PaperBLAST
PaperBLAST Hits for VIMSS5386 hypothetical protein (337 a.a., MVKIVVRIAT...)
Show query sequence
>VIMSS5386 hypothetical protein
MVKIVVRIATYASHSALQILKGAKDEGFETIAFGSERVKPLYTKYFPVADYFLVGKYPED
ELLELNAVVIPTGSFVAHLGVELVERMKVPYFGNKRVLKWESDRNLERKWLEKAKLKLPR
VYDDPDDIDRPVIVKPHGAKGGRGYFIAKDPQDFWTKVEKFLGIKDKEDLKNVQIQEYVI
GVPVYPHYFYSKLTRELELMSIDRRYESNVDAIGRIPSKDQLELELDITYTVIGNIPLVL
RESLLMDVIEAGERTVKAAEELMGGLWGPFCLEGVFTPDLDFVVFEISARIVAGTNPFIN
GSPYTWLKYDEPMSTGRRIAREIRLAIEEDKLDEVVS
Running BLASTp...
Found 17 similar proteins in the literature:
PAB0547 hypothetical protein from Pyrococcus abyssi GE5
100% identity, 100% coverage
- Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis
Gao, BMC genomics 2007 - “...characteristics of most Archaea. Of these proteins, 11 proteins (viz. PAB0654, PAB0950, PAB1135, PAB1906, PAB7388, PAB0547, PAB0552, PAB0623, PAB1272, PAB1429 and PAB1721) are mainly missing in the 4 Thermoplasmata species. Thermoplasmata are thermoacidophilic archaea which lack cell envelope [ 19 , 55 , 63 ](see Table...”
- “...COG1685 PAB7388 [NP_127197] Ribosomal_LX CDD2437 PAB0654 [NP_126650] CDD8168 PAB0469.1n [NP_877631] CDD8674 PAB0950 [NP_127106] TFIIE CDD480 PAB0547 [NP_126484] COG1759 PAB1112 [NP_127373] CDD5727 PAB0552 [NP_126501] Hjr CDD29957 PAB1135 [NP_127406] CDD8168 PAB0623 [NP_126611] CDD9586 PAB1241 [NP_127355] CDD9682 PAB1272 [NP_127310] COG1759 PAB1387 [NP_127161] flaJ COG1955 PAB1429 [NP_127105] COG2433 PAB1715 [NP_126667]...”
PURP_PYRFU / Q8U0R7 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase; 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate--formate ligase; EC 6.3.4.23 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (see paper)
2r86A / Q8U0R7 Crystal structure of purp from pyrococcus furiosus complexed with atp (see paper)
PF1517 hypothetical protein from Pyrococcus furiosus DSM 3638
85% identity, 99% coverage
- function: Catalyzes the ATP- and formate-dependent formylation of 5- aminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (FAICAR) in the absence of folates.
catalytic activity: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + formate + ATP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide + ADP + phosphate (RHEA:24836)
cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
subunit: Homotrimer and homohexamer. - Ligands: phosphate ion; adenosine-5'-triphosphate (2r86A)
- Purine biosynthesis in archaea: variations on a theme
Brown, Biology direct 2011 - “...cluster Ia, is the formate-dependent AICAR formyltransferase originally designated PurP [ 8 ]. Pyrococcus furiosus PF1517, in cluster Ib, and PF0421, in cluster II, have been reported to have no AICAR formyltransferase activity previously [ 66 ], although activity under different conditions or with different substrates...”
- Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii
Zhang, Biochemistry 2008 - “...also report structures from three crystal forms of a PF1517 (PfPurP), one of two PurP orthologs found in Pyrococcus furiosus. Although the MjPurP and PfPurP...”
- “...Purification of PfPurP Pyrococcus furiosus purP gene at loci Pf1517 was amplified by PCR from genomic DNA and subcloned into pT7-7 vector. The gene containing...”
- 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 - “...vs maltose 4.1 2.5 2.1 2.3 PF0426 PF1516 PF1517 4.3 2.3 4.8 4.0 2.4 3.1 SAICAR synthase Glutamine phosphoribosylpyrophosphate amidotransferase NCAIR synthetase...”
2r84B / Q8U0R7 Crystal structure of purp from pyrococcus furiosus complexed with amp and aicar (see paper)
79% identity, 99% coverage
- Ligands: adenosine monophosphate; aminoimidazole 4-carboxamide ribonucleotide (2r84B)
purP / Q57600 FAICAR synthetase monomer (EC 6.3.4.23) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see 2 papers)
PURP_METJA / Q57600 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase; 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate--formate ligase; EC 6.3.4.23 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see 2 papers)
Q57600 formate-phosphoribosylaminoimidazolecarboxamide ligase (EC 6.3.4.23) from Methanocaldococcus jannaschii (see 2 papers)
MJ0136 conserved hypothetical protein from Methanocaldococcus jannaschii DSM 2661
48% identity, 92% coverage
- function: Catalyzes the ATP- and formate-dependent formylation of 5- aminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (FAICAR) in the absence of folates.
catalytic activity: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + formate + ATP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide + ADP + phosphate (RHEA:24836)
cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
subunit: Homohexamer. Dimer of trimers. - Purine biosynthesis in archaea: variations on a theme
Brown, Biology direct 2011 - “...His 27 ( M. jannaschii numbering), which make contacts to the formyl group in the MJ0136 crystal structure [ 66 ]. Residues contacting the 5' monophosphate of AICAR were largely conserved, although we found conservative substitution with Thr at Ser 94. Ser 94 was not conserved...”
- “...only a few gene products in the PurP-like family have been experimentally characterized. M. jannaschii MJ0136, in cluster Ia, is the formate-dependent AICAR formyltransferase originally designated PurP [ 8 ]. Pyrococcus furiosus PF1517, in cluster Ib, and PF0421, in cluster II, have been reported to have...”
- Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii
Zhang, Biochemistry 2008 - “...NIH-PA Author Manuscript Methanocaldococcus jannaschii purP gene Mj0136 was cloned into the expression vector pET19b and overexpressed in Escherichia coli...”
- A Methanocaldococcus jannaschii archaeal signature gene encodes for a 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase. A new enzyme in purine biosynthesis
Ownby, The Journal of biological chemistry 2005 (PubMed)- “...the product of the Methanocaldococcus jannaschii purP gene (MJ0136), which is a signature gene for Archaea. As is characteristic of reactions catalyzed by this...”
- “...formate as substrates. Only the protein derived from the MJ0136 gene, which we designate as purP, catalyzed the desired reaction. Here we present the data on...”
2r7kA / Q57600 Crystal structure of faicar synthetase (purp) from m. Jannaschii complexed with amppcp and aicar (see paper)
48% identity, 93% coverage
- Ligands: phosphomethylphosphonic acid adenylate ester; aminoimidazole 4-carboxamide ribonucleotide (2r7kA)
MTH1201 conserved protein from Methanothermobacter thermautotrophicus str. Delta H
45% identity, 88% coverage
MTBMA_c15790 formate--phosphoribosylaminoimidazolecarboxamide ligase from Methanothermobacter marburgensis str. Marburg
44% identity, 91% coverage
D7DS15 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase from Methanococcus voltae (strain ATCC BAA-1334 / A3)
46% identity, 91% coverage
- Proteomic Analysis of Methanococcus voltae Grown in the Presence of Mineral and Nonmineral Sources of Iron and Sulfur
Steward, Microbiology spectrum 2022 - “...transporter-related proteins Extracellular solute-binding protein family 1 D7DV05 2.89244 2.05020 5-Formaminoimidazole-4-carboxamide-1-(beta)- d -ribofuranosyl 5-monophosphate synthetase D7DS15 11.55548 5.51428 ABC transporter-related protein D7DTS1 0.06359 0.01663 3.8233 0.0023623 ABC transporter-related protein D7DR50 0.23008 0.55915 2.43019 0.0003957 ABC transporter-related protein D7DT53 21.68802 15.94546 Formate/nitrite transporter D7DTM1 1.57738 1.21316 Substrate-binding...”
SSO0239 Conserved hypothetical protein from Sulfolobus solfataricus P2
46% identity, 93% coverage
MCP_2462 5-formaminoimidazole-4-carboxamide-1-(beta)-D- ribofuranosyl 5'-monophosphate synthetase from Methanocella paludicola SANAE
41% identity, 92% coverage
- Purine biosynthesis in archaea: variations on a theme
Brown, Biology direct 2011 - “...of the Methanococcales, Methanobacteriales, and Methanocella sp . RC-I, and one of the PurP-like proteins (MCP_2462) from Methanocella paludicola . As each of these organisms (except for M. paludicola ) has a single PurP with high similarity to M. jannaschii PurP and no PurH1, all are...”
PF0421 hypothetical protein from Pyrococcus furiosus DSM 3638
38% identity, 87% coverage
- Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus
Khatibi, Biotechnology and bioengineering 2017 - “...14 Energy metabolism PF0477 extracellular alpha amylase 3 17 50 Purines, pyrimidines, nucleosides, and nucleotides PF0421 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5-monophosphate synthetase --- 19 29 PF0422 phosphoribosylamine-glycine ligase --- 13 12 PF0426 phosphoribosylaminoimidazole carboxylase --- 7 8 PF0427 phosphoribosylaminoimidazole carboxylase 2 4 8 PF0430 phosphoribosylglycinamide formyltransferase 2 36 16...”
- Purine biosynthesis in archaea: variations on a theme
Brown, Biology direct 2011 - “...AICAR formyltransferase originally designated PurP [ 8 ]. Pyrococcus furiosus PF1517, in cluster Ib, and PF0421, in cluster II, have been reported to have no AICAR formyltransferase activity previously [ 66 ], although activity under different conditions or with different substrates cannot be ruled out. Crude...”
- Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii
Zhang, Biochemistry 2008 - “...P. furiosus, for example, has two purP genes (Pf0421 and Pf1517). In preliminary studies, neither P. furiosus gene product showed detectable FAICAR synthetase...”
- “...Author Manuscript subgroups; and the second P. furiosus PurP (Pf0421) belongs to group 3. No gene product from group 2 or group 3 has been functionally...”
PAB1272 hypothetical protein from Pyrococcus abyssi GE5
36% identity, 87% coverage
- Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis
Gao, BMC genomics 2007 - “...Archaea. Of these proteins, 11 proteins (viz. PAB0654, PAB0950, PAB1135, PAB1906, PAB7388, PAB0547, PAB0552, PAB0623, PAB1272, PAB1429 and PAB1721) are mainly missing in the 4 Thermoplasmata species. Thermoplasmata are thermoacidophilic archaea which lack cell envelope [ 19 , 55 , 63 ](see Table 1 ). Some...”
- “...[NP_127373] CDD5727 PAB0552 [NP_126501] Hjr CDD29957 PAB1135 [NP_127406] CDD8168 PAB0623 [NP_126611] CDD9586 PAB1241 [NP_127355] CDD9682 PAB1272 [NP_127310] COG1759 PAB1387 [NP_127161] flaJ COG1955 PAB1429 [NP_127105] COG2433 PAB1715 [NP_126667] CDD9801 PAB1721 [NP_126657] COG2248 PAB1906 [NP_126377] CDD2531 PAB2342 2 [NP_125707] CDD15774 PAB7094 [NP_126085] Alba CDD25844 PAB7309 [NP_126897] CDD2523 These...”
TK0203 hypothetical protein from Thermococcus kodakaraensis KOD1
36% identity, 87% coverage
TK0431 hypothetical protein from Thermococcus kodakaraensis KOD1
38% identity, 98% coverage
- Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis
Sanders, Frontiers in microbiology 2021 - “...Methyl-accepting chemotaxis protein Environmental information processing 5.19 TK0637 Chemotaxis protein CheC Environmental information processing 5.07 TK0431 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5-monophosphate synthetase Purine metabolism 4.51 TK0638 Methyl-accepting chemotaxis protein Environmental information processing 4.43 TK0432 Phosphonbosylam inoimidazole-succinocarboxamide synthase Purine metaboism 4.26 TK1139 ATPase, AAA superfamily unknown 4.23 TK0051 Protein- L...”
- Purine biosynthesis in archaea: variations on a theme
Brown, Biology direct 2011 - “...one protein closely related to the cluster Ib proteins of other Thermococci and one protein (TK0431 and the split TK1267 and TK1266) that is only distantly related to other PurP proteins in cluster I. The "extra" T. kodakaraensis gene product has been crystallized without substrates (PDB...”
- “...the loop from 161-165 for all the archaea studied. In this regard, the divergent sequences TK0431 and TGAM_1266-7 are members of cluster I. Figure 6 WebLOGOs for the combined cluster Ia/Ib P-loop (top) and corresponding cluster II loop region (bottom) . At this time, only a...”
2pbzA / Q5JD28 Crystal structure of an imp biosynthesis protein purp from thermococcus kodakaraensis
37% identity, 98% coverage
- Ligand: adenosine-5'-triphosphate (2pbzA)
TEU_09520 formate--phosphoribosylaminoimidazolecarboxamide ligase from Thermococcus eurythermalis
37% identity, 98% coverage
AF0256 conserved hypothetical protein from Archaeoglobus fulgidus DSM 4304
30% identity, 89% coverage
- Purine biosynthesis in archaea: variations on a theme
Brown, Biology direct 2011 - “...both purP -like genes to purine biosynthesis. The A. fulgidus cluster II purP -like gene (AF0256) is clustered with guaA1 (not shown), while the cluster Ib gene has no apparent linkage to purine biosynthesis. Pyrococcus abyssi and P. furiosus ' purP -like genes are both near...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 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