PaperBLAST
PaperBLAST Hits for metacyc::MONOMER-3165 protocatechuate 4,5-dioxygenase α subunit (EC 1.13.11.8; EC 1.13.11.57) (Comamonas testosteroni) (149 a.a., MALEKPYLDV...)
Show query sequence
>metacyc::MONOMER-3165 protocatechuate 4,5-dioxygenase α subunit (EC 1.13.11.8; EC 1.13.11.57) (Comamonas testosteroni)
MALEKPYLDVPGTIIFDAEQSRKGYWLNQFCMSLMKAENRERFRADERAYLDEWAMTEEQ
KQAVLARDLNWCMRTGGNIYFLAKIGATDGKSFQQMAGSMTGMTEEEYRAMMMGGGRSAE
GNRYVGEDGDAQAHHQPQGSAGNQNKEGN
Running BLASTp...
Found 30 similar proteins in the literature:
PmdA / Q8RNY0 protocatechuate 4,5-dioxygenase α subunit (EC 1.13.11.8; EC 1.13.11.57) from Comamonas testosteroni (see paper)
Q8RNY0 protocatechuate 4,5-dioxygenase (EC 1.13.11.8) from Comamonas testosteroni (see paper)
100% identity, 100% coverage
AAK73572.1 PmdA from Comamonas testosteroni (see paper)
99% identity, 100% coverage
proOa / BAD04057.1 alpha subunit of protocatechuate 4,5-dioxygenase from Pseudomonas straminea (see paper)
98% identity, 100% coverage
pmdA / BAI50714.1 protocatechuate 4,5-dioxygenase alpha subunit from Comamonas sp. E6 (see paper)
98% identity, 100% coverage
AA671_20045 protocatechuate 4,5-dioxygenase subunit alpha from Delftia tsuruhatensis
90% identity, 98% coverage
- Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity
Hou, Genome announcements 2015 - “...degrading plant-produced antimicrobial root exudates ( 13 , 14 ). Protocatechuate dioxygenase (AA671_06970, AA671_06975, AA671_20040, AA671_20045, AA671_25085, AA671_25090) may be related to the degradation of aromatic acid ( 15 ). Genes related to the degradation of phenylacetic acid (AA671_06085, AA671_20955, AA671_23770, AA671_24525, AA671_24535) and hydroxyatrazine (AA671_03765)...”
Rfer_0331 Protocatechuate 4,5-dioxygenase from Rhodoferax ferrireducens DSM 15236
81% identity, 97% coverage
D3M96_07060 protocatechuate 4,5-dioxygenase subunit alpha from Alcaligenes aquatilis
80% identity, 85% coverage
DelCs14_3008 protocatechuate 4,5-dioxygenase subunit alpha from Delftia sp. Cs1-4
79% identity, 85% coverage
AA671_25085 protocatechuate 4,5-dioxygenase subunit alpha from Delftia tsuruhatensis
78% identity, 85% coverage
- Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity
Hou, Genome announcements 2015 - “...plant-produced antimicrobial root exudates ( 13 , 14 ). Protocatechuate dioxygenase (AA671_06970, AA671_06975, AA671_20040, AA671_20045, AA671_25085, AA671_25090) may be related to the degradation of aromatic acid ( 15 ). Genes related to the degradation of phenylacetic acid (AA671_06085, AA671_20955, AA671_23770, AA671_24525, AA671_24535) and hydroxyatrazine (AA671_03765) were...”
Q9AGL8 Protocatechuate 4,5-dioxygenase from Arthrobacter keyseri
71% identity, 30% coverage
Asphe3_42380 protocatechuate 4,5-dioxygenase subunit alpha/beta from Pseudarthrobacter phenanthrenivorans Sphe3
71% identity, 30% coverage
- Elucidation of 4-Hydroxybenzoic Acid Catabolic Pathways in <i>Pseudarthrobacter phenanthrenivorans</i> Sphe3
Tsagogiannis, International journal of molecular sciences 2024 - “...4HB3H and the - and -subunits of PCD34 and CDO12 enzymes, respectively, whereas the genes Asphe3_42380 and Asphe3_40510, located on the plasmids, are considered to encode the PCD45 and CDO23 enzymes, respectively, according to the JGI database ( Table S1 from Supplementary Material ). According to...”
- “...Asphe3_38690 shares very high sequence identity (>93%) with 4HB3H from other Pseudarthrobacter strains; Asphe3_38850/Asphe3_38860 and Asphe3_42380 share over 90% identity with PCD34 and PCD45 enzymes, respectively, from Arthrobacter , Pseudarthrobacter and other Actinobacteria strains. Asphe3_35170 presents over 91% similarity with other Arthrobacter CDO12s, while Asphe3_40510 presents...”
- Characterization of Protocatechuate 4,5-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and In Situ Reaction Monitoring in the NMR Tube
Tsagogiannis, International journal of molecular sciences 2021 - “...C (Asphe3_ 42370), pcm C, pmd D, lig I, fld B, PDC hydrolase; pca A (Asphe3_42380), pcm A, PCA 4,5-dioxygenase; pmd A, lig A, fld V, -subunit of PCA 4,5-dioxygenase; pmd B, lig B, fld U, -subunit of PCA 4,5-dioxygenase; pca B (Asphe_42390), pcm B, pmd...”
ligA / P22635 protocatechuate 4,5-dioxygenase alpha chain (EC 1.13.11.8) from Sphingobium sp. (strain NBRC 103272 / SYK-6) (see 2 papers)
G2IQQ4 protocatechuate 4,5-dioxygenase (subunit 2/2) (EC 1.13.11.8) from Sphingobium sp. (see paper)
ligA / BAB88742.1 alpha subunit of protocatechuate 4,5-dioxygenase from Sphingomonas paucimobilis (see 5 papers)
P22635 Protocatechuate 4,5-dioxygenase alpha chain from Sphingobium sp. (strain NBRC 103272 / SYK-6)
66% identity, 79% coverage
- Plant-Soil-Microbiota Combination for the Removal of Total Petroleum Hydrocarbons (TPH): An In-Field Experiment
Zuzolo, Frontiers in microbiology 2020 - “...Q13ZY3), Homogentisate 1,2-dioxygenase (Uniprot code Q828S5 and B8H072), and Protocatechuate 4,5-dioxygenase (Uniprot code P20371 and P22635). The gene sequences from the isolates were deposited on European Nucleotide Archive (ENA) and are available at www.ebi.ac.uk/ena/submit/sra/#home . The short reads were determined by BLAST. All readings with an...”
- Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils.
Yergeau, PloS one 2012 - “...1.13.11.5; B8H072 and Q828S5), catechol 2,3-dioxygenase (EC 1.13.11.2; P06622 and Q53034), protocatechuate 4,5-dioxygenase (EC 1.13.11.8; P22635). All hits having an E-value below 0.10 were considered as significant and the corresponding sequences were recruited from the metagenomic datasets. We used a very low E-value for recruiting sequences,...”
- Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach.
Lin, BMC bioinformatics 2006 - “...Status Swiss-Prot AC Prediction Status P04390 - P20910 + P43589 - Q09824 - O13826 - P22635 - P49412 + Q17374 + O13862 + P23382 - P49659 + Q44009 + O26638 + P23485 + P50534 + Q45488 + O29031 + P23657 - P52283 - Q52982 - O29156...”
NSU_3625 protocatechuate 4,5-dioxygenase subunit alpha from Novosphingobium pentaromativorans US6-1
64% identity, 77% coverage
Saro_2813 Protocatechuate 4,5-dioxygenase from Novosphingobium aromaticivorans DSM 12444
59% identity, 79% coverage
- Redundancy in aromatic O-demethylation and ring opening reactions in Novosphingobium aromaticivorans and their impact in the metabolism of plant derived phenolics
Perez, Applied and environmental microbiology 2021 - “...only aromatic ring-opening dioxygenase that has been previously identified is a LigAB homologue, encoded by Saro_2813 ( ligA ) and Saro_2812 ( ligB ) ( 15 ), whose subunits have 67% and 70% amino acid sequence identity with LigA and LigB of Sphingobium sp. SYK-6, respectively....”
- “...Background used for strain construction Relevant characteristics 12444 ligAB 12444 1879 a 12444 1879 Saro_2812 Saro_2813 12444 ligAB2 12444 1879 12444 1879 Saro_1233 Saro_1234 12444 ligAB ligAB2 12444 ligAB 12444 1879 Saro_2812 Saro_2813 Saro_1233 Saro_1234 12444PDC ligAB 12444PDC a 12444PDC Saro_2812 Saro_2813 12444PDC ligAB2 12444PDC 12444PDC...”
ligA / BAA97117.1 protocatechuate 4,5-dioxygenase small subunit, partial from Sphingomonas paucimobilis (see 3 papers)
68% identity, 70% coverage
BRADO2379 Protocatechuate 4,5-dioxygenase (4,5-PCD), alpha chain from Bradyrhizobium sp. ORS278
39% identity, 70% coverage
SLG_37530 protocatechuate 4,5-dioxygenase subunit alpha from Sphingobium sp. SYK-6
42% identity, 70% coverage
NSU_3635 protocatechuate 4,5-dioxygenase subunit alpha from Novosphingobium pentaromativorans US6-1
40% identity, 70% coverage
AA671_06970 protocatechuate 4,5-dioxygenase subunit alpha from Delftia tsuruhatensis
41% identity, 69% coverage
- Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity
Hou, Genome announcements 2015 - “...bacterium involved in degrading plant-produced antimicrobial root exudates ( 13 , 14 ). Protocatechuate dioxygenase (AA671_06970, AA671_06975, AA671_20040, AA671_20045, AA671_25085, AA671_25090) may be related to the degradation of aromatic acid ( 15 ). Genes related to the degradation of phenylacetic acid (AA671_06085, AA671_20955, AA671_23770, AA671_24525, AA671_24535)...”
Saro_1233 Extradiol ring-cleavage dioxygenase LigAB, LigA subunit from Novosphingobium aromaticivorans DSM 12444
37% identity, 41% coverage
gllA / Q88JX5 gallate dioxygenase monomer (EC 1.13.11.57) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
GALA_PSEPK / Q88JX5 Gallate dioxygenase; Gallate degradation protein A; EC 1.13.11.57 from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see 2 papers)
30% identity, 29% coverage
- function: Ring-cleavage dioxygenase that acts specifically on gallate to produce the keto-tautomer of 4-oxalomesaconate. Mediates the first step of gallate degradation pathway.
catalytic activity: 3,4,5-trihydroxybenzoate + O2 = (1E)-4-oxobut-1-ene-1,2,4- tricarboxylate + 2 H(+) (RHEA:28927)
cofactor: Fe(2+) - Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases
Terrón-González, Applied and environmental microbiology 2016 - “...(Q9L3A6); GalA PSEPU, gallate dioxygenase, Pseudomonas putida KT2440 (Q88JX5 plus 80 aa at N terminus: the ORF for GalA apparently starts 240 nucleotides...”
- “...terminus compared to that of Q88JX5); HpaD ESCCO, 3,4-dihydroxyphenylacetate 2,3-dioxygenase, Escherichia coli (Q46980); MhpB ESCCO,...”
CBL13_00562 gallate dioxygenase from Pseudomonas putida
30% identity, 23% coverage
PP_RS13165 gallate dioxygenase from Pseudomonas putida KT2440
30% identity, 23% coverage
PPUTLS46_010694 gallate dioxygenase from Pseudomonas putida LS46
30% identity, 23% coverage
E2P69_RS13540 protocatechuate 3,4-dioxygenase subunit alpha from Xanthomonas perforans
28% identity, 66% coverage
A9762_21285 protocatechuate 3,4-dioxygenase from Pandoraea sp. ISTKB
31% identity, 68% coverage
XC_3426 protocatechuate degradation protein from Xanthomonas campestris pv. campestris str. 8004
28% identity, 65% coverage
- Xanthomonas transcriptome inside cauliflower hydathodes reveals bacterial virulence strategies and physiological adaptations at early infection stages
Luneau, Molecular plant pathology 2022 - “...component of plant cell walls and a source of aromatic compounds. Interestingly, the expression of XC_3426 and X C_3427 genes coding for protocatechuate (PCA) 4;5dioxygenase subunits was increased 6 and 8fold at 72hpi, respectively. PCA is a lignin degradation product (Brown et al., 2004 ) that...”
- “...PCA dioxygenases to enter the tricarboxylic acid (TCA) cycle (Wang et al., 2015 ). While XC_3426 and XC_3427 relevance for pathogenicity remains unknown, XC_0375 to XC_0383 genes cluster encoding 3 and 4hydroxybenzoate degrading enzymes are needed for full virulence of Xcc in radish (Wang et al.,...”
- Systematic Functional Analysis of Sigma (σ) Factors in the Phytopathogen Xanthomonas campestris Reveals Novel Roles in the Regulation of Virulence and Viability
Yang, Frontiers in microbiology 2018 - “...protein XC_3177 1.810 Type III effector XopXccQ XC_3178 1.009 Hypothetical protein XC_3425 1.177 Transcriptional regulator XC_3426 1.329 Protocatechuate 4,5-dioxygenase subunit alpha XC_3427 1.331 Protocatechuate 4,5-dioxygenase subunit beta XC_3676 1.268 Chorismate mutase XC_3802 1.402 Avirulence protein AvrXccB XC_3895 1.458 Disulfide-isomerase XC_3922 2.161 Hypothetical protein XC_4206 1.495 Hypothetical...”
XAC0879 protocatechuate degradation protein from Xanthomonas axonopodis pv. citri str. 306
27% identity, 66% coverage
desB / Q5NTE5 gallate dioxygenase monomer (EC 1.13.11.57) from Sphingomonas paucimobilis (see paper)
G2IKE5 gallate dioxygenase (EC 1.13.11.57) from Sphingobium sp. SYK-6 (see paper)
Q5NTE5 gallate dioxygenase (EC 1.13.11.57) from Sphingomonas paucimobilis (see paper)
desB / BAD80871.1 gallate dioxygenase from Sphingomonas paucimobilis (see 2 papers)
SLG_03330 gallate dioxygenase from Sphingobium sp. SYK-6
26% identity, 24% coverage
- Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases
Terrón-González, Applied and environmental microbiology 2016 - “...(A0A0A1GK74); DesB SPHPA, gallate dioxygenase, Sphingomonas paucimobilis (Q5NTE5). Terron-Gonzalez et al. FIG 5 Relative activities of clones bearing edo genes....”
- Regulation of vanillate and syringate catabolism by a MarR-type transcriptional regulator DesR in Sphingobium sp. SYK-6
Araki, Scientific reports 2019 - “...36 , 37 . In the case of SYK-6, ligM (SLG_12740), desA (SLG_25000), and desB (SLG_03330), involved in VA/SA, SA, and SA catabolism, respectively, are scattered throughout the chromosome 12 , 16 . However, it is thought that these genes are synchronously expressed which enables them...”
3wr9A / G2IKE5 Crystal structure of the anaerobic desb-gallate complex (see paper)
26% identity, 24% coverage
- Ligands: fe (ii) ion; 3,4,5-trihydroxybenzoic acid (3wr9A)
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