PaperBLAST
PaperBLAST Hits for mRNA_8428 (77 a.a., MMLSRQMTAI...)
Show query sequence
>mRNA_8428
MMLSRQMTAIFNFESLLLVILLVICTCTYVRATAPGLIDRNKQGVLGIFFKFARIGERLS
PYVALACVVMAVRSLVV
Running BLASTp...
Found 9 similar proteins in the literature:
KISHA_HUMAN / Q8TBQ9 Protein kish-A; Transmembrane protein 167; Transmembrane protein 167A from Homo sapiens (Human) (see paper)
NP_777569 protein kish-A precursor from Homo sapiens
72% identity, 84% coverage
Q5ZII6 Protein kish-A from Gallus gallus
69% identity, 92% coverage
Tmem167 protein kish-A precursor from Mus musculus
71% identity, 84% coverage
- Analyses of binding partners and functional domains for the developmentally essential protein Hmx3a/HMX3
Haws, Scientific reports 2023 - “...MGI:1,922,566 Tspan3 MGI:1,928,098 Commd4 MGI:1,913,449 Psmc3 MGI:1,098,754 Gfm2 MGI:2,444,783 Ahcyl MGI:3,643,647 Lat2 MGI:1,926,479 Uba3 MGI:1,341,217 Tmem167 MGI:1,913,324 Sdhb MGI:1,914,930 Ptpn2 MGI:97,806 We excluded from further analyses genes that either had no obvious ortholog in zebrafish or that were likely to be Y2H false positives because they,...”
- Structural and molecular characterization of paraventricular thalamic glucokinase-expressing neuronal circuits in the mouse
Gaspari, The Journal of comparative neurology 2022 - “...domain containing 7 (Spryd7) Frs2 0.39 .001650842 7.108316 Fibroblast growth factor receptor substrate 2 (Frs2) Tmem167 0.39 .005639071 6.600933 Transmembrane protein 167 (Tmem167) Pogz 0.39 .000558255 7.295534 Pogo transposable element with ZNF domain (Pogz) Rab3a 0.39 .000617378 8.68367 RAB3A, member RAS oncogene family (Rab3a) Tmem87b 0.39...”
- Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
Kubo, Nature structural & molecular biology 2021 - “...artificially tethered CTCF was also dependent on the presence of the promoter of Xrcc4 / Tmem167 gene located at 350 kb downstream of Vcan gene ( Fig. 3a , b , the cell line depicted on second from the bottom). PLAC-seq experiments showed that the Vcan...”
- “...the long-range chromatin contacts between Vcan promoter and the 350 kb downstream distal Xrcc4 / Tmem167 promoter was also re-established ( Fig. 3e , f , Extended Data Fig. 8d ). Taken together, our results demonstrated that promoter-proximal CTCF binding can promote long-range promoter-anchored chromatin contacts...”
- Long Term Response to Circulating Angiogenic Cells, Unstimulated or Atherosclerotic Pre-Conditioned, in Critical Limb Ischemic Mice
Beltrán-Camacho, Biomedicines 2021 - “...RPL37A, RPS17, S100A11, SCD1, SPARC, SEC16A, SPRR1A, SLMAP, SERPINF1, SERPINB6A, SERF2, SNRPD2, STMN1, TGTP1, TNC, TMEM167, TPP1, XIRP1 - ABCA1, APAF1, APBB1IP, APOBR, ARG2, ARL6IP1, ASS1, BC017643, CAPZA1, CAR13, CASP8, CD14, CYBB, DCAKD, DDX39, DHFR, DR1, DTYMK, ELANE, ELMO1, EMB, EMILIN1, EMILIN2, GCN1L1, GFPT1, GIT2, H2AFY,...”
- Temporal Integrative Analysis of mRNA and microRNAs Expression Profiles and Epigenetic Alterations in Female SAMP8, a Model of Age-Related Cognitive Decline
Cosín-Tomás, Frontiers in genetics 2018 - “.../ NM_023403.1 /2.71 Vps50 / NM_024260.5 /3.17 Tgfbr1 / NM_009370.3 /2.31 Irf6 / NM_016851.2 /2.03 Tmem167 / NM_025335.2 /2.85 Arl4d / NM_025404.3 /2.01 Thrb / NM_009380.3 /2.96 Slc5a3 / NM_017391.1 /2.5 Serbp1 / NM_025814.2 /2.14 Cdip1 / NM_025670.2 /1.99 Unc5c / NM_009472.4 /2.50 Chst2 / NM_018763.2...”
- “...Man1a2, Ndst2, Serf2, Skil, Coro1c, Abca1, Atp6v0d1, Tcp1, Pdk4, Pbx3, Hp, Pdlim4, Ykt6, Kox17, Mesdc2, Tmem167, Serpb1, Lipt2, Atg12, Loh12cr1, Mrpl19, Manba, Trps1, Kremen1 Regulation of membrane lipid distribution (GO:0097035) 0.00260 2.53 4.08 Cellular response to extracellular stimulius (GO:0031668) 0.00299 2.26 3.66 Regulation of extrinsic apoptotic...”
Q5BJC2 Protein kish-A from Danio rerio
68% identity, 86% coverage
KISH_SCHPO / G2TRS3 Protein kish from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
64% identity, 87% coverage
- function: Involved in the early part of the secretory pathway.
disruption phenotype: Inviable.
KISH_YEAST / Q8TGJ3 Protein Kish from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
YNL024C-A Putative protein of unknown function; YNL024C-A is an essential gene from Saccharomyces cerevisiae
61% identity, 86% coverage
- function: Involved in the early part of the secretory pathway.
disruption phenotype: Inviable. - A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection
Crook, PLoS computational biology 2020 - “...as core components of COPII vesicles and 6 associated with COPI vesicles. The protein Ksh1p (Q8TGJ3) is further suggested through homology with higher organisms to be part of the early secretory pathway [ 52 ]. The proteins Scw4p (P53334), Cts1p (P29029) and Scw10p (Q04951) [ 53...”
- A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family
Salzberg, PLoS genetics 2022 - “...protein, confers rapamycin resistance by binding Fpr1 YNL024C EFM6 Putative SAM-dependent lysine methyltransferase, methylates EF-1 YNL024C-A KSH1 Kish small membrane protein, role in secretory pathway YNCN0014W SNR66 snR66 small nucleolar RNA (snoRNA) YNCN0013W NME1 RNA component of RNAse MRP, cleaves pre-rRNA YNL025C SSN8 Cyclin-like component of...”
- Computational discovery and annotation of conserved small open reading frames in fungal genomes
Mat-Sharani, BMC bioinformatics 2019 - “...from this study Kastenmayer et al S.cerevisiae-gi14318502 YFL017W-A S.cerevisiae-gi6323292 #N/A S.cerevisiae-gi398364355 YFR032C-A S.cerevisiae-gi6323318 #N/A S.cerevisiae-gi398365385 YNL024C-A S.cerevisiae-gi6323506 #N/A S.cerevisiae-gi398365605 YLR287C-A S.cerevisiae-gi6323558 #N/A S.cerevisiae-gi398365775 YOR210W S.cerevisiae-gi6323634 #N/A S.cerevisiae-gi398365789 YDR139C S.cerevisiae-gi6323912 #N/A S.cerevisiae-gi398366075 YLR388W S.cerevisiae-gi6324184 #N/A S.cerevisiae-gi6321622 YGR183C S.cerevisiae-gi6324259 #N/A S.cerevisiae-gi6321937 YHR143W-A S.cerevisiae-gi6324313 #N/A S.cerevisiae-gi6323294 YLR264W S.cerevisiae-gi6324619 #N/A...”
- Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability
Bitton, Genetics 2011 - “...2); it has human (TMEM167A) and S. cerevisiae (YNL024C-A) orthologs whose functions are suggested to lie within the secretory pathway (Wendler et al. 2009)....”
- A genome-wide RNA interference screen identifies two novel components of the metazoan secretory pathway
Wendler, The EMBO journal 2010 - “...by the previously uncharacterised open reading frame (ORF) YNL024c-a. This yeast protein has only 72 residues and is 56% identical to the Drosophila protein,...”
- “...At Dd Hs Xl Ce CG14199 Tmem167A Tmem167A YNL024c-a At5g20165 TM167 Tmem167B Tmem167B K07F5.15 1 1 1 1 1 1 1 1 1...”
- Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
Kastenmayer, Genome research 2006 - “...YNR032C-A YOR167C YLR264W YKR057W YJL136C YDR139C YNL024C-A YLR038C YOR159C YGR037C YIL008W YER146W YOR298C-A YER048W-A YBL071W-A YFR032C-A YBR089C-A YPR052C...”
- “...YBR233W-A YDR320C-A YER074W-A YHR072W-A YKL138C-A YLR099W-A YNL024C-A YNL138W-A YBL071C-B YBL071W-A YGL007C-A YGL188C-A YPL096C-A YPL189C-A DAD3 DAD4 YOS1 NOP10...”
- Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii
Brachat, Genome biology 2003 - “...1 ). This suggests that they represent conserved fungal proteins. For two genes, YMR194C-B and YNL024C-A, we identified homologs in higher eukaryotes, including mouse and human. The conservation in other species, and particularly their syntenic positions in A. gossypii , strongly support the authenticity of these...”
- “...75 YLR307C-A 87 50.00 AFL165W 94 YMR194C-B 73 51.47 x x x x ADL210W 72 YNL024C-A 72 81.94 x x x x AFR059W 84 YNL138W-A 85 52.38 x AAR108W-A 70 YOR020W-A 90 35.71 x x ABR192C-A 71 YPL096C-A 68 45.59 x AFL069C 58 YPL189C-A 68 69.64...”
- Parallel identification of new genes in Saccharomyces cerevisiae
Oshiro, Genome research 2002 - “...YHR050W-A YHR132W-B YIL002W-A YIL046W-A YKR099C-A YLR154W-B YMR175W-A YNL024C-A YOR072W-A YOR192C-C YPR170W-A Chromosomal location Chr Chr Chr Chr Chr Chr Chr...”
KISH_DROME / Q9VWH8 Protein kish from Drosophila melanogaster (Fruit fly) (see paper)
65% identity, 84% coverage
- function: Involved in the early part of the secretory pathway.
C1LI02 Protein kish from Schistosoma japonicum
63% identity, 84% coverage
- iTRAQ-Based Comparative Proteomic Analysis of Adult Schistosoma japonicum from Water Buffalo and Yellow Cattle
Zhai, Frontiers in microbiology 2018 - “...TCCTTATCCGTATCAACTT C1LHC4 FP: GTCCTTATTGTACTTGTTGTC 0.73 1.53 RP: AAATCCCACCATCTTCTAAA C1LAT6 FP: TTATGTCGCAAGCAGATG 1.94 0.33 RP: TTGTAGGTCTTAGCAAGTT C1LI02 FP: TGCTTACATTAGACACTTCTCT 0.50 0.48 RP: TTGCGTTCACCAATCCTT Gene relative expression in schistosomes from water buffalo compared with those from yellow cattle has opposite expression regulation between qRT-PCR analysis and iTRAQ analysis....”
- “...protein 34.59 0.6568 Q5DGG9 Troponin T 63.21 0.6499 Q5BS32 Dynein light chain roadblock 12.37 0.5555 C1LI02 Transmembrane protein 167 precursor 13.89 0.4772 C1LEX2 Inner nuclear membrane protein Man1 (LEM domain-containing protein 3) 7.13 0.6609 Protein proteolysis F6LHR8 Tetraspanin 2 27.44 1.742 C1LBS5 Cathepsin L, a 34.14...”
KISHB_HUMAN / Q9NRX6 Protein kish-B; Transmembrane protein 167B from Homo sapiens (Human) (see paper)
42% identity, 84% coverage
- function: Involved in the early part of the secretory pathway.
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
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.
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.
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.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory