PaperBLAST

PaperBLAST Hits for XP_012812209.1 transmembrane protein 198 isoform X1 (Xenopus tropicalis) (354 a.a., MAFDLSTVVQ...)

Show query sequence

>XP_012812209.1 transmembrane protein 198 isoform X1 (Xenopus tropicalis)
MAFDLSTVVQPDMLQNIDNRTVDTGQDDPFDGFCSLESERHYDVVPTVVCSLCCLFGLVY
TFFGYRCFKAIMFLSGLLAGSAVIFLLCYKERIMDTQLSLELSAGIALGIGLLCGLVTML
VHSVGLFMTGLLLGLLLAIASLVGLEQFYHPPSAWIPVGLMMGSAMLFAVLTLQWQKLFT
VVSTATFGAAILTVCTDYFIELMLLVQYVYDRLRLETSHPLCWYSWVILGMWPVLSVLGI
VVQWKLTAEGFSHTDVIISRRQKRLQLLRIRQKDAKKRQNVASQEGTYRRKANPMKRYTG
DILAPSYLQSLRERQTGTGTSMSSLSTNMQTIVDMDYECGSTVPLTATTPVIHV

Running BLASTp...

Found 4 similar proteins in the literature:

XP_012812209 transmembrane protein 198 isoform X1 from Xenopus tropicalis
100% identity, 100% coverage

• Transmembrane protein 198 promotes LRP6 phosphorylation and Wnt signaling activation.
  Liang, Molecular and cellular biology 2011
  • GeneRIF: these results identified TMEM198 as a membrane scaffold protein that promotes LRP6 phosphorylation and Wnt signaling activation.

TM198_XENTR / Q6DFQ7 Transmembrane protein 198 from Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) (see paper)
100% identity, 97% coverage

• function: Promotes lrp6 phosphorylation by casein kinases and thereby plays a role in Wnt signaling. May be a membrane scaffold protein involved in the self-aggregation of lrp6 further enhancing its activity. Required for neural crest formation.
  subunit: Interacts with lrp6. Interacts with casein kinases.
  disruption phenotype: Morphants have defects in neural crest formation. At the tadpole stage, animals are often less pigmented with ventrally bent tails. Embryos develop smaller eyes and forebrain structures.

TM198_HUMAN / Q66K66 Transmembrane protein 198 from Homo sapiens (Human) (see paper)
NP_001290027 transmembrane protein 198 from Homo sapiens
51% identity, 96% coverage

• function: Promotes LRP6 phosphorylation by casein kinases and thereby plays a role in Wnt signaling. May be a membrane scaffold protein involved in the self-aggregation of LRP6 to further enhance its activity.
  subunit: Interacts with LRP6.
• Transmembrane protein 198 promotes LRP6 phosphorylation and Wnt signaling activation.
  Liang, Molecular and cellular biology 2011
  • GeneRIF: these results identified TMEM198 as a membrane scaffold protein that promotes LRP6 phosphorylation and Wnt signaling activation.
• Novel predictive biomarkers for atonic postpartum hemorrhage as explored by proteomics and metabolomics.
  Qu, BMC pregnancy and childbirth 2025
  • “...group Uniprot ID Protein name Gene name PPH vs. non-PPH P value Difference multiple Regulation Q66K66 Transmembrane protein 198 TMEM198 0.005 2.080 Up P25398 40S ribosomal protein S12 RPS12 0.023 2.037 Up Q9NZK5 Adenosine deaminase 2 ADA2 0.030 0.118 Down P01889 HLA class I histocompatibility antigen,...”
• A multi-omics study to monitor senescence-associated secretory phenotypes of Alzheimer's disease
  Yang, Annals of clinical and translational neurology 2024
  • “...0.46 0.09761194 Nucleus, Cytoplasm 25 P68871 Hemoglobin subunit beta HBB 0.444 0.080222037 Blood microparticle 26 Q66K66 Transmembrane protein 198 TMEM198 0.421 0.05588057 Membrane 27 P69905 Hemoglobin subunit alpha HBA1; HBA2 0.365 0.018902331 Blood microparticle 28 Q9Y623 Myosin4 MYH4 0.333 0.008978847 Cytoplasm 1 The subcellular location information...”
• Apolipoproteins have a major role in cellular tumor dormancy in triple negative breast cancer: In-silico study.
  El-Gammal, Scientific reports 2024
  • “...A1BG P04217 AF-P04217-F1 Clusterin CLUS P10909 AF-P10909-F1 Lumican LUM P51884 AF-P51884-F1 Transmembrane protein 198 TM198 Q66K66 AF-Q66K66-F1 Elongin-A2 ELOA2 Q8IYF1 AF-Q8IYF1-F1 Preparation of selected proteins Domain coverage, lack of mutations and gaps, resolution less than 3, and the experimental method of x-ray diffraction determine the best...”
• Biological Function Analysis of MicroRNAs and Proteins in the Cerebrospinal Fluid of Patients with Parkinson's Disease.
  Hwang, International journal of molecular sciences 2024
  • “...LV147 P01700 Increased LC-MS/MS [ 89 ] KLKB1 P03952 Increased LC-MS/MS [ 89 ] TM198 Q66K66 Increased LC-MS/MS [ 89 ] CBPB2 Q96IY4 Increased LC-MS/MS [ 89 ] RET4 P02753 Increased LC-MS/MS [ 89 ] LSAMP Q13449 Increased MRM-LC-MS/MS [ 112 ] APOH P02749 Increased MRM-LC-MS/MS...”
• Integrative Metabolome and Proteome Analysis of Cerebrospinal Fluid in Parkinson's Disease.
  Kim, International journal of molecular sciences 2024
  • “...89 ] TGFB1 P01137 Increased Meta-analysis (ELISA) TGON2 O43493 Decreased LC-MS/MS [ 114 ] TM198 Q66K66 Increased LC-MS/MS [ 110 ] TNFA P01375 Increased Meta-analysis [ 89 ] TTHY P02766 Decreased LC-MS/MS [ 26 ] VEGFA P15692 Decreased Systematic review [ 89 ] VGF O15240 Decreased...”
• Magnetic transferrin nanoparticles (MTNs) assay as a novel isolation approach for exosomal biomarkers in neurological diseases
  Jang, Biomaterials research 2023
  • “...HUMAN SLC2A3 Solute carrier family 2, facilitated glucose transporter member 3 Y N Cluster 3 Q66K66 HUMAN TMEM198 Transmembrane protein 198 N Y Cluster 1 P24821 HUMAN TNC Tenascin Y N Cluster 3 Q86YW5 HUMAN TREML1 Trem-like transcript 1 protein N Y Cluster 3 Discussion Exosomes...”
• Differential Expression of Serum Proteins in Chronic Obstructive Pulmonary Disease Assessed Using Label-Free Proteomics and Bioinformatics Analyses.
  Li, International journal of chronic obstructive pulmonary disease 2022
  • “...Stanniocalcin-2 0.33 DOWN P02768 ALB Albumin 0.32 DOWN Q9BWX5 GATA5 Transcription factor GATA-5 0.29 DOWN Q66K66 TMEM198 Transmembrane protein 198 0.27 DOWN Q9HCB6 SPON1 Spondin-1 0.26 DOWN Q07075 ENPEP Glutamyl aminopeptidase 0.24 DOWN Q5D862 FLG2 Filaggrin-2 0.23 DOWN P19440 GGT1 Glutathione hydrolase 1 proenzyme 0.22 DOWN...”
  • “...Number Protein-Coding Gene Name Protein Description FC UP P49913 CAMP Cathelicidin antimicrobial peptide 10.07 UP Q66K66 TMEM198 Transmembrane protein 198 9.27 UP P13611 VCAN Versican core protein 7.61 UP Q96EE4 CCDC126 Coiled-coil domain-containing protein 126 7.46 UP P08238 HSP90AB1 Heat shock protein HSP 90-beta 6.20 UP...”
• Proteomic analysis of synovial fluid from rheumatic arthritis and spondyloarthritis patients
  Birkelund, Clinical proteomics 2020
  • “...Q13790 Apolipoprotein F APOF 0.4627 3.02E03 Q96RL7 Vacuolar protein sorting-associated protein 13A VPS13A 0.5619 1.23E02 Q66K66 Transmembrane protein 198 TMEM198 0.5646 2.27E02 Correlation of proteins found changed/increased by proteomic in SF to regulatory pathways To identify underlying biological themes and pathways of the correlating proteins, a...”
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C9JXI5 Transmembrane protein 198 (Fragment) from Homo sapiens
56% identity, 61% coverage

• Proteomics investigation of the changes in serum proteins after high- and low-flux hemodialysis.
  Han, Renal failure 2018
  • “...A0A0B4J1X8 Immunoglobulin heavy variable 343 13077 5.18 Decreased P31327 Carbamoyl-phosphate synthase [ammonia], mitochondrial 164939 5.92 C9JXI5 Transmembrane protein 198 (fragment) 24329 NS K7ER74 Protein APOC4-APOC2 20049 5.25 A0A0J9YXX1 Uncharacterized protein (fragment) 12773 8.62 K7ERI9 Apolipoprotein C-I (fragment) 8647 6.13 C9JEE0 Immunoglobulin lambda-like polypeptide 1 (fragment) 19227...”

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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.