PaperBLAST

PaperBLAST Hits for BRENDA::I3RA71 acetyl-CoA C-acetyltransferase (subunit 1/2) (EC 2.3.1.9) (Haloferax mediterranei) (120 a.a., MTLEAGKCPN...)

Show query sequence

>BRENDA::I3RA71 acetyl-CoA C-acetyltransferase (subunit 1/2) (EC 2.3.1.9) (Haloferax mediterranei)
MTLEAGKCPNGHVSYPTHPRCRKCGEPQTETLDLSDRTGKVVTWTHSTATPPGVRQPNTM
AIVEFEVDGQAVRALGQVTTDDIETGDVVEPVYVEELRDPEVGIKAPESQSWDGYRWDPV

Running BLASTp...

Found 5 similar proteins in the literature:

I3RA71 acetyl-CoA C-acetyltransferase (subunit 1/2) (EC 2.3.1.9) from Haloferax mediterranei (see paper)
HFX_6003 Zn-ribbon domain-containing OB-fold protein from Haloferax mediterranei ATCC 33500
100% identity, 100% coverage

• Bioplastic Production from Agri-Food Waste through the Use of Haloferax mediterranei: A Comprehensive Initial Overview
  Longo, Microorganisms 2024
  • “...28 ]. Similarly, BktB is encoded by two co-transcribed genes, btkB and btkB (HFX_6004 and HFX_6003), and it consists of two subunits, the catalytic and the oligo-saccharide substrate-binding beta. The catalytic triad Ser-His-His of the alpha subunits of Btk and PhaA, which is distinct from the...”
• Optimising PHBV biopolymer production in haloarchaea via CRISPRi-mediated redirection of carbon flux
  Lin, Communications biology 2021
  • “...enzyme, involved in supply of 3HB-CoA and 3-hydroxyvaleryl-CoA (3HV-CoA), was encoded by cotranscribed HFX_6004 and HFX_6003 genes 39 . One crRNA (phaA-t1) targeting the template strand of phaA and two crRNAs (bktB-c1 and c2) targeting the coding strand of bktB were designed and expressed in DF50EPS...”
• Unusual Phosphoenolpyruvate (PEP) Synthetase-Like Protein Crucial to Enhancement of Polyhydroxyalkanoate Accumulation in Haloferax mediterranei Revealed by Dissection of PEP-Pyruvate Interconversion Mechanism
  Chen, Applied and environmental microbiology 2019 (secret)
• Haloarchaeal-type β-ketothiolases involved in Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis in Haloferax mediterranei
  Hou, Applied and environmental microbiology 2013
  • “...BktB) and encoded by cotranscribed HFX_6004 (bktB) and HFX_6003 (bktB). BktB and PhaA were the catalytic subunits and determined substrate specificities of BktB...”
  • “...HFX_6356 HFX_6051 37 37 26 24 19 HFX_6003 (protein with unknown function) HFX_1022 (protein with unknown function) HFX_6014 (superoxide dismutase) HFX_6016...”

I3R3D0 acetyl-CoA C-acetyltransferase (subunit 1/2) (EC 2.3.1.9) from Haloferax mediterranei (see paper)
HFX_1022 OB-fold domain-containing protein from Haloferax mediterranei ATCC 33500
62% identity, 95% coverage

• Bioplastic Production from Agri-Food Waste through the Use of Haloferax mediterranei: A Comprehensive Initial Overview
  Longo, Microorganisms 2024
  • “...oligo-saccharide binding domain, coded respectively according to the co-transcribed genes phaA and phaA (HFX_1023 and HFX_1022). PhaA catalyzes the condensation reaction (and the cleavage, as a reverse reaction) of two acetyl-coA units to form acetoacetyl-CoA or one acetyl- CoA and one propionyl-CoA to 3-keto valeryl-CoA, an...”
• Optimising PHBV biopolymer production in haloarchaea via CRISPRi-mediated redirection of carbon flux
  Lin, Communications biology 2021
  • “...(3HB-CoA) during PHBV biosynthesis in H. mediterranei , was encoded by the cotranscribed HFX_1023 and HFX_1022 genes. Likewise, BktB enzyme, involved in supply of 3HB-CoA and 3-hydroxyvaleryl-CoA (3HV-CoA), was encoded by cotranscribed HFX_6004 and HFX_6003 genes 39 . One crRNA (phaA-t1) targeting the template strand of...”
• Haloarchaeal-type β-ketothiolases involved in Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis in Haloferax mediterranei
  Hou, Applied and environmental microbiology 2013
  • “...and encoded by the cotranscribed HFX_1023 (phaA) and HFX_1022 (phaA) genes. Similarly, the BktB that was involved in generation of acetoacetyl-CoA and...”
  • “...24 19 HFX_6003 (protein with unknown function) HFX_1022 (protein with unknown function) HFX_6014 (superoxide dismutase) HFX_6016 (protein with unknown function)...”

PF0974 hypothetical protein from Pyrococcus furiosus DSM 3638
36% identity, 66% coverage

• Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome
  Menon, Molecular & cellular proteomics : MCP 2009
  • “...Acetyl-CoA acetyltransferase Hypothetical protein PF0974 Putative peroxiredoxin Orotate phosphoribosyltransferase CRISPR-associated protein Cas5, Tneap...”
  • “...PF0642 PF0643 PF0753 PF0754 PF0872 PF0873 PF0972 PF0973 PF0974 PF1033 PF1034 PF1121 PF1122 PF1123 PF1124 PF1125 PF1126 PF1186 PF1187 PF1268 PF1269 PF1283 PF1284...”
• Impact of substrate glycoside linkage and elemental sulfur on bioenergetics of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus
  Chou, Applied and environmental microbiology 2007
  • “...and PF1838), fatty acid metabolism (PF0972 to PF0974), and Downloaded from http://aem.asm.org/ on February 12, 2017 by University of California, Berkeley...”
  • “...homolog Acyl-CoA synthetase II Acetyl-CoA synthase PF0972 PF0973 PF0974 3.5 3.2 3.3 7.5 6.3 7.8 Acyl carrier protein synthase Acetyl-CoA synthase Hypothetical...”
• Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
  Schut, Journal of bacteriology 2003
  • “...PF0894 PF0913 PF0915 [Acetyl-CoA synthetase] PF0972 PF0973 PF0974 PF1057 [Amino acid metabolism] PF1245 PF1246 PF1253 PF1341 2-Keto acid ferredoxin...”

TON_1303 hypothetical protein from Thermococcus onnurineus NA1
35% identity, 67% coverage

• Genome-wide primary transcriptome analysis of H₂-producing archaeon Thermococcus onnurineus NA1
  Cho, Scientific reports 2017
  • “...TSSs (73.7%) ( Supplemental Table S2 ). For example, the transcription of TON_1301, TON_1302, and TON_1303 is initiated by a single TSS at the genomic position of 1,182,769 indicating that these genes are transcribed from a single TU (TU0722) ( Fig. 1A ). The operon harboring...”

TK0179 hypothetical protein from Thermococcus kodakaraensis KOD1
35% identity, 68% coverage

• Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing
  Liu, Frontiers in molecular biosciences 2022
  • “...TK2061 ), sulfur reductase subunits ( TK2071 and TK2072 ), and Acetyl-CoA acetyltransferase pathway ( TK0179 , TK0180 , and TK0181 ). The genes encoded within each operon were either enhanced or reduced to a similar extent in tk1545 KO. Transcriptome analysis from the small RNA-Seq...”
• An archaeal histone is required for transformation of Thermococcus kodakarensis
  Čuboňováa, Journal of bacteriology 2012
  • “...Downregulated by deletion of TK2289 (histone B) TK2289 TK0179 TK0180 TK0181 TK2076 TK2077 TK2078 TK2079 TK1830 TK1413 TK1405 TK1431 TK1046 TK1624 TK0560 TK1245...”

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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.