PaperBLAST
PaperBLAST Hits for BPHYT_RS02540 (84 a.a., MKQPNDVFND...)
Show query sequence
>BPHYT_RS02540
MKQPNDVFNDFQARMSELFKNSPAKDVERNVKAMLSQGFSKLDLVTREEFDTQTQVLVRT
RARLEELERRVAELEQKLPVTQTP
Running BLASTp...
Found 17 similar proteins in the literature:
Bmul_0436 accessory factor UbiK family protein from Burkholderia multivorans ATCC 17616
83% identity, 99% coverage
NMY220_0445 accessory factor UbiK family protein from Neisseria meningitidis NM220
57% identity, 65% coverage
Q9K0Z7 Ubiquinone biosynthesis accessory factor UbiK from Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)
51% identity, 74% coverage
BP2735 conserved hypothetical protein from Bordetella pertussis Tohama I
45% identity, 91% coverage
BB2036 conserved hypothetical protein from Bordetella bronchiseptica RB50
45% identity, 79% coverage
BPP2594 conserved hypothetical protein from Bordetella parapertussis 12822
46% identity, 78% coverage
PA5289 hypothetical protein from Pseudomonas aeruginosa PAO1
51% identity, 91% coverage
- Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains
Kwon, Journal of proteome research 2014 - “...1392.5 probable transcriptional regulator PA5261| algR 6.6 1.1 207.0 100.0 alginate biosynthesis regulatory protein AlgR PA5289 5.0 0.0 655.0 190.5 hypothetical protein a A comprehensive list of differentially expressed genes is available in Supporting Information Tables S1 and S2 . A >2-fold-change and FDR<0.05 were applied...”
UbiK / b3042 ubiquinone biosynthesis accessory factor UbiK from Escherichia coli K-12 substr. MG1655 (see 7 papers)
ubiK / Q46868 ubiquinone biosynthesis accessory factor UbiK from Escherichia coli (strain K12) (see 8 papers)
UBIK_ECOLI / Q46868 Ubiquinone biosynthesis accessory factor UbiK from Escherichia coli (strain K12) (see 2 papers)
NP_417514 ubiquinone biosynthesis accessory factor UbiK from Escherichia coli str. K-12 substr. MG1655
b3042 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
52% identity, 56% coverage
- function: Required for efficient ubiquinone (coenzyme Q) biosynthesis under aerobic conditions (PubMed:28559279, PubMed:30686758). UbiK is probably an accessory factor of Ubi enzymes and facilitates ubiquinone biosynthesis by acting as an assembly factor, a targeting factor, or both (PubMed:28559279). Dispensable for ubiquinone biosynthesis under anaerobiosis (PubMed:28559279).
subunit: Homotrimer (PubMed:28559279). Component of the Ubi complex metabolon, which regroups five ubiquinone biosynthesis proteins (UbiE, UbiF, UbiG, UbiH and UbiI) and two accessory factors (UbiK and the lipid-binding protein UbiJ) (PubMed:30686758). Interacts with the C- terminal part of UbiJ and forms a complex composed of 2 UbiK subunits and 1 UbiJ subunit. The UbiK-UbiJ complex interacts with palmitoleic acid (PubMed:28559279).
disruption phenotype: Deletion of the gene impacts ubiquinone biosynthesis in aerobic conditions but does not decrease menaquinone biosynthesis. Mutant accumulates octaprenylphenol, an early intermediate of the ubiquinone biosynthetic pathway. - Small genes/gene-products in Escherichia coli K-12.
Wasinger, FEMS microbiology letters 1998 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Structural assembly of the bacterial essential interactome
Gómez, eLife 2024 - “...ubiA: P0AGK1, ubiE: P0A887, ubiF: P75728, ubiG: P17993, ubiH: P25534, ubiI: P25535, ubiJ: P0ADP7, ubiK: Q46868. Through our analysis, we have identified high-confidence binary complexes involved in consecutive enzymatic steps, supporting the existence of the Ubi metabolon complex. Furthermore, we have predicted the UbiE-K assembly, shedding...”
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...P42632 TDCE Energy production and conversion Cytoplasm 78 P0DTT0 BIPA Signal transduction mechanisms Cytoplasm 79 Q46868 UBIK Function unknown Cytoplasm 80 P07913 TDH Function unknown Cytoplasm 81 P0A717 KPRS Function unknown Cytoplasm 82 P0A7G2 RBFA Translation, ribosomal structure and biogenesis Cytoplasm 83 P26646 ACUI Function unknown...”
- Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies
Launay, International journal of molecular sciences 2022 - “...is aimed at modelling UbiJ (Uniprot ID: P0ADP7, 201 amino acids) and UbiK (Uniprot ID: Q46868, 96 amino acids) from E. coli in monomeric forms. Given the limited available structural data on these proteins, we opted to use AF2 in order to predict the three-dimensional models...”
- “...to yellow and red/blue circles, respectively. Residue numbering corresponds to the Uniprot sequence (Uniprot ID: Q46868). Figure 3 Modelling of UbiJ monomer. ( A ) Best AF2 model of the whole UbiJ represented as a cartoon and is coloured as a function of the pLDDT value....”
- The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ
Loiseau, The Journal of biological chemistry 2017 - “...present in Proteobacteria E. coli UbiK (UniProtKB entry Q46868) is a 96-residue protein that belongs to the BMFP (Brucella membrane fusogenic protein)...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...Q46856 YqiC YqiK YqjD YraM YraP YraR YrbC YrbF Q46868 P77306 P64581 P45464 P64596 P45469 P0ADV7 P63386 YrdA YrdC P0A9W9 P45748 YrfE YtfJ YtfQ P39187 P39325 ZnuA...”
- Identification of genes with fast-evolving regions in microbial genomes
Zheng, Nucleic acids research 2004 - “...GenBank id Name Annotation 1788436 1789421 1790051 yehI b3042 rfaC 1789805 1790469 yhgE lamB 1786335 folK 1788309 flu putative regulator orf, hypothetical...”
YPTB3405 hypothetical protein from Yersinia pseudotuberculosis IP 32953
YPO0656 conserved hypothetical protein from Yersinia pestis CO92
54% identity, 58% coverage
UBIK_SALTY / Q8ZLY9 Ubiquinone biosynthesis accessory factor UbiK from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 3 papers)
NP_462111 putative cytoplasmic protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
52% identity, 44% coverage
- function: Required for efficient ubiquinone (coenzyme Q) biosynthesis under aerobic conditions. UbiK is probably an accessory factor of Ubi enzymes and facilitates ubiquinone biosynthesis by acting as an assembly factor, a targeting factor, or both. Dispensable for ubiquinone biosynthesis under anaerobiosis (PubMed:28559279). Required for proliferation in macrophages and virulence in mice (PubMed:21554724, PubMed:28559279). Significantly contributes to colonization and invasion as well as host inflammation and innate immunity after infection (PubMed:27777572). In vitro, has membrane fusogenic activity at acidic pH (PubMed:21554724).
subunit: Homotrimer.
disruption phenotype: Mutant is growth-deficient under aerobic conditions and is impaired to replicate at physiological and high temperatures (PubMed:21554724, PubMed:28559279). Mutant is defective for proliferation in macrophages and mice infection and has a severe attenuation in virulence in the murine model when inoculated both orally and intraperitoneally (PubMed:21554724, PubMed:28559279). Deletion inhibits colonization and invasion of four human cell lines, impairs flagella formation, activates the expression of type-1 fimbriae-like structures on the cell surface, enhances biofilm formation and reduces bacterial motility. The deletion mutant is menaquinone-deficient (PubMed:27777572). - YqiC of Salmonella enterica serovar Typhimurium is a membrane fusogenic protein required for mice colonization.
Carrica, BMC microbiology 2011 - GeneRIF: The authors show that a Salmonella typhimurium yqiC deficient strain had a severe attenuation in virulence in the murine model when inoculated both orally and intraperitoneally
APL_1138 hypothetical protein from Actinobacillus pleuropneumoniae L20
52% identity, 64% coverage
KPHS_45820 accessory factor UbiK family protein from Klebsiella pneumoniae subsp. pneumoniae HS11286
48% identity, 64% coverage
SO4329 conserved hypothetical protein from Shewanella oneidensis MR-1
47% identity, 69% coverage
A1S_0217 hypothetical protein from Acinetobacter baumannii ATCC 17978
40% identity, 69% coverage
- Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii
Mujawar, Frontiers in cellular and infection microbiology 2019 - “...ABAYE3490 KeF HMPREF0010_03689 A1S_0003 HMPREF0010_03360 A1S_0028 HMPREF0010_03276 A1S_0061 HMPREF0010_03274 A1S_0063 HMPREF0010_03221 A1S_0114 HMPREF0010_03191 A1S_0147 HMPREF0010_02008 A1S_0217 HMPREF0010_01991 A1S_0236 HMPREF0010_01903 A1S_0334 HMPREF0010_01875 A1S_0364 HMPREF0010_01854 A1S_0388 HMPREF0010_01851 A1S_0391 HMPREF0010_01810 A1S_0428 HMPREF0010_01791 A1S_0447 HMPREF0010_01758 A1S_0469 HMPREF0010_01757 A1S_0470 HMPREF0010_01723 A1S_0506 HMPREF0010_01691 A1S_0561 HMPREF0010_01682 A1S_0571 KFC HMPREF0010_02522 HMPREF0010_02769 HMPREF0010_03233 HMPREF0010_00091 A1S_2232...”
ABAYE3550 hypothetical protein from Acinetobacter baumannii AYE
HMPREF0010_02008 accessory factor UbiK family protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
40% identity, 69% coverage
- Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1
Álvarez, Frontiers in microbiology 2020 - “...among GC1 chromosomes; at loci ABAYE1410 to ABAYE1438, ABAYE2053 to ABAYE2054, ABAYE2822 to ABAYE3048 and ABAYE3550 to ABAYE3552 in AYE genome; these regions also showed signs of microevolution identified as Regions of Genomic Plasticity (RGP) RGP2/HS8, RGP3/HS12, RGP5 and RGP6 with HS15 and HS16, and RGP7/HS18...”
- Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii
Mujawar, Frontiers in cellular and infection microbiology 2019 - “...HMPREF0010_01948 ABAYE3490 KeF HMPREF0010_03689 A1S_0003 HMPREF0010_03360 A1S_0028 HMPREF0010_03276 A1S_0061 HMPREF0010_03274 A1S_0063 HMPREF0010_03221 A1S_0114 HMPREF0010_03191 A1S_0147 HMPREF0010_02008 A1S_0217 HMPREF0010_01991 A1S_0236 HMPREF0010_01903 A1S_0334 HMPREF0010_01875 A1S_0364 HMPREF0010_01854 A1S_0388 HMPREF0010_01851 A1S_0391 HMPREF0010_01810 A1S_0428 HMPREF0010_01791 A1S_0447 HMPREF0010_01758 A1S_0469 HMPREF0010_01757 A1S_0470 HMPREF0010_01723 A1S_0506 HMPREF0010_01691 A1S_0561 HMPREF0010_01682 A1S_0571 KFC HMPREF0010_02522 HMPREF0010_02769 HMPREF0010_03233 HMPREF0010_00091...”
FTN_1666 conserverd protein of unknown function from Francisella tularensis subsp. novicida U112
38% identity, 71% coverage
PD0463 conserved hypothetical protein from Xylella fastidiosa Temecula1
49% identity, 44% coverage
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