PaperBLAST

PaperBLAST Hits for GFF1810 (49 a.a., MSFVDVQALK...)

Show query sequence

>GFF1810
MSFVDVQALKDNHATGIVQLNQHNLQVIIGPQVQSVKDEMVGLMNTVQA

Running BLASTp...

Found 3 similar proteins in the literature:

c2013 bifunctional maltose and glucose-specific PTS system components IICB from Escherichia coli CFT073
84% identity, 9% coverage

• The Saccharomyces cerevisiae TAN1 gene is required for N4-acetylcytidine formation in tRNA
  Johansson, RNA (New York, N.Y.) 2004
  • “...Bystrom 2002) into the SalI/ NruI sites of plasmid c2013 (Cvrckova and Nasmyth 1993), removing the spADHCLN2 construct. The TRP1 variant of the ADE3 sup61+...”
• Dual function of the tRNA(m(5)U54)methyltransferase in tRNA maturation
  Johansson, RNA (New York, N.Y.) 2002
  • “...by replacing the Sal I spADH::CLN2 fragment in plasmid c2013 (Cvrckova & Nasmyth, 1993) with a Sal I RHO4-TRM2 fragment from pMJ1342 that is pRS316-RHO4-TRM2...”
• Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus
  Watanabe, American journal of human genetics 1996 (secret)

MalX / b1621 PTS enzyme IIBC component MalX from Escherichia coli K-12 substr. MG1655 (see 5 papers)
MalX / P19642 PTS enzyme IIBC component MalX from Escherichia coli (strain K12) (see 4 papers)
PTOCB_ECOLI / P19642 PTS system maltose-specific EIICB component; EC 2.7.1.208 from Escherichia coli (strain K12) (see 2 papers)
TC 4.A.1.1.3 / P19642 Maltose porter (MalX) from Escherichia coli (see 6 papers)
malX / RF|NP_416138.1 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 from Escherichia coli K12 (see paper)
NP_416138 PTS enzyme IIBC component MalX from Escherichia coli str. K-12 substr. MG1655
b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component from Escherichia coli str. K-12 substr. MG1655
84% identity, 9% coverage

• function: The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. This system is involved in maltose transport. MalX can also recognize and transport glucose even though this sugar may not represent the natural substrate of the system.
  catalytic activity: D-maltose(out) + N(pros)-phospho-L-histidyl-[protein] = alpha- maltose 6'-phosphate(in) + L-histidyl-[protein] (RHEA:49300)
• substrates: Maltose
• A phosphoenolpyruvate-dependent phosphotransferase system is the principal maltose transporter in Streptococcus mutans
  Webb, Journal of bacteriology 2007
  • “...coli PtsG (NP_415619); ecMalX, E. coli MalX (P19642); efMalT, Enterococcus faecalis MalT (NP_814695); SMU.2047 PtsG/MalT, S. mutans PtsG/MalT (NP_722340);...”
• Genomic analysis of a pathogenicity island in uropathogenic Escherichia coli CFT073: distribution of homologous sequences among isolates from patients with pyelonephritis, cystitis, and Catheter-associated bacteriuria and from fecal samples
  Guyer, Infection and immunity 1998
  • “...glucosespecific IIabc component sacpa operon antiterminator 7.1e2100 3.5e2155 U65013 P19642 2.6e253 P26212 R1 f447 C C C C C C C 58724-57843 C 60267-58885 C...”
• Pathogenicity island sequences of pyelonephritogenic Escherichia coli CFT073 are associated with virulent uropathogenic strains
  Kao, Infection and immunity 1997
  • “...numbers for homologs are as follows: 1, P26212; 2, P19642. Probe 5/684-707, a 2.1-kb PCR product amplified from a region of 0.8 kb inside the right junction,...”
• Transcription initiation in the Escherichia coli K-12 malI-malX intergenic region and the role of the cyclic AMP receptor protein.
  Lloyd, FEMS microbiology letters 2008 (PubMed)
  • GeneRIF: Expression from the malX promoter is dependent on binding of the cyclic AMP receptor protein (CRP) to a DNA site centred 41.5 bp upstream of the transcript start.
• FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization
  Hassani, Microbial cell factories 2024
  • “...b3946, b3916, b1723 Triple ACKr, GLCpts, PYK 0.56 54.88 b2296, b3115, b1849, b1819, b2415, b2416, b1621, b1101, b2417, b1817, b1818, b1854, b1676 DHAPT, GART, PPAKr Quadruple ACKr, ARGDC, GLCpts, PYK 0.56 64.72 b2296, b3115, b1849, b2938, b4117, b1819, b2415, b2416, b1621, b1101, b2417, b1817, b1818, b1854,...”
• Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
  Bonocora, PLoS genetics 2015
  • “...2593 10.373 IA13 1693966 2 C TGGC ACAGCAA TTGC C 1693959 + b1617 uidA - b1621 malX 3401 11.352 IA14 1724329 2 C TGG TTCAGTGT TTGC T 1724326 - b1649 nemR + b1648 ydhL 363 8.27 IA15 1781364 6 GC GGC ACGGAAAC TGC A 1781359 -...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
  Polen, Applied and environmental microbiology 2003
  • “...1.25* 1.16 1.32 2.08* 2.16* 1.72* 0.82 1.15* 0.95 b1621 b1622 malX malY 2 2 PTS, maltose- and glucose-specific enzyme II Enzyme that may degrade or block...”

EAE_18025 maltose/glucose-specific PTS transporter subunit IIBC from Klebsiella aerogenes KCTC 2190
78% identity, 9% coverage

• Transcriptional effects of melatonin on the gut commensal bacterium Klebsiella aerogenes
  Graniczkowska, Genomics 2022
  • “...ID Product Description Growth stage fold change EAE_06200 MtlA mannitol transporter IIBC component exponential 1.835 EAE_18025 MalX maltose transporter exponential 1.788 EAE_03850 DhaK dihydroxyacetone kinase subunit exponential 2.633 EAE_03855 DhaL dihydroxyacetone kinase subunit exponential 2.292 EAE_10515 CelB lactose/cellobiose-specific enzyme IIC stationary 1.330 EAE_09655 MtlA2 transcriptional regulator/PTS...”

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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.