PaperBLAST
PaperBLAST Hits for W6QU90 DUF934 domain-containing protein (Pseudomonas pseudoalcaligenes (strain CECT 5344)) (159 a.a., MTLIDTAGTP...)
Show query sequence
>W6QU90 DUF934 domain-containing protein (Pseudomonas pseudoalcaligenes (strain CECT 5344))
MTLIDTAGTPLADPYQYPAADQELTEADHCVVLLSQWDTYQELFGKTATGVWVTGDQDPA
DLLALLNRTRVVVIEFPKSRDGRGFTLARVLRERHRYDGDIRAAGPLLPDQFSMLIQCGY
TSVLAEAAIPLVRWKEAAMALDQSKARPRTLLDRLSQNR
Running BLASTp...
Found 28 similar proteins in the literature:
W6QU90 DUF934 domain-containing protein from Pseudomonas pseudoalcaligenes (strain CECT 5344)
100% identity, 100% coverage
BTH_I0815 Bacterial protein of unknown function (DUF934) superfamily from Burkholderia thailandensis E264
38% identity, 56% coverage
BPHYT_RS04730 required for sulfate utilization, putative electron transport protein for sulfite reductase from Burkholderia phytofirmans PsJN
41% identity, 41% coverage
- mutant phenotype: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic
PA1837 hypothetical protein from Pseudomonas aeruginosa PAO1
36% identity, 61% coverage
- Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa
Drabinska, International journal of molecular sciences 2021 - “...Alkaline metalloproteinase PA1493 cysP 0.55 Sulphate ABC transporter substrate-binding protein PA1756 cysH 0.98 Phosphoadenosinephosphosulphate reductase PA1837 PA1837 1.52 Hypothetical protein/ oxidoreductase probably involved in sulphite reduction PA1838 cysI 1.29 Sulphite reductase PA1912 femI 0.39 ECF sigma factor FemI PA2062 PA2062 1.00 Probable pyridoxal-phosphate dependent protein/ IscS...”
- The LysR-Type Transcriptional Regulator BsrA (PA2121) Controls Vital Metabolic Pathways in Pseudomonas aeruginosa
Modrzejewska, mSystems 2021 - “...180 07670 PA3488 305 07670 PA3488 2.09 2.45 Hypothetical protein 410 16485 PA1838 7 16490 PA1837 2.10 2.02 DUF934 domain-containing protein 348 13300 PA2440 374 13295 PA2441 2.10 2.45 Hypothetical protein 389 15535 PA2020 72 15535 PA2020 2.11 2.50 MexZ, transcriptional regulator 652 25380 PA4673.1 28...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...Alkaline proteinase inhibitor AprI PA1384 galE 1.3 UDP-glucose 4-epimerase PA1784 1.2 1.6 + Hypothetical protein PA1837 2 Hypothetical protein PA1838 cysI 1.5 Sulfite reductase PA1869 acp1 2.4 2.2 + Acp1 PA1871 lasA 2 3.4 + LasA protease precursor PA1899 phzA2 2.1 2.8 Probable phenazine biosynthesis protein...”
- Molecular mechanism for sphingosine-induced Pseudomonas ceramidase expression through the transcriptional regulator SphR
Okino, Scientific reports 2016 - “...cysN ATP sulfurylase GTP-binding subunit/APS kinase 2.294 0.0304196 PA2426 pvdS sigma factor PvdS 2.285 0.0049072 PA1837 hypothetical protein 2.271 0.0095659 PA4351 OlsA 2.238 0.0282751 PA0280 cysA sulfate transport protein CysA 2.171 0.0079830 PA0843 plcR phospholipase accessory protein PlcR precursor 2.074 0.0009660 PA0844 plcH hemolytic phospholipase C...”
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
Lecoutere, MicrobiologyOpen 2012 - “...54 * PA1800 tig Trigger factor O C 48.6 54 4.83 4.76 0.699 0.395 55 PA1837 Hypothetical protein S C 18.8 19 4.88 4.88 0.69 0.378 56 PA2001 atoB Acetyl CoA acetyltransferase I C 40.4 40 6.03 6.02 0.716 0.121 57 PA2064 pcoB Copper resistance protein...”
- “...Pseudomonas database, 12 of which so far lacked experimental confirmation (PA0446, PA0664, PA0976, PA1597, PA1677, PA1837, PA2806, PA3302, PA3481, PA3801, PA4458, and PA5339). Among those 19 proteins, 12 are conserved in other organisms. Obviously, their substantial expression suggests that they have biological roles in P. aeruginosa...”
- Indole and 7-hydroxyindole diminish Pseudomonas aeruginosa virulence
Lee, Microbial biotechnology 2009 - “...1.3 Hypothetical protein PA0939 1.1 5.3 1.6 Hypothetical protein PA1190 5.7 1.6 1.2 Hypothetical protein PA1837 4.6 2.1 1.1 Hypothetical protein PA1914 1.1 6.1 1.1 Hypothetical protein PA1953 3.2 6.1 1.5 Hypothetical protein PA2036 2.0 7.0 1.1 Hypothetical protein PA2078 3.0 5.7 1.6 Hypothetical protein PA2419...”
HP15_1796 required for sulfate utilization, putative electron transport protein for sulfite reductase from Marinobacter adhaerens HP15
ACP86_21365 DUF934 domain-containing protein from Marinobacter sp. CP1
35% identity, 52% coverage
PP_2370 conserved hypothetical protein from Pseudomonas putida KT2440
31% identity, 64% coverage
- Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440
Avendaño, Microbial biotechnology 2023 - “...Cmethyltransferase Sulphur metabolism/Porphyrins Delayed RF31 PP_3999 cysG UroporphyrinIII Cmethyltransferase JJ3 PP_3999 cysG UroporphyrinIII Cmethyltransferase JJ7 PP_2370 Hypothetical conserved protein Sulphur metabolism JJ13 PP_0051 sqrR Putative dependant sigma54 transcriptional regulator Fast JJ33 PP_0052 pdo2 Persulphide dioxygenase JJ14 PP_0053 sqr Sulphidequinone oxidoreductase RF16 PP_4189 sucA 2oxoglutarate dehydrogenase Central...”
- “...related to selenium metabolism were obtained (Table 1 ). Twelve mutants (in genes cysG , PP_2370, sucA , D2HGDH , gqr , ccmF , ldcA , msbA and wzy ) had a phenotype delayed in the production of elemental selenium nanoparticles, meaning that the colonies had...”
CCNA_01178 oxidoreductase from Caulobacter crescentus NA1000
43% identity, 53% coverage
RR42_RS16265 required for sulfate utilization, putative electron transport protein for sulfite reductase from Cupriavidus basilensis FW507-4G11
33% identity, 65% coverage
- mutant phenotype: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic
Psyr_2461 Uncharacterised conserved protein UCP030820 from Pseudomonas syringae pv. syringae B728a
30% identity, 63% coverage
Ga0059261_1499 required for sulfate utilization, putative electron transport protein for sulfite reductase from Sphingomonas koreensis DSMZ 15582
39% identity, 57% coverage
- mutant phenotype: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic
PfGW456L13_2842 required for sulfate utilization, putative electron transport protein for sulfite reductase from Pseudomonas fluorescens GW456-L13
27% identity, 64% coverage
- mutant phenotype: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic
Pf6N2E2_2074 required for sulfate utilization, putative electron transport protein for sulfite reductase from Pseudomonas fluorescens FW300-N2E2
28% identity, 61% coverage
- mutant phenotype: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic
AO356_00560 required for sulfate utilization, putative electron transport protein for sulfite reductase from Pseudomonas fluorescens FW300-N2C3
28% identity, 61% coverage
- mutant phenotype: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase, auxotrophic
RSc2424 CONSERVED HYPOTHETICAL PROTEIN from Ralstonia solanacearum GMI1000
31% identity, 56% coverage
- A CysB regulator positively regulates cysteine synthesis, expression of type III secretion system genes, and pathogenicity in Ralstonia solanacearum
Chen, Molecular plant pathology 2022 - “...function for sulphate transportation (Figure 3a ). A further five genes, cysI ( RSc2425 ), RSc2424 (hypothetical protein), cysH ( RSc2423 ), cysD ( RSc2422 ), and cysN ( RSc2422 ), are located together, possibly forming a cysI regulon to function for sulphate reduction (Figure 3b...”
AL066_11190 DUF934 domain-containing protein from Pseudomonas nunensis
39% identity, 45% coverage
PA14_10560 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
37% identity, 46% coverage
PA4129 hypothetical protein from Pseudomonas aeruginosa PAO1
37% identity, 46% coverage
- The secondary metabolite hydrogen cyanide protects Pseudomonas aeruginosa against sodium hypochlorite-induced oxidative stress
da, Frontiers in microbiology 2023 - “...0.359 7.617 0.615 PA3022 PA3022 PW6063 9.181 0.331 7.228 2.425 PA14_24980 8.038 0.505 6.325 1.978 PA4129 PA4129 PW7993 9.113 0.397 6.482 1.977 PA4130 PA4130 PW7996 9.290 0.083 7.835 0.936 PA14_10550 6.401 0.398 6.176 0.577 PA4131 PA4131 PW7998 9.367 0.115 7.331 0.316 PA14_10540 8.238 0.105 7.278 0.483...”
- A VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of Pseudomonas aeruginosa TBCF10839
Wiehlmann, Frontiers in cellular and infection microbiology 2023 - “...T6SS) 29.5 PA3908 tsiT, immunity protein, TsiT (part of T6SS) 173.7 PA3928 Hypothetical protein 7.5 PA4129 Hypothetical protein 16.6 PA4130 nirA, ferredoxin-dependent nitrite reductase, NirA 24.2 PA4132 mpaR, MvfR-mediated PQS, and anthranilate regulator MpaR 8.1 PA4133 Cytochrome c oxidase subunit (cbb3-type) 40.6 PA4134 Hypothetical protein 35.3...”
- NirA Is an Alternative Nitrite Reductase from Pseudomonas aeruginosa with Potential as an Antivirulence Target
Fenn, mBio 2021 - “...hypothetical protein with homology to nitrite and sulfite reductases, and forming a predicted operon with PA4129 ( Fig.1E ). To ensure the attenuation in virulence traits observed was not due a polar effect on PA4129, located in the same predicted transcriptional unit as PA4130, in-frame deletion...”
- “...incubated at 37C for 16h. (E) Diagram displaying operon structure and transcriptional start sites of PA4129- PA4130 and PA4131- PA4132 with the PAJD21 Tn 5 insertion site indicated by the red arrow. Data were collated from three independent experiments with at least three replicates each. Values...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...terminal oxidase PA4078 2.1 3.9 + Probable non-ribosomal peptide synthetase PA4079 1.4 NaD(P)H-dependent carbonyl reductase PA4129 2.1 2.1 + Hypothetical protein PA4130 2.5 2 + Probable sulfite or nitrite reductase PA4131 2.3 1.9 + Probable ironsulfur protein PA4132 1.9 1.9 + Conserved hypothetical protein PA4133 4.2...”
- Conditional quorum-sensing induction of a cyanide-insensitive terminal oxidase stabilizes cooperating populations of Pseudomonas aeruginosa
Yan, Nature communications 2019 - “...the presence of 150M KCN; grid, in the absence of 150M KCN. b cioA , PA4129, PA4131, PA4133, and rhdA expression from either WT PAO1 (policing, black) or RhlR-null cooperators (non-policing, white) when grown in co-culture with cheaters, with the populations separated by dialysis membranes. Expression...”
- “...cooperators in these experiments with dialysis membranes and compared expression by cooperators of cioA , PA4129, PA4131, PA4133, or rhdA in both the policing and non-policing conditions. We added analysis of PA4129 and PA4131 in this analysis because differences in PA4133 expression were markedly different than...”
- A novel cyanide-inducible gene cluster helps protect Pseudomonas aeruginosa from cyanide
Frangipani, Environmental microbiology reports 2014 (PubMed)- “...These genes are predicted to encode hypothetical proteins (PA4129, PA4132 and PA4134), proteins possibly involved in electron transfer (PA4131 and PA4133), and...”
- “...translational fusion. This choice was made as PA4130 and PA4129 are homologues of two genes that form a transcriptional unit together with cioAB in P....”
- Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon
Chugani, Proceedings of the National Academy of Sciences of the United States of America 2012 - “...PA3332 PA3475 PA3476 PA3535 PA3724 PA3904 PA3907 PA4128 PA4129 PA4130 PA4131 PA4132 PA4134 PA4677 clpP2 pheC rhlI lasB Description RahU Chitin-binding protein...”
- Food as a source for quorum sensing inhibitors: iberin from horseradish revealed as a quorum sensing inhibitor of Pseudomonas aeruginosa
Jakobsen, Applied and environmental microbiology 2012 - “...PA3361 PA3477 PA3478 PA3479 PA3520 PA3692 PA3724 PA3923 PA4129 PA4130 PA4131 PA4132 PA4133 PA4134 PA4141 PA4142 PA4175 PA4209 PA4211 PA4217 PA4738 PA4739 PA5170...”
- More
CLJ1_0708 DUF934 domain-containing protein from Pseudomonas aeruginosa
38% identity, 44% coverage
SMc02123 required for sulfate utilization, putative electron transport protein for sulfite reductase from Sinorhizobium meliloti 1021
SMc02123 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
35% identity, 53% coverage
ABUW_0644 DUF934 domain-containing protein from Acinetobacter baumannii
32% identity, 73% coverage
ACIAD2981 conserved hypothetical protein from Acinetobacter sp. ADP1
30% identity, 77% coverage
RL2291 hypothetical protein from Rhizobium leguminosarum bv. viciae 3841
28% identity, 73% coverage
RSc1863 CONSERVED HYPOTHETICAL PROTEIN from Ralstonia solanacearum GMI1000
32% identity, 54% coverage
BCAM1677 hypothetical protein from Burkholderia cenocepacia J2315
34% identity, 51% coverage
- Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum
Drevinek, BMC infectious diseases 2008 - “...reactive oxygen and nitrogen species upregulated BCAL1766 2.23 OsmC-like protein BCAM1676 19.99 putative nitrite/sulfite reductase BCAM1677 26.75 conserved hypothetical protein BCAM2753 8.00 putative organic hydroperoxide resistance protein, ohr gene Downregulated (none) Motility and adherence upregulated BCAL0124 2.02 flagellar regulon master regulator subunit FlhD BCAL0525 2.17 flagellar...”
- “...dehydrogenase BCAL1156 2.02 putative 4-hydroxybenzoate transporter BCAL1157 2.51 putative monooxygenase BCAM1676 19.99 putative nitrite/sulfite reductase BCAM1677 26.75 conserved hypothetical protein BCAM2749 31.39 carboxymuconolactone decarboxylase family protein BCAM2750 14.06 putative exported protein BCAM2751 7.13 LysR family regulatory protein BCAM2752 12.35 NAD dependent epimerase/dehydratase family protein BCAM2753 8.00...”
BP3433 conserved hypothetical protein from Bordetella pertussis Tohama I
39% identity, 32% coverage
- Combined RNAseq and ChIPseq Analyses of the BvgA Virulence Regulator of Bordetella pertussis
Coutte, mSystems 2020 - “...bp2226 , bp2227 , bp2232, bp2233 , bp2256, bp2257, bp2749 , bp2907 ( fhaL ), bp3433 , and bp3439 ( dnt ), identified as vag s(3) in the RNAseq analysis. 10.1128/mSystems.00208-20.6 FIGS6 Representation of the ChIPseq reads mapping on the fim2 and fim3 loci. (A) ChIPseq-mapped...”
LPU83_2531 DUF934 domain-containing protein from Rhizobium favelukesii
29% identity, 69% coverage
BCAN_A0188 uncharacterised conserved protein UCP030820 from Brucella canis ATCC 23365
BMEI1764 OXIDOREDUCTASE from Brucella melitensis 16M
26% identity, 71% coverage
Ac3H11_576 required for sulfate utilization, putative electron transport protein for sulfite reductase from Acidovorax sp. GW101-3H11
41% identity, 41% coverage
- mutant phenotype: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 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