PaperBLAST
PaperBLAST Hits for IAI46_16305 (82 a.a., MGIISWIIFG...)
Show query sequence
>IAI46_16305
MGIISWIIFGLIAGILAKWIMPGKDGGGFIVTVILGIIGAVVGGYISTFFGMGRVDGFNL
GSFVVAVIGALVVLFVYRKIRN
Running BLASTp...
Found 19 similar proteins in the literature:
YPO1181 putative membrane protein from Yersinia pestis CO92
89% identity, 77% coverage
YPTB1222 putative membrane protein from Yersinia pseudotuberculosis IP 32953
89% identity, 100% coverage
YeaQ / b1795 PF04226 family protein YeaQ from Escherichia coli K-12 substr. MG1655 (see paper)
ECs_2504 hypothetical protein from Escherichia coli O157:H7 str. Sakai
b1795 conserved inner membrane protein from Escherichia coli str. K-12 substr. MG1655
E2348C_1922 GlsB/YeaQ/YmgE family stress response membrane protein from Escherichia coli O127:H6 str. E2348/69
82% identity, 100% coverage
- Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
Tyagi, Toxins 2019 - “...peroxide resistance OB fold protein 2.2 1.7 ECs_2355 sodC superoxide dismutase [Cu-Zn] SodC2 3.4 2.9 ECs_2504 yeaQ stress response membrane protein 2.7 2.7 ECs_2558 yebG damage-inducible protein YebG 2.3 1.8 ECs_3271 mntH manganese/divalent cation transporter 1.5 ECs_3476 grpE molecular chaperone GrpE 1.8 ECs_3553 csrA carbon storage...”
- 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
Militello, BMC microbiology 2016 - “...by indole transport regulation; global regulator. e.g. of AI-2 transport and motility genes 1.52 5.23E-05 b1795 yeaQ UPF0410 family protein, function unknown 1.56 1.65E-03 b2414 cysK Cysteine synthase A, O-acetylserine sulfhydrylase A; homodimeric; selenate, azaserine, chromate resistance; alkali-inducible, sulfate starvation-inducible protein SSI5; cysteine desulfhydrase 1.58 2.86E-03...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
González, Journal of bacteriology 2006 - “...ymgC yeaQ amyA gatC b1454 b3864 b4078 b1166 b1167 b1795 b1927 b2092 dsdX ygdI b3254 yiaG tra5_3 yhjS rbsC b2365 b2809 b3254 b3555 b0372 b3536 b3750 Hypothetical...”
- The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli
Lease, Journal of bacteriology 2004 - “...Alias Alias Alias Alias Alias Alias b0287 b1450 b1787 b1794 b1795 b1969 b2253 2.6-2.8 2.1-4.4 2-2.9 2-2.2 2.9-3.3 2.3-4 2.1-3.2 26 -- -- 3.5 2.6 3.5 NS NS --...”
- Global analyses of transcriptomes and proteomes of a parent strain and an L-threonine-overproducing mutant strain
Lee, Journal of bacteriology 2003 - “...on L-threonine production. Upregulation of aceBA and downregulation of b1795, hdeAB, oppA, and yfiD seem to be linked to a low accumulation of acetate in...”
- “...b0859 hypothetical protein b1200 hypothetical protein b1795 hypothetical protein dadA D-amino acid dehydrogenase dadX alanine racemase dapB dihydrodipicolinate...”
- Gene expression profiling of the pH response in Escherichia coli
Tucker, Journal of bacteriology 2002 - “...of acid-induced gene comparisons b no. Gene b1661 cfa b1795 yeaQ b2254 yfbF b3506 slpc b3509 hdeB c b3511 hdeDc b4376 osmY b1000 cbpA b3510 hdeAc b0329...”
- Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
Pomposiello, Journal of bacteriology 2001 - “...b0485 b0881 b1112 b1164 b1165 b1200 b1450 b1452 b1643 b1795 b2174 b2266 b2672 b3004 b3024 b3238 b3242 b1661 b3806 b2414 b4382 b4383 b0014 b0812 b0593 b3289...”
- “...artP b0485 b0881 b1112 b1164 b1165 b1200 b1450 b1452 b1643 b1795 b2174 b2266 b2672 b3004 b3024 b3238 b3242 cfa cyaA cysK deoA deoB dnaK dps entC fmu fumC gadA...”
- Microarray analysis of the Ler regulon in enteropathogenic and enterohaemorrhagic Escherichia coli strains
Bingle, PloS one 2014 - “...- fruR leader peptide E2348C_0318 2 iraP hypothetical protein E2348C_1098 2 - hypothetical protein IE2 E2348C_1922 2 yeaQ conserved inner membrane protein E2348C_2034 3 sdiA DNA-binding transcriptional activator E2348C_2114 2 - hypothetical protein IE3 E2348C_3744 5 chuT putative hemin binding protein E2348C_3745 6 chuW putative coproporphyrinogen...”
STM14_2173 GlsB/YeaQ/YmgE family stress response membrane protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
65% identity, 98% coverage
- Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation
Lago, Scientific reports 2017 - “...63 Yes yaiA 12 -Proteobacteria STM14_1271 YccJ-like protein IPR025600 75 Yes yccJ 1114 - Proteobacteria STM14_2173 Transglycosylase motif IPR007341, 3TM fragments 84 ymgE 1114 Bacteria and Archaea STM14_2188 45 Yes Enterobacteriaceae STM14_2189 32 Salmonella STM14_2239 Start codon re-annotated, 88% identity with E . coli YebV, DUF1480...”
- “...coding capacity of the uncharacterized small ORFs, for which no protein was identified by LC-MS (STM14_2173, STM14_2189, STM14_5292, STM14_5469, STM14_5479, STM14_5481), was assessed by immunodetection of the corresponding 3xFlag-tagged proteins. Proteins were detected for all of them, except STM14_5469 and STM14_5479 (Fig. 1b ). In the...”
Z1960 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs1692 hypothetical protein from Escherichia coli O157:H7 str. Sakai
67% identity, 98% coverage
- Genome evolution in major Escherichia coli O157:H7 lineages
Zhang, BMC genomics 2007 - “...upstream region ECs1691 (Z1959) orf, hypothetical protein; ycgR 100% 100% 0% S-loop#83/OI#55 upstream region ECs1692 (Z1960) orf, hypothetical protein; ymgE 100% 100% 0% S-loop#83/OI#55 ECs1693 (Z1961) putative TonB dependent outer membrane receptor 100% 100% 0% S-loop#83/OI#55 ECs1694 (Z1962) molybdenum transport protein 100% 100% 0% S-loop#83 ECs1695...”
- Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
King, Molecular & cellular proteomics : MCP 2016 - “...ECs4212 ), and encoding hypothetical proteins ( ECs0383 , ECs0886 , ycaC / ECs0982 , ECs1692 , ECs2695 , ECs2785 , ECs2888 , ECs3588 , ECs4112 , yhfG / ECs4213 , ECs4323 , ysgA / ECs4760 , ECs5089 ). Cluster II contains genes involved in fatty...”
- Genome evolution in major Escherichia coli O157:H7 lineages
Zhang, BMC genomics 2007 - “...S-loop#83/OI#55 upstream region ECs1691 (Z1959) orf, hypothetical protein; ycgR 100% 100% 0% S-loop#83/OI#55 upstream region ECs1692 (Z1960) orf, hypothetical protein; ymgE 100% 100% 0% S-loop#83/OI#55 ECs1693 (Z1961) putative TonB dependent outer membrane receptor 100% 100% 0% S-loop#83/OI#55 ECs1694 (Z1962) molybdenum transport protein 100% 100% 0% S-loop#83...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...ompT -2.72 1 ECs2346 tyrS -2.97 1 ECs1683 ycgB 5.36 2 ECs2385 ynhG 3.80 2 ECs1692 ymgE 2.35 2 ECs2387 sufS 2.88 2 ECs1705 - 2.55 2 ECs2389 sufC 3.58 2 ECs1722 chaB 2.85 2 ECs2390 sufB 2.93 2 ECs1729 narG -2.70 4 ECs2391 sufA 3.68...”
Tag / b1195 PF04226 family protein YmgE from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b1195 predicted inner membrane protein from Escherichia coli str. K-12 substr. MG1655
65% identity, 98% coverage
- 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
Militello, BMC microbiology 2016 - “...protein; BCCP; homodimeric 1.05 6.41E-04 b0083 ftsL Cell division and growth, membrane protein 1.01 9.70E-04 b1195 ymgE UPF0410 family predicted inner membrane protein; function unknown 1.01 2.15E-03 b0255 insN' Pseudogene reconstruction, fused IS911 transposase AB 1.08 2.42E-04 b4107 yjdN Metalloprotein superfamily protein, function unknown 1.30 4.90E-04...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
Zhang, Journal of bacteriology 2007 - “...ymgE b0806 b0456 b1050 b4045 b4107 b2672 b1195 Hypothetical protein Hypothetical protein Hypothetical protein Highly abundant nonessential protein Hypothetical...”
- Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
Smulski, Journal of bacteriology 2001 - “...b1105 b1107 b1108 b1111 b1112 b1128 b1145 b1168 b1178 b1195 b1205 b1256 b1257 b1273 b1285 b1321 b1333 b1376 b1378 b1414 b1446 b1454 b1586 b1598 b1667 b1678...”
A4U42_RS19150 GlsB/YeaQ/YmgE family stress response membrane protein from Dickeya solani IPO 2222
79% identity, 100% coverage
IMX11_18495, IMX12_18995 GlsB/YeaQ/YmgE family stress response membrane protein from Streptomyces sp. Babs14
45% identity, 89% coverage
- Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara
Zerouki, BMC genomics 2021 - “...was found in Babs14 (IMX12_04415, IMX12_08985, IMX12_18995, IMX12_21360) and in Osf17 (locus tag IMX11_03925, IMX11_08485, IMX11_18495, IMX11_20860). The alkaline shock Asp23/Gls24 family that envelope stress response was also predicted in Babs14 (locus tagIMX12_09080) and Osf17 (IMX11_08580), as well as 50S ribosomal protein L25/general stress protein Ctc...”
- “...The GlsB/YeaQ/YmgE family stress response related to the membrane was found in Babs14 (IMX12_04415, IMX12_08985, IMX12_18995, IMX12_21360) and in Osf17 (locus tag IMX11_03925, IMX11_08485, IMX11_18495, IMX11_20860). The alkaline shock Asp23/Gls24 family that envelope stress response was also predicted in Babs14 (locus tagIMX12_09080) and Osf17 (IMX11_08580), as...”
asr3089 transglycosylase-associated protein from Nostoc sp. PCC 7120
43% identity, 86% coverage
BAB1_0459 Transglycosylase-associated protein from Brucella melitensis biovar Abortus 2308
47% identity, 94% coverage
CC_1682 conserved hypothetical protein from Caulobacter crescentus CB15
45% identity, 77% coverage
- Regulatory response to carbon starvation in Caulobacter crescentus
Britos, PloS one 2011 - “...protein NC 7.67 No No Yes CC_3473 Entericidin B homolog NC 2.57 Yes No Yes CC_1682 Transglycosylase associated protein S 2.57 Yes No Yes CC_0201 Outer membrane protein M 2.11 Yes Yes Yes CC_0428 Methyl-accepting chemotaxis protein N 2.82 Yes No No CC_0164 Chain length regulator...”
SCO4613 integral membrane protein from Streptomyces coelicolor A3(2)
44% identity, 89% coverage
- Defining the regulon of genes controlled by σE , a key regulator of the cell envelope stress response in Streptomyces coelicolor
Tran, Molecular microbiology 2019 - “...AGT AACC GGGGCGTACCGTTGACC CGTCT G 19 sco4582 Membrane protein GGC AACC CGACCGGAACCTGTGC CCTCC C 345 sco4613 Membrane protein CGC AACC ACCCGGCGCGGTCGGAA CGTCC T 88 sco4651 Putative lipoprotein AGA AACC ACAAGATCGTTCGAAC CGTTT C 105 sco4847 LMW PBP; cell wall biosynthesis CGC AACC CGATGACCCCGACGAC CGTCC C 271 sco4849...”
- “..., pkaA , sco3396 , mprF , sco4120 , sco4134 , sco4439 , sco4471 , sco4613 , sco4934 , sco5030 , sco5039 , sco5358 , sco5742 , sco7657 ) include 9 targets ( mreB , sco3396 , mprF , sco4134 , sco4471 , sco4934 , sco5030...”
IMX11_20860, IMX12_21360 GlsB/YeaQ/YmgE family stress response membrane protein from Streptomyces sp. Osf17
42% identity, 89% coverage
- Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara
Zerouki, BMC genomics 2021 - “...found in Babs14 (IMX12_04415, IMX12_08985, IMX12_18995, IMX12_21360) and in Osf17 (locus tag IMX11_03925, IMX11_08485, IMX11_18495, IMX11_20860). The alkaline shock Asp23/Gls24 family that envelope stress response was also predicted in Babs14 (locus tagIMX12_09080) and Osf17 (IMX11_08580), as well as 50S ribosomal protein L25/general stress protein Ctc in...”
- “...GlsB/YeaQ/YmgE family stress response related to the membrane was found in Babs14 (IMX12_04415, IMX12_08985, IMX12_18995, IMX12_21360) and in Osf17 (locus tag IMX11_03925, IMX11_08485, IMX11_18495, IMX11_20860). The alkaline shock Asp23/Gls24 family that envelope stress response was also predicted in Babs14 (locus tagIMX12_09080) and Osf17 (IMX11_08580), as well...”
BCAL2998 transglycosylase associated protein from Burkholderia cenocepacia J2315
48% identity, 96% coverage
G8E09_19180 GlsB/YeaQ/YmgE family stress response membrane protein from Acinetobacter pittii
37% identity, 94% coverage
- Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii
Zhang, Frontiers in microbiology 2020 - “...0.0012 0.0318 G8E09_12925 OprD family porin 1.73 0.0001 0.0064 G8E09_10340 Hypothetical protein 1.72 0.0001 0.0067 G8E09_19180 GlsB/YeaQ/YmgE family stress response membrane protein 1.71 0.0020 0.0463 G8E09_01795 Hemerythrin domain-containing protein 1.71 0.0008 0.0244 G8E09_12835 Heavy-metal-associated domain-containing protein -1.70 0.0002 0.0091 G8E09_07185 Hypothetical protein 1.67 0.0008 0.0229 G8E09_18175...”
ZMO1289 Transglycosylase-associated protein from Zymomonas mobilis subsp. mobilis ZM4
45% identity, 100% coverage
- The Magnesium Concentration in Yeast Extracts Is a Major Determinant Affecting Ethanol Fermentation Performance of Zymomonas mobilis
Li, Frontiers in bioengineering and biotechnology 2020 - “...stress protein CsbD 1.44 2.56 ZMO1521 Hypothetical protein 1.70 2.41 ZMO1237 Lactate dehydrogenase 1.70 2.19 ZMO1289 Putative transglycosylase-associated protein 2.06 3.23 ZMO1522 TonB-dependent receptor 2.75 3.88 Down-regulated gene in ZM4 cultured in RM OXOID compared with RM BD ZMO0934 Secretion-related protein 1.65 3.28 ZMO0374 Levansucrase 1.45...”
- “...DUF541 domain-containing protein 1.31 2.40 ZMO1754 Succinate-semialdehyde dehydrogenase SSADH 1.21 2.47 ZMO0918 Catalase 1.18 2.49 ZMO1289 Putative transglycosylase-associated protein 1.17 2.35 ZMO1776 Aminopeptidase N 1.17 2.86 ZMO1113 NADH dehydrogenase 1.15 2.47 ZMO0968 Hypothetical protein 1.09 2.37 ZMO0740 General stress protein CsbD 1.03 2.05 ZMO1285 Sorbitol dehydrogenase...”
HZ99_RS16790 GlsB/YeaQ/YmgE family stress response membrane protein from Pseudomonas canadensis
38% identity, 100% coverage
BP0987 putative membrane protein from Bordetella pertussis Tohama I
43% identity, 92% coverage
- The multifaceted RisA regulon of Bordetella pertussis
Coutte, Scientific reports 2016 - “..., while the remaining genes were not identified as BvgA/S-regulated genes. With the exception of bp0987 , the gene with the strongest decrease in transcript abundance in BPSMRisA (42 fold), all the other genes showed only a 5-fold decrease in transcript abundance ( Fig. 1B )....”
BCAM1775 putative transglycosylase associated protein from Burkholderia cenocepacia J2315
35% identity, 94% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory