PaperBLAST

PaperBLAST Hits for SM_b20031 (82 a.a., MVDVIKGEIL...)

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>SM_b20031
MVDVIKGEILRKGRVTEPYSKDGHWRDPRPRLAAADGQIVITDPRHSLIRVIDAETLKET
RTIPIDGQPFAIVAVGGSGASH

Running BLASTp...

Found 5 similar proteins in the literature:

AZTD_CITK8 / A8AF35 Zinc chaperone AztD from Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (see paper)
60% identity, 19% coverage

• function: Acts as a zinc chaperone in the AztABCD zinc transport system (By similarity). Directly transfers one zinc cation to the solute binding protein AztC; the transfer occurs without the formation of a stable interaction (By similarity). Binds 3 Zn(2+), two with high affinity and one with low affinity, and transfers only Zn(2+) bound to site 2 to AztC (PubMed:31428696).
  subunit: Monomer.

6cmkA / A8AF35 Crystal structure of citrobacter koseri aztd (see paper)
60% identity, 22% coverage

• Ligand: zinc ion (6cmkA)

AZTD_PARDP / A1B2F4 Zinc chaperone AztD from Paracoccus denitrificans (strain Pd 1222) (see 4 papers)
WP_011747897 zinc metallochaperone AztD from Paracoccus denitrificans
52% identity, 20% coverage

• function: Acts as a zinc chaperone in the AztABCD zinc transport system (PubMed:26468286, PubMed:30353723, PubMed:31428696, PubMed:32781785). Directly transfers one zinc cation to the solute binding protein AztC; the transfer occurs without the formation of a stable interaction (PubMed:26468286, PubMed:31428696, PubMed:32781785). Binds 3 Zn(2+), two with high affinity and one with low affinity, and transfers only Zn(2+) bound to site 2 to AztC (PubMed:26468286, PubMed:31428696). Likely functions to store zinc in the periplasm and may be important for zinc accumulation in zinc-limited environments (PubMed:32781785).
  subunit: Monomer.
  disruption phenotype: No effect on growth and no effect on zinc cellular level in zinc repleted media (PubMed:30353723). In zinc limited media, growth is reduced in a znuA mutant background and also in an aztC mutant background (PubMed:30353723). In zinc depleted media, zinc cellular levels are reduced and levels are further reduced in a znuA mutant background, an aztC mutant background or a znuA and aztC mutant background (PubMed:30353723).
• Two ABC Transporters and a Periplasmic Metallochaperone Participate in Zinc Acquisition in Paracoccus denitrificans.
  Neupane, Biochemistry 2019
  • GeneRIF: ZnuA can bind as many as 5 zinc ions with a high affinity.ZnuA does not interact with AztD.[ZnuA] AztD cannot support transport of zinc into the cytoplasm, it likely functions to store zinc in the periplasm for transfer through the AztABCD system.
• Two ABC Transporters and a Periplasmic Metallochaperone Participate in Zinc Acquisition in Paracoccus denitrificans
  Neupane, Biochemistry 2019
  • “...39 , 41 43 Second, the aztABCD operon encodes a novel metallochaperone AztD (UniProt KB A1B2F4), which we have shown to stoichiometrically transfer zinc to the SBP AztC 44 ( Figure 1 ). This process requires the presence of the AztC flexible loop and its three...”
• Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins
  Neupane, Communications biology 2019
  • “...transfer. Methods Phylogenetic analysis of AztD The protein sequence of Pd AztD (UniProtKB accession number A1B2F4) was used to perform a BLAST search of the UniProtKB database 53 . Sequences were filtered to include only those with E values below 10 20 . These sequences were...”

6ck1A / A1B2F4 Crystal structure of paracoccus denitrificans aztd (see paper)
52% identity, 22% coverage

• Ligand: zinc ion (6ck1A)

MSMEG_6049 secreted protein from Mycobacterium smegmatis str. MC2 155
MSMEG_6049 zinc metallochaperone AztD from Mycolicibacterium smegmatis MC2 155
28% identity, 18% coverage

• Identification and Characterization of Mycobacterium smegmatis and Mycobacterium avium subsp. paratuberculosis Zinc Transporters
  Goethe, Journal of bacteriology 2021 (secret)
• Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
  Goethe, mSystems 2020
  • “...43.8 Cation ABC transporter periplasmic cation-binding protein MSMEG_6048 MAP3772c (72.6) <0.0001 456.0 Cobalamin synthesis protein/P47K MSMEG_6049 <0.0001 624.5 Secreted protein MSMEG_6050 <0.0001 556.5 ABC-type Zn uptake system solute-binding lipoprotein MSMEG_6051 <0.0001 227.0 Pseudo-ABC transporter trans-membrane protein MSMEG_6052 <0.0001 54.0 ABC transporter ATP-binding protein MSMEG_6055 <0.0001 28.0...”
  • “...ABC transporter periplasmic cation-binding protein **MSMEG_6048 MAP3772c (72.6) 1 3288.50 456.0 2,903.00 Cobalamin synthesis protein/P47K MSMEG_6049 <0.0001 494.44 624.5 443.56 Secreted protein MSMEG_6050 <0.0001 917.25 556.5 849.0 ABC-type Zn uptake system solute-binding lipoprotein MSMEG_6051 <0.0001 777.0 227.0 632.0 Pseudo ABC transporter transmembrane protein * MSMEG_6052 <0.0001...”
• Association of Mycobacterium Proteins with Lipid Droplets
  Armstrong, Journal of bacteriology 2018
  • “...MSMEG_0919 MSMEG_2695 MSMEG_6282 MSMEG_1030 MSMEG_5048 fadA2 MSMEG_6049 fabG groL1 MSMEG_1077 rpsC MSMEG_0098 MSMEG_4188 hup MSMEG_0863 MSMEG_3767 atpD...”
• A Screen for Protein-Protein Interactions in Live Mycobacteria Reveals a Functional Link between the Virulence-Associated Lipid Transporter LprG and the Mycolyltransferase Antigen 85A
  Touchette, ACS infectious diseases 2017
  • “...& Cell Processes ABC Fe3+-siderophores transporter; periplasmic binding protein MSMEG_4692 Rv2468c Conserved hypotheticals Conserved protein MSMEG_6049 Secreted protein MSMEG_6394 Rv3802c Cell Wall & Cell Processes Probable conserved membrane cutinase MSMEG_6398 Rv3804c ag85A Lipid Metabolism Secreted antigen 85-a, mycolyl transferase 85A, fibronectin-binding protein A MSMEG_6595 Cell Wall...”

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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.