 - “...in the periplasm. For the degradation of - l- Ara f , - l -arabinofuranosidase (BT3675) was characterized to hydrolyze 1,3-Ara f linkage but not 1,4-Ara f linkage, but 1,4-Ara f -specific - l -arabinofuranosidase has not been detected yet. In bifidobacteria, we found a key...”
- “...follows: Ba. Cell_Abf, B. cellulosilyticus - l -arabinofuranosidase (GenPept accession no. ALJ58905.1 ); Ba. The_Abf (BT3675), B. thetaiotaomicron - l -arabinofuranosidase encoded by BT3675 (GenPept accession no. AAO78780.1 ); R. Jos_Abf, Ruminiclostridium josui exo-1,5-arabinofuranosidase (GenPept accession no. BBA94052.1 ); Ba. Ova_Bgf, B. ovatus - d -galactofuranosidase...”
- Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi
Solanki, The ISME journal 2022 - “...genes are most closely related to the - l -arabinofuranosidases of B. thetaiotaomicron VPI-5482 T (BT3675, GH43) [ 28 ] and Thermotoga thermarum DSM 5069 (TtAFase, GH2) [ 76 ]. Known members of the GH92 family are exo-acting -mannosidases [ 77 ], and members of the...”
- A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation
Cartmell, Nature microbiology 2018 - “...PULs removed the -Gal (discussed below). PUL AGPS also encodes two arabinofuranosidases; a GH43 enzyme (BT3675) and the non-specific arabinofuranosidase, BT3679, active against wheat AGP (WH-AGP), arabinoxylan and sugar beet arabinan ( Supplementary Fig. 7b , Supplementary Table 2 ). BT3679 establishes a GH family (GH155)...”
- “...backbone irrespective of whether the Gal was decorated at O4 ( Supplementary Fig. 8 ). BT3675 hydrolysed the Ara f -1,3-Gal glycosidic bond, but not when Gal also contained -L-Ara f at O4. The two enzymes and cell-free extracts of B. thetaiotaomicron cultured on AGPs did...”
VDAG_01866 xylosidase/arabinosidase from Verticillium dahliae VdLs.17
39% identity, 8% coverage
- Deleting an xylosidase-encoding gene VdxyL3 increases growth and pathogenicity of Verticillium dahlia
Li, Frontiers in microbiology 2024 - “...cotton varieties resistant or susceptible to V. dahliae . Among the 13 VdxyL genes, only VDAG_01866 ( VdxyL3 ) of the GH43 subfamily showed obvious up-regulation in response to the root exudate (VdX6) from the susceptible cotton variety (Xinluzao 7) and no significant change in response...”
- Transcriptomic analysis of gene expression of Verticillium dahliae upon treatment of the cotton root exudates
Zhang, BMC genomics 2020 - “...3' 5' GCCTCCTCCTCGTACTCCTC 3' VDAG_01193 high-affinity nicotinic acid transporter 5' GTGCCATCTCCGGCTTCATC 3' 5' TTGCGTTGTCACCCTTCTCG 3' VDAG_01866 xylosidase/arabinosidase 5' CAGCTCCGTGCTCAATGTGCC 3' 5' TCCAACTGAGATGCCCGCCTT 3' VDAG_03038 periplasmic trehalase 5' GGCAACAACCTCACTCGC 3' 5' GCACTACGGCTACCAAACTTCT 3' VDAG_03526 alpha-glucuronidase 5' GTGACGGCGGACAACTCTAC 3' 5' TGCACGCCCTTGAATGTAAT 3' VDAG_04513 hexose transporter protein 5' TCAACATTGCCATCCAGGTC...”
- “...Alpha-glucosidase 0.525139 1.351249 0.631004 0.348396 0.365856 2 VDAG_01781 Polygalacturonase 4.42107 9.593065 6.264324 4.446467 3.902134 3 VDAG_01866 Xylosidase/arabinosidase 2.999633 6.737425 3.158829 1.499116 1.280038 4 VDAG_02175 Beta-glucosidase 0 0.230686 0.231927 0.113611 0.277088 5 VDAG_02469 Glucan 1,3-beta-glucosidase 9.092852 19.9074 14.55665 10.28952 7.637805 6 VDAG_02542 Beta-glucosidase 1.740641 3.559025 2.760439 1.618581...”
BBMN68_RS07385 family 43 glycosylhydrolase from Bifidobacterium longum subsp. longum BBMN68
35% identity, 4% coverage
BLGA_18450 family 43 glycosylhydrolase from Bifidobacterium longum subsp. longum
35% identity, 4% coverage
BL105A_1857 family 43 glycosylhydrolase from Bifidobacterium longum
35% identity, 4% coverage
BLLJ_1850 family 43 glycosylhydrolase from Bifidobacterium longum subsp. longum JCM 1217
35% identity, 4% coverage
- The Bifidobacterium adolescentis BAD_1527 gene encodes GH43_22 α-L-arabinofuranosidase of AXH-m type
Fathallah, AMB Express 2024 - “...contrast to -1,2- and -1,3-isomers (Komeno et al. 2019 ). Bl AbfE (a product of BLLJ_1850 gene) and specifically its GH43_22 domain liberated arabinose, which was 1,3-linked to side chain galactose, readily from gum arabic arabinogalactan but hardly from larch arabinogalactan having less complicated side chains...”
- Bifidobacterial GH146 β-L-arabinofuranosidase for the removal of β1,3-L-arabinofuranosides on plant glycans
Fujita, Applied microbiology and biotechnology 2024 - “...BlArafC (BLLJ_1852) (Komeno et al. 2022 ), BlArafD (BLLJ_1851) (Komeno et al. 2022 ), BlArafE (BLLJ_1850) (Sasaki et al. 2022 ), GH43_24 exo--1,3-galactanase Bl1,3Gal (BLLJ_1840) (Fujita et al. 2014a ), and GH30_5 exo--1,6-galactobiohydrolase Bl1,6Gal (BLLJ_1841) (Fujita et al. 2019a ). The aa sequence of the catalytic...”
- “...on the arabinan side chains (Komeno et al. 2019 ). Recently, BlArafD (BLLJ_1851) and BlArafE (BLLJ_1850) with tandem GH43 domains have been characterized. The GH43_UC (uncharacterized subfamily of GH43) domain of BlArafD acts on the 1,2-linked Ara f of the 1,2- and 1,3-Ara f doubly substituted...”
- Two α-L-arabinofuranosidases from Bifidobacterium longum subsp. longum are involved in arabinoxylan utilization
Komeno, Applied microbiology and biotechnology 2022 (PubMed)- “...In this study, we characterized two genes, BLLJ_1850 and BLLJ_1851, in the hemicellulose-degrading gene cluster (BLLJ_1836-BLLJ_1859) of B. longum subsp. longum...”
- “...activity toward p-nitrophenyl--l-arabinofuranoside. BlArafE (encoded by BLLJ_1850) contains the glycoside hydrolase family 43 (GH43), subfamily 22 (GH43_22),...”
- Mechanism of Cooperative Degradation of Gum Arabic Arabinogalactan Protein by Bifidobacterium longum Surface Enzymes
Sasaki, Applied and environmental microbiology 2022 - “...and modified sugar. In this study, we identified an - l -arabinofuranosidase (BlArafE; encoded by BLLJ_1850), a multidomain enzyme with both GH43_22 and GH43_34 catalytic domains, as a critical enzyme for the degradation of modified - l -arabinofuranosides in gum arabic AGP. Site-directed mutagenesis approaches revealed...”
- “...-l -Ara f -(12)-- l -Ara f -(12)- -l -Ara f -Hyp ( 10 ). BLLJ_1850 to BLLJ_1854 are arranged in tandem in the gene cluster, and we previously reported that BlArafA (BLLJ_1854) contained the GH43 subfamily 22 (GH43_22) domain acting on the 1,3-Ara f residue...”
- Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population
Chung, Microbiology spectrum 2021 - “...subunits shared >70% nucleotide identity with the - l -arabinofuranosidases, arafB (BLLJ_1853, GH43_22) and arafE (BLLJ_1850, GH43_34), of B. longum JCM1217, which encode degradative enzymes targeting the arabinan backbone and arabinoxylan, respectively ( 35 ). The remaining GH43_22 subunit of RS09395 showed no ortholog in B....”
- Two Novel α-l-Arabinofuranosidases from Bifidobacterium longum subsp. longum Belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan
Komeno, Applied and environmental microbiology 2019 - “...strain lacking the GH43 gene cluster that includes BLLJ_1850 to BLLJ_1853 did not grow in arabinan medium, suggesting that BlArafC and BlArafB are important...”
- “...JCM 1217. Notably, five previously uncharacterized GH43 ORFs, BLLJ_1850 to BLLJ_1854, form a gene cluster. In this study, we cloned and characterized two GH43...”
- Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan
Odamaki, Scientific reports 2018 - “...a cluster of five tandemly arrayed genes that are all predicted to encode extracellular -L-arabinofuranosidases (BLLJ_1850 to BLLJ_1854 homologues) as well as genes encoding a putative multidrug-family ABC transporter with an associated two-component system (TCS), a genetic cluster containing an Hsp20-family heat shock chaperone, and various...”
- Bifidobacterium longum subsp. longum Exo-β-1,3-Galactanase, an enzyme for the degradation of type II arabinogalactan
Fujita, Applied and environmental microbiology 2014 - “...(BLLJ_1848) and five duplicated genes of GH43 -L-arabinofuranosidases (BLLJ_1850 to BLLJ_1854) in B. longum subsp. longum JCM1217. In the presence of AG-II, the...”
- “...endo--1,6-galactanase (BLLJ_1841), and GH43 -L-arabinofuranosidases (BLLJ_1850 to BLLJ_1854) on the bifidobacterial cell surface. Next, the released...”
WP_024834488 family 43 glycosylhydrolase from Ruminiclostridium josui JCM 17888
32% identity, 4% coverage
FGSG_03003 hypothetical protein from Fusarium graminearum PH-1
38% identity, 20% coverage
- Comparison of Fusarium graminearum Transcriptomes on Living or Dead Wheat Differentiates Substrate-Responsive and Defense-Responsive Genes
Boedi, Frontiers in microbiology 2016 - “...Uncharacterized protein FGSG_01829 Related to aldose 1-epimerase FGSG_01831 Related to trihydrophobin precursor FGSG_02914 Uncharacterized protein FGSG_03003 Related to alpha-N-arabinofuranosidase/alpha-L-arabinofuranosidase FGSG_03178 Uncharacterized protein FGSG_03190 Uncharacterized protein FGSG_03343 Related to beta-galactosidase FGSG_03394 Uncharacterized proteinrelated to NPP1 domain protein FGSG_03454 Uncharacterized protein FGSG_03467 Probable extracellular elastinolytic metalloproteinase precursor FGSG_03968...”
- “...for proteolytic protein processing and extracellular polysaccharide degradation. Examples are proteins similar to secreted alpha-N-arabinofuranosidase/alpha-L-arabinofuranosidase (FGSG_03003), to vacuolar aminopeptidase Y precursor (FGSG_03027), to endo-1,4-beta-xylanase A precursor (FGSG_03624) and a predicted cellulase (FGSG_11184). The one gene that is positively affected by AP and PP impact factors, FGSG_00028,...”
BBPC_RS09395 family 43 glycosylhydrolase from Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505
31% identity, 3% coverage
BF9343_1139 glycoside hydrolase family 43 protein from Bacteroides fragilis NCTC 9343
35% identity, 21% coverage
- Multi-omics approach for understanding the response of Bacteroides fragilis to carbapenems
Zholdybayeva, Heliyon 2024 - “...BF9343_0934 metallophosphoesterase (I6J55_RS09055) 1,66E+00 xylanase activit BF9343_1273 alpha/beta hydrolase family protein (I6J55_RS07960) 2,37E+00 alpha-L-arabinofuranosidase activity BF9343_1139 Putative xylosidase/arabinosidase (xynD_3) 7,99E-01 galactosidase activity BF9343_0230 Alpha-galactosidase (aga_1) 2,71E+00 unknown function BF9343_1393 Bacteriophage-related replication protein (BF9343_1393) 5,05E+00 BF9343_2497 DUF169 domain-containing protein (I6J55_RS01150) 8,11E-01 BF9343_0291 Exported glutaminase (BF9343_0291) 1,02E+00 BF9343_0624...”
- “...ligase activity BF9343_2640 RNA ligase 4,88E+00 lyase activity, BF9343_0873 O-acetylhomoserine synthase (mdeA_2) 7,84E-01 arabinofuranosidase activity, BF9343_1139 Putative xylosidase/arabinosidase (xynD_3) 7,51E-01 unknown function BF9343_0308 Conserved hypothetical exported protein 4,77E+00 BF9343_3666 Conserved hypothetical membrane protein 3,36E+00 BF9343_3099 Conserved hypothetical phospholipase 2,39E+00 BF9343_2744 DUF2589 domain-containing protein 1,15E+00 BF9343_0326 Exported...”
BT3516 arabinan endo-1,5-alpha-L-arabinosidase A precursor from Bacteroides thetaiotaomicron VPI-5482
38% identity, 11% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
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by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory