PaperBLAST

PaperBLAST Hits for BWI76_RS23600 (76 a.a., MDKELLEAGY...)

Show query sequence

>BWI76_RS23600
MDKELLEAGYRAYTGEKIDVYFNTDICQHSGNCVRGSAKLFNLKRKPWIVPDEVDVATVV
KVIDTCPSGALKYRQK

Running BLASTp...

Found 10 similar proteins in the literature:

YjdI / b4126 PF06902 family protein YjdI from Escherichia coli K-12 substr. MG1655
yjdI / RF|NP_418550 uncharacterized protein yjdI from Escherichia coli K12 (see paper)
ECs5108 hypothetical protein from Escherichia coli O157:H7 str. Sakai
b4126 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
87% identity, 100% coverage

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...gadW 2.10 2 ECs4396 gadX 2.76 2 ECs4534 intL 2.50 2 ECs4673 atpC -2.24 1 ECs5108 yjdI 2.20 2 ECs5269 yjhT 3.09 2 Expression of LEE island genes upon entry to stationary phase Of the 41 LEE island ORFs, 23 had a significant ( p <...”
• Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains
  McGuire, BMC genomics 2023
  • “...b3779 guanosine-5'-triphosphate,3'-diphosphate phosphatase FS 387/494 cytR b3934 DNA-binding transcriptional repressor CytR FS 112/341 yjdI * b4126 PF06902 family protein YjdI FS 9/76 cutA * b4137 copper binding protein CutA T 106/112 dcuA * b4138 C4-dicarboxylate transporter DcuA FS 19/433 serB b4388 phosphoserine phosphatase FS 311/322 a...”
• Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
  Bonocora, PLoS genetics 2015
  • “...459 11.876 IS49 4342113 8 TG GG TATGGCTC TTGC T 4342109 + b4120 melB + b4126 yjdI 7753 8.401 IS50 4370368 2 TG GG TATCAAAG TTGC A 4370368 + b4143 groL + b4144 yjeI 464 7.795 IS51 4445887 1 CA GGC ACTGGAT TTGC T 4445887 +...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...b2672 b2809 b2856 b2857 b3099 b3170 b3184 b3260 b3512 b4068 b4126 b4127 Change in expression (fold) SdiA vs no SdiA SdiA1E11 vs SdiA 6.5 5.3 5.3 9.2 5.3 2.5...”
• Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
  Weber, Journal of bacteriology 2005
  • “...b2732 b2886 b2922 b3003 b3024 b3362 b3448 b3524 b4045 b4126 b4127 b4178 b4247 b4263 b4310 b1165 b1449 b1678 b1758 b1957 b1953 b2137 b3097 b3098 b3099 b3102...”
• 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
  • “...b3818 b3827 b3861 b3875 b3923 b3928 b3937 b3995 b4030 b4126 b4127 b4135 b4178 b4189 b4199 b4206 b4234 b4255 b4311 b4325 b4326 b2300 b2302 b2303 b2442 b2529...”
  • “...b3698 b3818 b3827 b3861 b3875 b3923 b3928 b3937 b3995 b4030 b4126 b4127 b4135 b4178 b4189 b4199 b4206 b4234 b4255 b4311 b4325 b4326 3.2 3.6 2.8 2.2 2.1 2.7 23.6...”

LMRG_02382 hypothetical protein from Listeria monocytogenes 10403S
64% identity, 99% coverage

• PrfA-like transcription factor gene lmo0753 contributes to L-rhamnose utilization in Listeria monocytogenes strains associated with human food-borne infections
  Salazar, Applied and environmental microbiology 2013
  • “...LMRG_01479 LMRG_01173 LMRG_01172 LMRG_00557 LMRG_02808 LMRG_02382 LMRG_02094 LMRG_02304 LMRG_00196 LMRG_01948 LMRG_02041 LMRG_00236 LMRG_02013 LMRG_00280...”
• Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
  Oliver, BMC genomics 2009
  • “...panel indicates the normalized RNA-Seq coverage represented by the horizontal line shown. Panel (A) depicts LMRG_02382 and LMRG_02383 (shown as blue bars), which form an operon (indicated by a long white bar) with a defined Rho-independent terminator (purple bar) downstream of LMRG_02383; the three positive frames...”

lmo0133 similar to E. coli YjdI protein from Listeria monocytogenes EGD-e
61% identity, 99% coverage

• Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella
  Lee, Applied and environmental microbiology 2019 (secret)
• Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
  Oliver, Applied and environmental microbiology 2010
  • “...February 11, 2017 by University of California, Berkeley lmo0133 lmo0134 lmo0169 lmo0170 lmo0210 lmo0211 Productb 4222 OLIVER ET AL. APPL. ENVIRON. MICROBIOL....”
• Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
  Oliver, BMC genomics 2009
  • “...a putative membrane-associated protein and a putative transcriptional regulator similar to PspC, respectively, and (iv) lmo0133 and lmo0134 (Figure 4A ), which encode proteins similar to E. coli YjdI and YjdJ, respectively. Figure 4 Examples of B -dependent transcripts identified by RNA-Seq . In each panel...”

LACR_0714 hypothetical protein from Lactococcus lactis subsp. cremoris SK11
53% identity, 81% coverage

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
  Dijkstra, PloS one 2016
  • “...4.4 LACR_E7 hypothetical protein positive 4.1 LACR_1450 fibronectin-binding protein positive 1.1 LACR_0073 esterase positive 10.0 LACR_0714 hypothetical protein positive 3.7 LACR_C16 replication initiator protein positive 3.3 LACR_0074 lactoylglutathione lyase related lyase positive 7.0 LACR_1221 hypothetical protein positive 2.1 LACR_0072 hypothetical protein positive 8.5 LACR_0920 copper-potassium transporting...”

Alvin_0680, YP_003442661 protein of unknown function DUF1271 from Allochromatium vinosum DSM 180
42% identity, 30% coverage

• A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
  Weissgerber, Applied and environmental microbiology 2014
  • “...University of California, Berkeley Alvin_0492 Alvin_0680 Alvin_1172 Alvin_1295 Alvin_1317 Alvin_1323 Alvin_1324 Alvin_1365 Alvin_1366 Alvin_1394 Alvin_1502...”
  • “...Among the remaining proteins listed in Table 1, Alvin_0680 exhibits features that point to a possible role in sulfur metabolism. The protein contains an...”
• Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
  Weissgerber, Journal of bacteriology 2013
  • “...Alvin_0316 Alvin_0345 Alvin_0476 Alvin_0492 Alvin_0562 Alvin_0680 Alvin_0750 Alvin_0804 Alvin_0805 Alvin_0961 Alvin_0962 Alvin_1188 Alvin_1196 Alvin_1197...”
• Structure and molecular evolution of CDGSH iron-sulfur domains
  Lin, PloS one 2011
  • “...CISD in subtypes DCC and CDC. Ppac: Plesiocystis pacifica , ZP_01908188; Avin: Allochromatium vinosum , YP_003442661; Mbur: Methanococcoides burtonii , YP_566882; Jann: Jannaschia sp. CCS1 , YP_509212; Flav: Flavobacteriales bacterium , ZP_02182054; Rbif: Robiginitalea biformata , YP_003195727. (D) Alignment of type 3 CISDs. Pcal: Pyrobaculum calidifontis...”

YP_566882 protein of unknown function DUF1271 from Methanococcoides burtonii DSM 6242
36% identity, 30% coverage

• Structure and molecular evolution of CDGSH iron-sulfur domains
  Lin, PloS one 2011
  • “...CDC. Ppac: Plesiocystis pacifica , ZP_01908188; Avin: Allochromatium vinosum , YP_003442661; Mbur: Methanococcoides burtonii , YP_566882; Jann: Jannaschia sp. CCS1 , YP_509212; Flav: Flavobacteriales bacterium , ZP_02182054; Rbif: Robiginitalea biformata , YP_003195727. (D) Alignment of type 3 CISDs. Pcal: Pyrobaculum calidifontis , YP_001056297; Aper: Aeropyrum pernix...”

YP_509212 protein of unknown function DUF1271 from Jannaschia sp. CCS1
38% identity, 26% coverage

• Structure and molecular evolution of CDGSH iron-sulfur domains
  Lin, PloS one 2011
  • “...Avin: Allochromatium vinosum , YP_003442661; Mbur: Methanococcoides burtonii , YP_566882; Jann: Jannaschia sp. CCS1 , YP_509212; Flav: Flavobacteriales bacterium , ZP_02182054; Rbif: Robiginitalea biformata , YP_003195727. (D) Alignment of type 3 CISDs. Pcal: Pyrobaculum calidifontis , YP_001056297; Aper: Aeropyrum pernix , NP_148024; Tvol: Thermoplasma volcanium ,...”

ZP_01908188 hypothetical protein from Plesiocystis pacifica SIR-1
40% identity, 29% coverage

• Structure and molecular evolution of CDGSH iron-sulfur domains
  Lin, PloS one 2011
  • “...indicate the first and second CISD in subtypes DCC and CDC. Ppac: Plesiocystis pacifica , ZP_01908188; Avin: Allochromatium vinosum , YP_003442661; Mbur: Methanococcoides burtonii , YP_566882; Jann: Jannaschia sp. CCS1 , YP_509212; Flav: Flavobacteriales bacterium , ZP_02182054; Rbif: Robiginitalea biformata , YP_003195727. (D) Alignment of type...”

ZP_02182054 hypothetical protein from Flavobacteriales bacterium ALC-1
33% identity, 45% coverage

• Structure and molecular evolution of CDGSH iron-sulfur domains
  Lin, PloS one 2011
  • “...Mbur: Methanococcoides burtonii , YP_566882; Jann: Jannaschia sp. CCS1 , YP_509212; Flav: Flavobacteriales bacterium , ZP_02182054; Rbif: Robiginitalea biformata , YP_003195727. (D) Alignment of type 3 CISDs. Pcal: Pyrobaculum calidifontis , YP_001056297; Aper: Aeropyrum pernix , NP_148024; Tvol: Thermoplasma volcanium , NP_110689; Cmaq: Caldivirga maquilingensis ,...”

YP_003195727 hypothetical protein from Robiginitalea biformata HTCC2501
35% identity, 46% coverage

• Structure and molecular evolution of CDGSH iron-sulfur domains
  Lin, PloS one 2011
  • “...Jann: Jannaschia sp. CCS1 , YP_509212; Flav: Flavobacteriales bacterium , ZP_02182054; Rbif: Robiginitalea biformata , YP_003195727. (D) Alignment of type 3 CISDs. Pcal: Pyrobaculum calidifontis , YP_001056297; Aper: Aeropyrum pernix , NP_148024; Tvol: Thermoplasma volcanium , NP_110689; Cmaq: Caldivirga maquilingensis , YP_001540894; Hwal: Haloquadratum walsbyi ,...”

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Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.