PaperBLAST

PaperBLAST Hits for Atu4095 (83 a.a., MEDAQVGWIA...)

Show query sequence

>Atu4095
MEDAQVGWIAAIIIGGVAGWLAEQFMKSNMGVFMNIILGIIGAIVANFLLGLIGVSLGGW
IGYLIAGFIGACILIAVGRAFRR

Running BLASTp...

Found 7 similar proteins in the literature:

RL1172 putative transmembrane protein from Rhizobium leguminosarum bv. viciae 3841
80% identity, 67% coverage

• Role of O2 in the Growth of Rhizobium leguminosarum bv. viciae 3841 on Glucose and Succinate
  Wheatley, Journal of bacteriology 2017
  • “...2017 by University of California, Berkeley Gene RL0036 RL1172 RL3424 RL4283 RL4284 aInsertion density is defined as the proportion of TA insertion sites...”
  • “...with that of strains mutated in RL0037 (pckA), RL1172, RL3424 (dctA), RL4283 (ptsP), and RL4284 (ask) (Table S1). Each mutant strain had a significantly...”

RL2489A hypothetical protein from Rhizobium leguminosarum bv. viciae 3841
71% identity, 99% coverage

• Factors governing attachment of Rhizobium leguminosarum to legume roots at acid, neutral, and alkaline pHs
  Parsons, mSystems 2024
  • “...is apparent, as again genes encoding proteins involved in peptidoglycan metabolism are required (these include RL2489A, encoding a transglycosylase-associated protein, and RL2778, encoding an exopolysaccharide biosynthesis protein). Also required is RL2644 ( sixA, the only known bacterial phosphohistidine dephosphorylase), part of the Npr system that acts...”
• Factors governing attachment ofRhizobium leguminosarumto legume roots
  Parsons, 2022

BQ09200 hypothetical protein from Bartonella quintana str. Toulouse
71% identity, 100% coverage

• Bartonella quintana deploys host and vector temperature-specific transcriptomes
  Abromaitis, PloS one 2013
  • “...0.63 1.72 0 2.76 2 5.10 BQ11730 hypothetical protein 0.62 1.59 0 2.46 7 4.62 BQ09200 hypothetical protein 0.87 1.33 0 3.07 1 4.59 BQ10980 sensory transduction regulatory protein phyR 0.38 1.63 0.78 2.18 8 4.00 BQ01390 variable outer membrane protein vompD 0.40 1.34 0.36 1.91...”
  • “...BQ08670 - - - PF11015.3 n/a Protein of unknown function (DUF2853) 2 100 9.40E-35 DUF2853 BQ09200 Transglycosylase-associated protein 3.00E-26 YP_002290717.1 transglycosylase-associated protein 3.20E-30 306843863 BQ09410 cation diffusion facilitator family transporter 1.00E-126 ZP_04680778.1 cation diffusion facilitator family transporter 8.40E-117 306844567 BQ10150 trm112p-like family protein 3.00E-17 ZP_08269540.1 Trm112p-like...”

BCAL2998 transglycosylase associated protein from Burkholderia cenocepacia J2315
49% identity, 86% coverage

• Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
  O'Grady, Frontiers in cellular and infection microbiology 2011
  • “...1.56 BCAL2969a Hypothetical protein 1.68 BCAL2971 Hypothetical phage protein 1.55 BCAL2973 Putative exported protein 1.64 BCAL2998 Transglycosylase associated protein 2.82 BCAL3006 Cold shock-like protein 3.81 BCAL3018 Conserved hypothetical protein 2.19 BCAL3109 Urease accessory protein 1.69 BCAL3178 LysR family regulatory protein 1.72 BCAL3179 Probable d -lactate dehydrogenase...”

DR_2389 transglycosylase associated protein from Deinococcus radiodurans R1
37% identity, 53% coverage

• The Construction of an Extreme Radiation-Resistant Perchlorate-Reducing Bacterium Using <i>Deinococcus deserti</i> Promoters
  Chen, International journal of molecular sciences 2024
  • “...top-five promoters, with gene_1 corresponding to dr_1942 , gene_2 to dr_2330 , and gene_8 to dr_2389 ; however, homologous genes for gene_21 and gene_22 were not identified. Subsequently, we compared these homologs with the transcriptome data from D. radiodurans under radiation stress [ 47 ] and...”

Deide_01280 putative transglycosylase associated protein from Deinococcus deserti VCD115
36% identity, 88% coverage

• The Construction of an Extreme Radiation-Resistant Perchlorate-Reducing Bacterium Using <i>Deinococcus deserti</i> Promoters
  Chen, International journal of molecular sciences 2024
  • “...13,108.6 gene_6 RS10680 Deide_18600 putative Thioredoxin 11,626.1 gene_7 RS11895 Deide_20641 hypothetical protein 8012.08 gene_8 RS00720 Deide_01280 putative transglycosylase associated protein 6118.36 gene_9 RS00860 Deide_01461 putative adenylate/guanylate cyclase 5842.14 gene_10 RS13035 Deide_22810 hypothetical protein 5471.95 gene_11 RS10440 Deide_18130 hypothetical protein 5034.39 gene_12 RS10375 Deide_18000 hypothetical protein 4916.47...”

Rv1861 PROBABLE CONSERVED TRANSMEMBRANE PROTEIN from Mycobacterium tuberculosis H37Rv
BCG_1897 putative transmembrane protein from Mycobacterium bovis BCG str. Pasteur 1173P2
38% identity, 60% coverage

• Methionine Antagonizes para-Aminosalicylic Acid Activity via Affecting Folate Precursor Biosynthesis in Mycobacterium tuberculosis
  Howe, Frontiers in cellular and infection microbiology 2018
  • “...++ BCG_3873 ( Rv3811 ) Cell surface protein involved in virulence no ++ BCG_1897 ( Rv1861 ) Conserved transmembrane protein no ++ BCG_2026 ( vapB15 ) Antitoxin component of an toxin-antitoxin operon with BCG_2027 ( vapC15 ) no ++ kgtP ( kgtP ) Ketoglutarate transport protein...”
• Single nucleotide polymorphisms may explain the contrasting phenotypes of two variants of a multidrug-resistant Mycobacterium tuberculosis strain
  Bigi, Tuberculosis (Edinburgh, Scotland) 2017 (PubMed)
  • “...components, others in drug resistance and a SNP in Rv1861, a gene encoding a putative transglycosylase that produces a truncated protein in Mp. The mutation in...”
  • “...nucleotide deletion produced a predicted reading frameshifting for the Rv1861 protein of Mp and the insertion of three nucleotides added a proline in Rv0668 of...”
• FurA contributes to the oxidative stress response regulation of Mycobacterium avium ssp. paratuberculosis
  Eckelt, Frontiers in microbiology 2015
  • “...-4.67 Hypothetical protein MAP1388 MAP1418c Rv3821 (56.25) MAV_3059 (84.67) 0.00950 -4.00 Hypothetical protein MAP1418c MAP1570 Rv1861 (50.49) MAV_2858 (65.16) <0.0001 -5.52 Membrane protein MAP1639c Rv0854 (75.86) MAV_2785 (99.32) 0.00074 -4.21 Cyclase/dehydratase I furA MAP1669c* Rv1909c (88.02) MAV_2752 (100) <0.0001 -52.80 FurA P MAP1706 Rv1987 (73.1) MAV_2710...”
• Assignment of oriented sample NMR resonances from a three transmembrane helix protein
  Murray, Journal of magnetic resonance (San Diego, Calif. : 1997) 2014
  • “...to assist in a tertiary structure calculation, we have chosen to study the membrane protein Rv1861 from Mycobacterium tuberculosis ( Mtb ). Tuberculosis is responsible for 1.4 million deaths per year and currently there exist extensively drug resistant strains. Many small membrane proteins in the cell...”
  • “...a strategy is demonstrated for assigning the resonances of TM sites in SLF spectra of Rv1861 in a synthetic lipid bilayer. Due to a high level of congestion in OS ssNMR data for uniformly labeled protein, a series of AA specific 15 N-labeled samples were prepared...”
• Lipid bilayer preparations of membrane proteins for oriented and magic-angle spinning solid-state NMR samples
  Das, Nature protocols 2013
  • “...oriented-sample solid-state NMR. the procedure is demonstrated using two proteins: CrgA (two transmembrane helices) and rv1861 (three transmembrane helices), both from Mycobacterium tuberculosis . the success of this procedure relies on two points. First, for samples for both types of NMR experiment, the reconstitution of the...”
  • “...small helical membrane proteins from M. tuberculosis , H37Rv strain: CrgA (two transmembrane helices) and Rv1861 (three transmembrane helices) ( Table 1 ) 19 21 . In addition, we provide some data for gramicidin A that we use as a test sample. Once conditions for protein...”
• Solid state NMR strategy for characterizing native membrane protein structures
  Murray, Accounts of chemical research 2013
  • “..., CrgA that has two TM helices and is involved in cell division 28 and Rv1861 that has three TM helices and binds nucleotide triphosphates 29 . Structural Restraints Orientational restraints are typically obtained from Separated Local Field (SLF) spectroscopy when the anisotropic chemical shift and...”
  • “...a PISA wheel within a TM helical sequence. We have recently assigned the resonances for Rv1861 having three TM helices, as well as the resonances from the two helices of CrgA (Murray et al., unpublished and Das et al., unpublished). These both represented challenging problems; the...”
• De novo prediction of the structures of M. tuberculosis membrane proteins
  Bu, Journal of the American Chemical Society 2008 (PubMed)
  • “...infection. Recently, one M. tuberculosis membrane protein, Rv1861, has been studied using solid-state NMR.3 However, due to difficulties of sample preparation...”
  • “...structures of four M. tuberculosis membrane proteins, Rv2433, Rv1861, Rv1616, and Rv3069, are predicted using de novo methods. The number of transmembrane (TM)...”
• The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
  Fu, BMC microbiology 2007
  • “...Rv2044C LIPF Rv2670C CPSY Rv2297 Rv0165C PKS11 Rv1362C Rv2799 Rv1363C Rv2255C Rv1931C Rv3501C VIUB APT Rv1861 SECG Rv3860 Rv0149 Rv0269C Rv2639C Rv1151C Rv0230C MOAC3 Rv2722 TRXA Rv3891C Rv0188 Rv1535 Rv2288 Rv2657C Rv3764C Rv1230C Rv3288C LPQH Rv0695 Rv3633 Rv3616C Rv3399 LPRF Rv2638 Rv3615C Rv3614C PAPA3 FRDC Rv2129C...”
• More
• Methionine Antagonizes para-Aminosalicylic Acid Activity via Affecting Folate Precursor Biosynthesis in Mycobacterium tuberculosis
  Howe, Frontiers in cellular and infection microbiology 2018
  • “...regulator no ++ BCG_3873 ( Rv3811 ) Cell surface protein involved in virulence no ++ BCG_1897 ( Rv1861 ) Conserved transmembrane protein no ++ BCG_2026 ( vapB15 ) Antitoxin component of an toxin-antitoxin operon with BCG_2027 ( vapC15 ) no ++ kgtP ( kgtP ) Ketoglutarate...”

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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.