PaperBLAST

PaperBLAST Hits for 15989 (79 a.a., MDERRRRPRP...)

Show query sequence

>15989
MDERRRRPRPQPLARRNEPVLPTMLGFVGLSDDNKERISKAIEVAKTIVHYGWIPTILLV
AYRASNPRPPLMRLISPLA

Running BLASTp...

Found 1 similar proteins in the literature:

TOM7_YEAST / P53507 Mitochondrial import receptor subunit TOM7; Translocase of outer membrane 7 kDa subunit from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
TC 3.A.8.1.1 / P53507 Tom7 aka MOM7 aka YNL070W aka N2378, component of Mitochondrial protein translocase (MPT) (Chacinska et al., 2005; Mokranjac et al., 2005; Bihlmaier et al., 2007). The crystal structure of the intermembrane space domain of yeast Tim50 has been solved to 1.83 Å resolution (Qian et al., 2011). A protruding beta-hairpin of Tim50 is crucial for interaction with Tim23, providing a molecular basis for the cooperation of Tim50 and Tim23 in preprotein translocation to the protein-conducting channel of the mitochondrial inner membrane from Saccharomyces cerevisiae (Baker's yeast) (see 7 papers)
TOM7 / RF|NP_014329.1 mitochondrial import receptor subunit TOM7 from Saccharomyces cerevisiae
YNL070W Component of the TOM (translocase of outer membrane) complex responsible for recognition and initial import steps for all mitochondrially directed proteins; promotes assembly and stability of the TOM complex from Saccharomyces cerevisiae
NP_014329 Tom7p from Saccharomyces cerevisiae S288C
45% identity, 62% coverage

• function: Component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. TOM7 is involved in assembly and stability of the TOM complex.
  subunit: Forms part of the preprotein translocase complex of the outer mitochondrial membrane (TOM complex) which consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70).
• substrates: proteins
  tcdb comment: TIM23-mediates insertion of transmembrane α-helices into the mitochondrial inner membrane (Botelho et al., 2011). The TIM23 channel undergoes structural changes in response to the energized state of the membrane, the pmf (Malhotra et al. 2013). TMS1 in TIM23 is required for homodimerization while it and TMS2 are involved in pre-protein binding in the channel (Pareek et al. 2013). The Tom40 outer membrane channel may be a 19 β-stranded barrel, possibly homologous to the VDAC porins (TC# 1.B.8) (Lackey et al. 2014). Tim23 and Tim17 interact with each other as well as Tim44 and Pam17, respectively. These last two proteins may serve regulatory functions (Ting et al. 2014). Tom20, 22, 40 and 70 recognize presequences in various mitochondrially targetted proteins (Melin et al. 2015; Melin et al. 2014). In the 4 TMS TIM17 protein, mutations in TMSs1 and 2 impair the interaction of Tim17 with Tim23, whereas mutations in TM3 compromise binding of the import motor (Demishtein-Zohary et al. 2017); further, residues in the matrix-facing region of Tim17 involved in binding of the import motor were identified. TIM22, forms an intramolecular disulfide bond in yeast and humans. If not oxidized, they do not properly integrate into the membrane complex, and the lack of Tim17 oxidation disrupts the TIM23 translocase complex (Wrobel et al. 2016). Mgr2 (TC# 1.A.111.1.3) and Pam18 are involved in precursormembrane protein quality control (Schendzielorz et al. 2018). Tom7 and OMA1 play reciprocal roles during mitochondrial import and activation of the PTEN-induced kinase 1, PINK1, in humans (Sekine et al. 2019). Organellar beta-barrel proteins are unique as most of them do not contain typical targeting information in the form of an N-terminal cleavable targeting signal. Instead, targeting and surface recognition of mitochondrial beta-barrel proteins in yeast, humans and plants depends on the hydrophobicity of the last beta-hairpin of the beta-barrel.Klinger et al. 2019 demonstrated that hydrophobicity is not sufficient for the discrimination of targeting to chloroplasts or mitochondria. Using atVDAC1 (TC# 1.B.8.1.15) and psOEP24 (1.B.28.1.1) they showed that the presence of a hydrophilic amino acid at the C-terminus of the penultimate beta-strand is required for mitochondrial targeting. A mutation of the chloroplast beta-barrel protein psOEP24 which mimics such a profile is efficiently targeted to mitochondria (Klinger et al. 2019). The high-resolution cryo-EM structures of the core TOM complex from Saccharomyces cerevisiae in dimeric and tetrameric forms have been determined (Tucker and Park 2019). Dimeric TOM consists of two copies each of five proteins arranged in two-fold symmetry: pore-forming beta-barrel protein Tom40 and four auxiliary alpha-helical transmembrane proteins. The pore of each Tom40 has an overall negatively charged inner surface due to multiple functionally important acidic patches. The tetrameric complex is a dimer of dimeric TOM, which may be capable of forming higher-order oligomers. Negatively charged residues in the N-terminus of Tim17 are critical for the preprotein-induced gating of the TIM23 translocase, possibly by recognizing the positive charges in the leader sequence of the substrate proteins (Meier et al. 2005)
• The Endoplasmic Reticulum-Mitochondria Encounter Structure and its Regulatory Proteins
  Cheema, Contact (Thousand Oaks (Ventura County, Calif.)) 2021
  • “...sites (null mutant) GFP-Mdm34 Mmm1-RFP N.D. ( Ackema et al., 2016 ) Tom7 Saccharomyces cerevisiae YNL070W Mitochondrial outer membrane Aggregated /unevenly distributed mitochondria N.D. Mdm10 Mmm1, Mdm12, Mdm10, Mdm34 ( Ellenrieder et al., 2016 ) Arf1 Candida albicans YDL192W Golgi Fragmented Increased number of ERMES foci...”
• Identifying longevity associated genes by integrating gene expression and curated annotations
  Townes, PLoS computational biology 2020
  • “...of cytochrome c oxidase (Complex IV) HOR7 0.999 YMR251W-A Protein of unknown function TOM7 0.999 YNL070W Component of the TOM (translocase of outer membrane) complex MFA1 0.999 YDR461W Mating pheromone a-factor TAR1 0.999 YLR154W-C Protein potentially involved in regulation of respiratory metabolism To assess the accuracy...”
• Human stefin B role in cell's response to misfolded proteins and autophagy
  Polajnar, PloS one 2014
  • “...0.499 YML032C (RAD52 Nuclear protein involved in the repair of double-strand breaks in DNA 0.429 YNL070W (TOM7) Component of the translocase of outer membrane complex 0.462 Functions of the encoded proteins according to SGD ( http://www.yeastgenome.org/ ) are shown. R denotes relative growth rate compared to...”
• Mitochondrial protein synthesis, import, and assembly
  Fox, Genetics 2012
  • “...Tom40 Tom70 Tom71 YOL026C YLR099W-A YPR133W-A YOR045W YNL070W YGR082W YNL131W YMR203W YNL121C YHR117W a Known function Insertion of transmembrane helix proteins...”
• A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae
  Addinall, Genetics 2008
  • “...YNL081C YLR354C YIL011W YPR074C YER007C-A YJR014W YGR260W YNL070W YNL121C YIL138C YPL030W YLR425W YER151C YFR010W YMR067C YBR273C YDL190C YNL229C YKR042W...”
• Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins
  Zahedi, Molecular biology of the cell 2006
  • “...28.0 YOR285w 45 15.4 5.9 27.5 YBR179c 32 97.7 6.6 26.5 YNL070w 27 6.9 8.3 24.0 YIL124w YNL055c 49 64 32.8 30.4 9.2 7.7 YIR038c YDR470c 21 21 26.8 57.4 6.2 6.6...”
• Biogenesis of mitochondria: dual role of Tom7 in modulating assembly of the preprotein translocase of the outer membrane.
  Becker, Journal of molecular biology 2011 (PubMed)
  • GeneRIF: The authors report here that the third small Tom protein, Tom7, plays an inhibitory role at two distinct steps in the biogenesis of the translocase of the outer mitochondrial membrane (TOM) complex.
• Tom7 regulates Mdm10-mediated assembly of the mitochondrial import channel protein Tom40.
  Yamano, The Journal of biological chemistry 2010
  • GeneRIF: Tom7 recruits Mdm10, enhancing its association with the MMM1 complex, to regulate timing of the release of Tom40 from the TOB complex for subsequent assembly into the TOM40 complex
• Reconstructing the mitochondrial protein import machinery of Chlamydomonas reinhardtii
  Figueroa-Martínez, Genetics 2008
  • “...Mas22, Mom22 Tom20 (NP_011596) Mas20, Mom19 Tom7 (NP_014329) Mom7, Yok22 Tom6 (NP_014688) Tom5 (NP_015459) Isp6, Mom8B Mim1 (NP_014616) Tob55 (NP_014372) Tob38...”
• Mitochondrial protein sorting: differentiation of beta-barrel assembly by Tom7-mediated segregation of Mdm10.
  Meisinger, The Journal of biological chemistry 2006 (PubMed)
  • GeneRIF: Tom7-mediated segregation of Mdm10 functions by a differentiation of beta-barrel assembly

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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.