PaperBLAST

PaperBLAST Hits for NIAGMN_24555 (71 a.a., MYQMEKITTG...)

Show query sequence

>NIAGMN_24555
MYQMEKITTGVSYTTSAVGTGYWLLQLLDKVSPSQWVAIGVLGSLLFGLLTYLTNLYFKI
REDRRKAARGE

Running BLASTp...

Found 11 similar proteins in the literature:

Z3106 putative holin protein of prophage CP-933U from Escherichia coli O157:H7 EDL933
99% identity, 68% coverage

• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z0984, Z1484a Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371, Z3104, Z3339, Z6051 Z1352, Z1469, Z1796,a...”

Z1794 putative holin protein from Escherichia coli O157:H7 EDL933
97% identity, 68% coverage

• Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933
  Dong, BMC genomics 2009
  • “...45 Unknown (bacteriophage BP-933W) Z1503 8.0 0.5 10.2 0.5 -4 O-Island 45 Unknown (bacteriophage BP-933W) Z1794 5.6 0.3 6.8 0.3 -2 O-Island 50 Putative holin protein Z1878 13.0 0.2 14.7 0.1 -3 O-Island 52 Putative Bor protein Z2146 5.8 0.2 7.0 0.1 -2 O-Island 57 Putative...”
• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z1484a Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371, Z3104, Z3339, Z6051 Z1352, Z1469, Z1796,a Z6051,...”

Z3340 putative lysis protein S of prophage CP-933V from Escherichia coli O157:H7 EDL933
94% identity, 79% coverage

• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z3073, Z3306,a Z6026 Z0984, Z1484a Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371, Z3104, Z3339, Z6051 Z1352,...”

Z1468 putative lysis protein S of bacteriophage BP-933W from Escherichia coli O157:H7 EDL933
94% identity, 100% coverage

• Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence
  Bansal, FEMS immunology and medical microbiology 2012
  • “...* 1.7 * 1760248_s_at Z1467 1.5 * 1.7 * 1761222_s_at Z1469 1.4 1.9 * 1767360_s_at Z1468 1.3 1.5 * Fimbrial and Flagellar Genes 1766324_s_at sfmH 1.6 * 1.6 * Fimbrial assembly protein 1763064_s_at sfmD 1.7 * 1.1 Putative outer membrane protein 1766811_s_at sfmC 1.9 * 1.2...”
• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z1484,a Z2148, Z3073, Z3306,a Z6026 Z0984, Z1484a Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371, Z3104,...”

Z2374 putative holin protein of prophage CP-933R from Escherichia coli O157:H7 EDL933
100% identity, 96% coverage

• Complex effects of the exo-xis region of the Shiga toxin-converting bacteriophage Φ24_B genome on the phage development and the Escherichia coli host physiology
  Bloch, Journal of applied genetics 2024
  • “...bacteriophage Z1874 Putative antiterminator Q +0.997 1.9E02 Z1878 Putative Bor protein 0.585 2.0E02 CP-933R bacteriophage Z2374 Putative holin protein of prophage 0.560 2.3E02 CP-933V bacteriophage Z3356 Putative DNA replication protein O +2.490 7.3E03 Z3366 Putative recombination protein Bet +1.157 1.2E04 Z3367 Putative exonuclease +2.062 4.3E06 CP-933P...”

Z1350 putative holin protein of cryptic prophage CP-933M from Escherichia coli O157:H7 EDL933
Z2069 putative holin protein of prophage CP-933O from Escherichia coli O157:H7 EDL933
Z6053 putative holin protein encoded by cryptic prophage CP-933P from Escherichia coli O157:H7 EDL933
99% identity, 96% coverage

• Engineering Escherichia coli for succinate production from hemicellulose via consolidated bioprocessing
  Zheng, Microbial cell factories 2012
  • “...4 5.10 0.03 0.08 0.01 0.21 0.01 1098 28 13.22 1.05 7.3 0.2 88 7 Z1350 E 3 , X 5 3.97 0.09 0.22 0 0.51 0.04 1512 2 6.88 0 10.9 0.5 49 1 Z1360 E 3 , X 6 4.93 0.10 0.08 0 0.25...”
  • “...about 8 h for the three strains. Strains expressed other enzyme combinations including Z1170 and Z1350 were also tested. When the expression of xylanases reduced, the performance of the two strains were not as good as predicted. For strain Z1170, the maximum OD 600 was restored...”
• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z1383, Z1484,a Z2148, Z3073, Z3306,a Z6026 Z0984, Z1484a Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371,...”
• Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC)
  Michelacci, Frontiers in microbiology 2016
  • “...Z2060 ATGCGGAGCTGCAGAGTGAA 18655161865652 137 TTCTGCCGGTTTTTCGCACG Z2065 CACAGCAACCTGCGCTTGTT 18673691867445 77 TGGCACTGCGCGTTAAACAC Z2066 TTACGGTGCGGCATCGAGAA 18676591867735 77 TGCGCGCCCATGAACTGAAA Z2069 TGTCATACACCACGTCAGCGGT 18689621869084 123 ATGTCAGCAGCCCAAACAGCA Z2071 TTCTGGCGCTGATTGGTGCA 18695831869674 92 ACGGTATGCTGTGGTGTGGT Z2073 ATGCTCTCAGCCATCGCGTT 18712701871454 185 ACATTCGTGCTGGATGCGCT Z2082 AACGCCATCGAGTCGCTGAA 18781291878228 100 TTGCCAGCCACACGACCTTT Z2084 ATGGTTGGGGCAAACTCGCTT 18788301878951 122 AACCAGATGGGCCATGCAGA Z2085 TCTTCGCCGTTGACGTTGGT 18802181880319 102 AAAAGGCGGGGAAGATGGCA Z2086...”
  • “...in more than 95% of the strains tested, while genes Z2037, Z2039, Z2056, Z2057, Z2060, Z2069, Z2071, Z2084, Z2086, Z2096, Z2118, Z2131, and Z2146, were positive in more than 50% of the population assayed. As a whole, a mean of 15.9 targets out of the 41...”
• Genomic instability in regions adjacent to a highly conserved pch prophage in Escherichia coli O157:H7 generates diversity in expression patterns of the LEE pathogenicity island
  Yang, Journal of bacteriology 2009
  • “...hit No hit No hit No hit Z0165 (hemL) Z0268 to Z2069 (open reading frames in Rhs element) Z0318 (pinH from CP-933H); same as RDOBGS 7 Z196 to Z1204 (perC-like...”
• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z3306,a Z6026 Z0984, Z1484a Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371, Z3104, Z3339, Z6051 Z1352, Z1469,...”
• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371, Z3104, Z3339, Z6051 Z1352, Z1469, Z1796,a Z6051, Z2120,...”

TC 1.E.1.1.3 / O48430 Holin (see 2 papers)
99% identity, 96% coverage

• substrates: endolysin, small molecules

Z2122 putative holin protein of prophage CP-933O from Escherichia coli O157:H7 EDL933
97% identity, 96% coverage

• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...Z6026 Z0984, Z1484a Z1350, Z1468, Z2374,a Z3340, Z2069, Z2122, Z3106, Z1794, Z6053 Z1352, Z1469, Z1796,a Z2120, Z2371, Z3104, Z3339, Z6051 Z1352, Z1469, Z1796,a...”

EssD / b0554 DLP12 prophage; putative phage lysis protein from Escherichia coli K-12 substr. MG1655 (see 4 papers)
b0554 DLP12 prophage; predicted phage lysis protein from Escherichia coli str. K-12 substr. MG1655
c1561 Lysis protein S homolog from lambdoid prophage DLP12 from Escherichia coli CFT073
79% identity, 100% coverage

• Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment
  Tucker, BMC microbiology 2007
  • “...lysis emrE b0543 yes -2.02 0.0001 multidrug resistance pump, methylviologen resistance inner mem. orthologue essD b0554 yes -2.57 0.0001 orf, phage lambda S lysis protein homolog mem. lysis ybcS b0555 yes -2.19 0.0001 orf, bacteriophage lambda lysozyme homolog wall lysis orthologue rzpD b0556 yes -2.41 0.0001...”
• Genome-wide localization of mobile elements: experimental, statistical and biological considerations
  Martinez-Vaz, BMC genomics 2005
  • “...tra8_1, ykfC, yi52_1 , ykfD, yagD, insB_2 2. b0546, b0547, b0548, b0550, b0551, yi52_2 , b0554, b0555, b0556 3. gltL, gltK, gltJ, ybeJ, yi52_3 , b0658 4. b1328, b1329, b1330, yi52_4, b1332, fnr 5. b1361, b1362, trkG, b1368, yi52_5, b1371, b1372, b1374 6. motB, motA, flhC,...”
• The aquaporin water channels
  Agre, Proceedings of the American Thoracic Society 2006

YdfS / b1556 Qin prophage; putative prophage lysis protein EssQ from Escherichia coli K-12 substr. MG1655 (see paper)
TC 1.E.1.1.2 / P77237 Lysis protein S from Escherichia coli (see 3 papers)
b1556 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
79% identity, 100% coverage

• substrates: endolysin, small molecules
  tcdb comment: Identical to EssD, a holin from lambdoid prophage DLP12 with two TMSs (Srividhya and Krishnaswamy 2007)
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013

HOLIN_BPP21 / P27360 Antiholin from Enterobacteria phage P21 (Bacteriophage 21) (Bacteriophage P21) (see 5 papers)
TC 1.E.1.1.1 / P27360 Lysis protein S; also called ''pinholin''; forms small heptameric pores that depolarize the membrane (see paper)
76% identity, 100% coverage

• function: [Isoform Holin]: Accumulates harmlessly in the cytoplasmic membrane until it reaches a critical concentration that triggers the formation of nanometer-scale pores (pinholes) causing host cell membrane depolarization and endolysin refolding and release into the periplasmic space (PubMed:17827300, PubMed:19861547, PubMed:23671069). Once the pinholin has permeabilized the host cell membrane, the SAR- endolysin is released into the periplasm and breaks down the peptidoglycan layer (PubMed:17827300, PubMed:19861547). Determines the precise timing of host cell lysis (PubMed:23671069). Participates with the SAR-endolysin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles from the host cell (Probable) (PubMed:17827300).
  function: [Isoform Antiholin]: Counteracts the aggregation of the holin molecules and thus of pore formation.
  subunit: [Isoform Holin]: Homoheptamer; forms small heptameric channels of about 2 nm (pinholes) (PubMed:19861547). Interacts with isoform Antiholin; this interaction blocks the holin homomultimerization and delays host cell lysis (Probable).
• substrates: endolysin, small molecules
  tcdb comment: This holin is of topological Class II, forming 2 TMSs, with the N- and C-termini inside (Park et al. 2006). TMS1 partially externalizes from the lipid bilayer and interacts with the membrane surface, whereas TMS2 remains buried in the lipid bilayer in the active conformation (Ahammad et al. 2019)

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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.