PaperBLAST

PaperBLAST Hits for BWI76_RS17950 (47 a.a., MKKLRWVLLT...)

Show query sequence

>BWI76_RS17950
MKKLRWVLLTVIIAGCLLLWTQMLNVMCDQDVQFFSGICTINKFIPW

Running BLASTp...

Found 4 similar proteins in the literature:

MAKP3_17680 PhoP/PhoQ regulator MgrB from Klebsiella pneumoniae
B5XQ45 PhoP/PhoQ regulator MgrB from Klebsiella pneumoniae (strain 342)
KP1_3468 hypothetical protein from Klebsiella pneumoniae NTUH-K2044
98% identity, 100% coverage

• Stepwise Evolution of a Klebsiella pneumoniae Clone within a Host Leading to Increased Multidrug Resistance
  Yoshino, mSphere 2021
  • “...regulator KdgR (MAKP3_17660) Ins (IS Ecp1 ) Del (6,792bp) Hypothetical protein (MAKP3_17670) Del (6,792bp) MgrB (MAKP3_17680) Del (6,792bp) Hypothetical protein (MAKP3_17690) Del (6,792bp) Cold shock-like protein CspC (MAKP3_17700) Del (6,792bp) Cell division protein FtsI (MAKP3_17710) Del (6,792bp) 23S rRNA [guanine(745)-N(1)]-methyltransferase (MAKP3_17720) Del (6,792bp) Putative manganese efflux...”
• Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes
  Gomes, Scientific reports 2023
  • “...for genomic regions similar to K. pneumoniae strain 342's mgr B-coding protein (SwissProt registry number B5XQ45) with BLAST version 2.9.0+< https://ftp.ncbi.nlm.nih.gov/blast/executables/blast + > 103 , with the following command-lines and parameters: makeblastdb -in 'scaffolds_fasta_file' -dbtype nucl -out 'database_name' ; tblastn -outfmt 4 -query'mgrb-gene_fasta_file' -db 'database_name' -out...”
• Comparative genomic analyses of Polymyxin-resistant Enterobacteriaceae strains from China
  He, BMC genomics 2022
  • “...Uniprot ID: P37661 Uniprot ID: P37661 mcr-like genes mcr-1.1 mcr-1.1 None mcr-8 mgrB Uniprot ID: B5XQ45 Uniprot ID: P64512 Uniprot ID: B5XQ45, IS 903 is inserted upstream Uniprot ID: B5XQ45 opgE Uniprot ID: P75785 Uniprot ID: P75785*2 Uniprot ID: P75785 Uniprot ID: P75785 phoP Uniprot ID:...”
• Identification of Genetic Alterations Associated with Acquired Colistin Resistance in Klebsiella pneumoniae Isogenic Strains by Whole-Genome Sequencing
  Choi, Antibiotics (Basel, Switzerland) 2020
  • “...alterations were identified in five pairs of isogenic K. pneumoniae strains. Genetic alterations related to KP1_3468 , including the insertion of an IS 5 -like element in an intergenic or coding region and amino acid substitutions, were identified in three separate derivative strains. Amino acid substitutions...”
  • “...inserted between KPN_02065 and KPN_02066. In B0704-039R1, an IS 5 -like element was inserted between KP1_3468 and KP1_3469. Alterations in KP1_3468 were also seen in B0704-039R2, a colistin-resistant strain derived from the same parent strain as B0704-039R1. However, these changes were in the coding region. Specifically,...”

MGRB_SALT1 / D0ZK39 PhoP/PhoQ regulator MgrB from Salmonella typhimurium (strain 14028s / SGSC 2262) (see paper)
t1038 putative membrane protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
72% identity, 100% coverage

• function: PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing. MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway (Probable). Represses PhoP/PhoQ signaling, possibly by binding to the periplasmic domain of PhoQ, altering its activity and that of downstream effector PhoP.
  subunit: May form homooligomers. Probably interacts with the periplasmic domain of PhoQ (Probable).
• Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium
  Wong, PloS one 2013
  • “...ATP synthase SpaI I -1.46E+00 2.23E-02 pipB t1830 hypothetical protein t1830 I -1.54E+00 2.61E-02 - t1038 hypothetical protein t1038 II 1.03E+00 4.21E-02 yiiD t3592 Acetyltransferase IV -8.89E-01 4.21E-02 ppc t3505 phosphoenolpyruvate carboxylase VII -1.25E+00 4.21E-02 Nth t1321 endonuclease III VI 1.26E+00 4.21E-02 - t3408 hypothetical protein...”
  • “...encodes endonuclease III involved in the DNA repair system [ 60 , 61 ] and t1038 , which encodes an unknown hypothetical protein. The differential expression of several genes, including cstA1 , t4581 , t4580 , spaM , spaN , spaI and sopE , were validated...”

YobG / b1826 PhoQ kinase inhibitor from Escherichia coli K-12 substr. MG1655 (see 14 papers)
MGRB_ECOLI / P64512 PhoP/PhoQ regulator MgrB from Escherichia coli (strain K12) (see 7 papers)
S1515 hypothetical protein from Shigella flexneri 2a str. 2457T
NP_416340 PhoQ kinase inhibitor from Escherichia coli str. K-12 substr. MG1655
b1826 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
SF1400 orf, conserved hypothetical protein from Shigella flexneri 2a str. 301
Z2872 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs2536 hypothetical protein from Escherichia coli O157:H7 str. Sakai
72% identity, 100% coverage

• function: Represses PhoP/PhoQ signaling, possibly by binding to the periplasmic domain of PhoQ, altering its activity and that of downstream effector PhoP. PhoP-regulated transcription is redox- sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway; the 2 periplasmic Cys residues of MgrB are required for its action on PhoQ, and thus PhoP.
  subunit: May form homooligomers. Probably interacts with the periplasmic domain of PhoQ.
  disruption phenotype: Induction of genes regulated by PhoP, not suppressed by a dsbA deletion or 50 uM CuSO(4).
• A One-Pot Convenient RPA-CRISPR-Based Assay for Salmonella enterica Serovar Indiana Detection
  Gong, Microorganisms 2024
  • “...of Industrial Culture Collection). The origins of strains used in this study (S1105, S1467, and S1515) were recovered from aquatic product, broiler, and duck, and the detailed information can be found in our previous publication [ 22 ]. These strains were archived at 80 C in...”
  • “...19 Salmonella Typhimurium ATCC14028 20 Salmonella Indiana S1467 21 Salmonella Derby CMCC50112 22 Salmonella Indiana S1515 Non- Salmonella strains 1 Proteus vulgaris CMCC49027 2 Escherichia coli ATCC25922 3 Klebsiella pneumoniae CMCC46117 4 Shigella sonnei CMCC51592 5 Enterococcus faecium ATCC35667 6 Staphylococcus aureus ATCC25923 7 Bacillus cereus...”
• MgrB affects the acid stress response of Escherichia coli by modulating the expression of iraM.
  Xu, FEMS microbiology letters 2019 (PubMed)
  • GeneRIF: data suggest that MgrB affects the acid resistance of E. coli by modulating the expression of iraM, but not completely through PhoP/Q.
• Pervasive gene deregulation underlies adaptation and maladaptation in trimethoprim-resistant E. coli
  Vinchhi, mBio 2023
  • “...against the proteome of the query organism (amino acid similarity with wild-type E. coli MgrB-Uniprot: P64512 and PhoQ-Uniprot: P23837). A positive hit in at least one of the above searches was taken to mean that PhoQ/MgrB was present in the query organism. Gene expression analysis Transcriptome...”
• Comparative genomic analyses of Polymyxin-resistant Enterobacteriaceae strains from China
  He, BMC genomics 2022
  • “...Uniprot ID: P37661 mcr-like genes mcr-1.1 mcr-1.1 None mcr-8 mgrB Uniprot ID: B5XQ45 Uniprot ID: P64512 Uniprot ID: B5XQ45, IS 903 is inserted upstream Uniprot ID: B5XQ45 opgE Uniprot ID: P75785 Uniprot ID: P75785*2 Uniprot ID: P75785 Uniprot ID: P75785 phoP Uniprot ID: P13792; Uniprot ID:...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim
  Sangurdekar, BMC genomics 2011
  • “...with MoaD ybhN b0788 Function unknown yliE b0833 Function unknown ymfQ b1153 Function unknown yobG b1826 Function unknown yecN b1869 Function unknown crr b2417 Phosphocarrier protein for glucose of the PTS; Enzyme IIA(Glc); formerly EIII(glc) recJ b2892 Single-stranded DNA-specific exonuclease, 5'-3' ygjT b3088 Function unknown; induced...”
• Escherichia coli gene expression responsive to levels of the response regulator EvgA
  Masuda, Journal of bacteriology 2002
  • “...protein, cryptic ynaI gadC gadB ydeO ydeP rstA yobG yegZ b1826 b2083 b2084 b2085 b2368 b2369 yegR emrK evgA b2371 b2372 b2373 b2374 b2375 b3238 b3491 b3506 yfdE...”
• mRNA expression profiles for Escherichia coli ingested by normal and phagocyte oxidase-deficient human neutrophils
  Staudinger, The Journal of clinical investigation 2002
  • “...abundance after 7 minutes of phagocytosis cpxA stress response), b1826 (mgrB, magnesium limi- was ahpCF: 5.4; dps: 8.8; katG: 4.4; and trxC: 23 (n = 1)....”
  • “...trpE b1264 2.2 0.03 N2 ppiA b3363 2.1 0.009 hemH b3095 b1826 napA yqjF glpF b1171 htpX apaG cspD trxB yejO b0475 b3095 b1826 b2206 b3101 b3927 b1171 b1829 b0050...”
• Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli
  Reitzer, Microbiology and molecular biology reviews : MMBR 2001
  • “...secE, mog, ybiH, b0836, ymdD, dnaA, sapABCDF, slyA, b1826, sanA, yjdE, intB, hyaABCDEF, yhcL, yjhA, b2444-2445, tktA, bglX, yafW, dsbB, yfjZ-ypjF, yicK, panD,...”
• Virulence and Stress Responses of Shigella flexneri Regulated by PhoP/PhoQ
  Lin, Frontiers in microbiology 2017
  • “...ND Chromosome Putative L-serine deaminase FUNCTION UNKNOWN yrbL 0.02 <0.0001 0.07 0.01 Chromosome Hypothetical protein SF1400 0.04 0.0005 0.21 0.04 Chromosome Hypothetical protein ycgW 0.09 <0.0001 ND Chromosome Hypothetical protein SF2261 0.17 0.0051 0.04 0.01 Chromosome Hypothetical protein SF1401 0.34 0.0034 ND Chromosome Hypothetical protein ygaM...”
• Bacterial MgrB peptide activates chemoreceptor Fpr3 in mouse accessory olfactory system and drives avoidance behaviour
  Bufe, Nature communications 2019
  • “...International). MgrB expression in bacteria A sequence containing the E. coli EDL933 mgrB gene (Genbank Z2872) fused to a C-terminal His-6 tag (Supplementary Fig. 1d ) was designed, synthesised (Eurofins), and subcloned into the XbaI and XhoI restriction sites of pBluescript KS(-) to obtain plasmid p...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs2289 ECs2292 ECs2303 ECs2392 ECs2449 ECs2505 ECs2506 ECs2536 ECs2544 ECs2558 ECs2581 ECs2614 ECs2622 ECs2623 ECs2692 ECs2714 ECs2737 ECs2758 ECs2759 ECs2987...”

UTI89_C2026 low magnesium induced hypothetical protein from Escherichia coli UTI89
70% identity, 100% coverage

• Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
  García, Microbial genomics 2021
  • “...dehydrogenase Purine metabolism (F) 2.11 UTI89_C1543 topA DNA topoisomerase 1 DNA topological change (L) 2.11 UTI89_C2026 mgrB PhoP/PhoQ regulator MgrB Transcription regulation/response to Mg2 +ion (S) 2.05 UTI89_C0736 tolB Tol-Pal system protein TolB Protein transport/cell cycle, cell division (U) 2.03 UTI89_C2053 eda KHG/KDPG aldolase Carbohydrate metabolism...”

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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.