PaperBLAST
PaperBLAST Hits for MMP_RS06755 (52 a.a., MEILDKCVGC...)
Show query sequence
>MMP_RS06755
MEILDKCVGCAGCVPFCPVGAISAFGKAEIDTEMCTNCAVCKDYCPLDAISE
Running BLASTp...
Found 25 similar proteins in the literature:
Cphy_2056 hydrogenase, Fe-only from Clostridium phytofermentans ISDg
40% identity, 8% coverage
B2M23_RS02975 DUF362 domain-containing protein from Eubacterium limosum
47% identity, 88% coverage
P14073 Ferredoxin from Butyribacterium methylotrophicum
46% identity, 91% coverage
AF0355 ferredoxin (fdx-3) from Archaeoglobus fulgidus DSM 4304
53% identity, 65% coverage
D9PW01 Polyferredoxin from Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)
41% identity, 20% coverage
hymB / GI|14250934 protein HymB from Eubacterium acidaminophilum (see paper)
50% identity, 8% coverage
TON_0957 3'-phosphoadenosine 5'-phosphosulfate reductase from Thermococcus onnurineus NA1
44% identity, 7% coverage
AHA_1496 pyridine nucleotide-disulphide oxidoreductase family protein from Aeromonas hydrophila subsp. hydrophila ATCC 7966
A0KID3 Pyridine nucleotide-disulphide oxidoreductase family protein from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
43% identity, 8% coverage
- Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila
Li, Biology 2023 - “...5 , the top 20 hub proteins are A0KEL7 (gene ID: AHA_0149 ), A0KID3 ( AHA_1496 ), A0KLH4 ( AHA_2616 ), A0KLK7 ( AHA_2649 ), A0KN49 ( AHA_3209 ), EutE, FrdA, Icd, IlvB-2, LeuA-1, LeuB, PpsA, RnpA, RplF, RpmA, RpmG, RpmH, RpsB, RpsF, and YfiA-1, and...”
- Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila
Li, Biology 2023 - “...in Figure 5 , the top 20 hub proteins are A0KEL7 (gene ID: AHA_0149 ), A0KID3 ( AHA_1496 ), A0KLH4 ( AHA_2616 ), A0KLK7 ( AHA_2649 ), A0KN49 ( AHA_3209 ), EutE, FrdA, Icd, IlvB-2, LeuA-1, LeuB, PpsA, RnpA, RplF, RpmA, RpmG, RpmH, RpsB, RpsF, and...”
- Mechanisms of low susceptibility to the disinfectant benzalkonium chloride in a multidrug-resistant environmental isolate of Aeromonas hydrophila
Chacón, Frontiers in microbiology 2023 - “...1.217 0.015 A0KJK6 Succinate dehydrogenase iron-sulfur subunit 1.286 0.000 A0KKI6 Paraquat-inducible protein B 1.076 0.023 A0KID3 Pyridine nucleotide-disulfide oxidoreductase family protein 1.191 0.027 A0KK76 3-ketoacyl-CoA thiolase 1.251 0.000 A0KQF0 Sodium: dicarboxylate symporter family 1.031 0.002 A0KJK6 Succinate dehydrogenase iron-sulfur subunit 1.188 0.011 A0KNV4 DUF469 domain-containing protein...”
- “...A0KFP6 AHA_0539 0 A0KHF4 AHA_1164 1 A0KFQ1 AHA_0544 3 A0KIA0 AHA_1463 5 A0KFV9 AHA_0602 1 A0KID3 AHA_1493 9 A0KG30 ptsI-1 0 A0KIK8 AHA_1573 8 A0KG31 lgt 0 A0KIM8 moaD 3 A0KH11 alr-1 2 A0KIT7 AHA_1652 2 A0KH45 AHA_1053 13 A0KIY8 AHA_1703 5 A0KHA5 AHA_1114 3 A0KJK6...”
MCP_0638 putative phosphoadenosine phosphosulfate reductase from Methanocella paludicola SANAE
46% identity, 6% coverage
SWOL_RS10890 4Fe-4S binding protein from Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
52% identity, 81% coverage
GSU2708 ferredoxin family protein from Geobacter sulfurreducens PCA
48% identity, 88% coverage
CD1142 electron transport complex protein from Clostridium difficile 630
47% identity, 14% coverage
- Is there a Function for a Sex Pheromone Precursor?
Vasieva, Journal of integrative bioinformatics 2019 - “...(a.k.a. CD630_11410, YP_001087632.1, CD1141, Electron transport complex protein), rnfB Electron transport complex protein (a.k.a. CD630_11420, CD1142, YP_001087633.1, Electron transport complex protein). The neighbourhood and co-occurrence STRING views were chosen for graphical outputs of the associations between the input genes. For automated co-occurrence profiles STRING uses a...”
CD630_31210 EFR1 family ferrodoxin from Clostridioides difficile 630
CD3121 putative flavodoxin from Clostridium difficile 630
41% identity, 18% coverage
- Characterizing the flavodoxin landscape in Clostridioides difficile
Troitzsch, Microbiology spectrum 2024 - “...identifiers: CD630_08100 , CD630_14580 , CD630_16790 , CD630_19990 , CD630_22070 , CD630_26840 , CD630_28250 and CD630_31210 . Hereinafter, we will use the abbreviated notation of the flavodoxin names, CD0810 (floX), CD1458 (wrbA), CD1679, CD1999 (fldX), CD2207, CD2684, CD2825, and CD3121 . Table 1 lists characteristics specific...”
- Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile
Boudry, RNA biology 2021 - “...Putative CRISPR-associated Cas1 family protein 13.77 3.39713 CD630_30620 - Transcriptional regulator, RpiR family 57.58 4.15443 CD630_31210 + Putative flavodoxin/nitric oxide synthase 25.97 4.17693 CD630_31450 ( cbpA ) - Surface-exposed adhesin 20.96 3.0304 CD630_32040 - Putative membrane protein 173.22 4.93516 CD630_32050 + Putative nitroreductase 16.38 5.73797 CD630_35040...”
- Characterizing the flavodoxin landscape in Clostridioides difficile
Troitzsch, Microbiology spectrum 2024 - “...of the flavodoxin names, CD0810 (floX), CD1458 (wrbA), CD1679, CD1999 (fldX), CD2207, CD2684, CD2825, and CD3121 . Table 1 lists characteristics specific to each gene and associated protein ( Table 1 ). The eight flavodoxin sequences are distributed over the entire 4,290,252 bp genome of C....”
- “...a protein mass of 19 kDa, these putative flavodoxins are comparatively small proteins, except for CD3121 being much larger with 28.5 kDa. An alignment of all eight amino acid sequences shows that the proteins are not very similar in sequence. A one-to-one comparison reveals a sequence...”
- Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile
Boudry, RNA biology 2021 - “..., the nitroreductase gene CD3205 ( Fig. 3E ) and the flavodoxin/nitric oxide synthase gene CD3121 (Supplementary Figure S5G) (24-, 16- and 26-fold enrichment). Interestingly, in addition to CRISPR RNAs, the mRNAs for Cas1, Cas2 and Cas4 (CD2975-2976-2977 with 38-fold enrichment) CRISPR-associated adaptation proteins were co-immunoprecipitated...”
CTK_C26290 4Fe-4S dicluster domain-containing protein from Clostridium tyrobutyricum
45% identity, 10% coverage
CIBE_4899 glycyl-radical enzyme activating protein from Clostridium beijerinckii
39% identity, 14% coverage
- l-Rhamnose Metabolism in Clostridium beijerinckii Strain DSM 6423
Diallo, Applied and environmental microbiology 2019 - “...11 10 7.54 CIBE_4898 BMC-T shell protein S . Typhimurium PduB (67) 10 8.99 7.04 CIBE_4899 Propanediol dehydratase activator Clostridium butyricum DhaB2 (56) 11 11 7.69 CIBE_4900 Propanediol dehydratase C. butyricum DhaB1 (58) 12 10 6.94 CIBE_4901 Glutamine amidotransferase 6.3 5.94 5.44 CIBE_4902 Propanediol utilization protein...”
MMP1692 polyferredoxin, associated with F420-non-reducing hydrogenase from Methanococcus maripaludis S2
50% identity, 13% coverage
- An extracellular [NiFe] hydrogenase mediating iron corrosion is encoded in a genetically unstable genomic island in Methanococcus maripaludis
Tsurumaru, Scientific reports 2018 - “...and Mmp0817 - 0820 ), those for two non-F 420 -reducing hydrogenases ( vhu : Mmp1692 1696 ; and vhc : Mmp0821 - 0824 ) and those for two energy-conserving hydrogenases ( eha : Mmp1448 -1467 ; and ehb : Mmp0400 , 0940, 1049, 1073, 1074,...”
- Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
Hendrickson, Journal of bacteriology 2004 - “...non-F420-reducing hydrogenases, which also contain selenocysteine (Vhu) (Mmp1692 to -1696) and cysteine Downloaded from http://jb.asm.org/ on February 11, 2017...”
- “...Vhc contains Mmp0824 (a polyferredoxin), Vhu contains Mmp1692 (a polyferredoxin), Fru contains Mmp1384, and Frc contains Mmp0818. Among the multisubunit...”
TKV_c09620 indolepyruvate ferredoxin oxidoreductase subunit alpha from Thermoanaerobacter kivui
42% identity, 86% coverage
- A Versatile Aldehyde: Ferredoxin Oxidoreductase from the Organic Acid Reducing Thermoanaerobacter sp. Strain X514
Nissen, International journal of molecular sciences 2024 - “..., 13 , 15 ]. Here, we used four potential Fds from T. kivui (TKV_c16450; TKV_c09620; TKV_c10420; TKV_c19530), as they can be overproduced in T. kivui and subsequently purified using a His-tag [ 48 ]. Of these four putative Fds, two were used by the AOR...”
- “...carried out by Katsyv et al. (2023), it was found, that His- TKV_c16450 and His- TKV_c09620 are most likely ferredoxins involved in T. kivui metabolism [ 48 ]. The affinity for TKV_c09620 was higher than that for the artificial electron acceptors (50 to 200 M) (...”
- Characterization of ferredoxins from the thermophilic, acetogenic bacterium Thermoanaerobacter kivui
Katsyv, The FEBS journal 2023 (PubMed)- “...protein. Here, we show that the genome of T. kivui encodes four putative ferredoxin-like proteins (TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530). All four genes were cloned, a His-tag encoding sequence was added and the proteins were produced from a plasmid in T. kivui. The purified proteins had...”
- “...The determined iron-sulfur content is consistent with the presence of two predicted [4Fe4S] clusters in TKV_c09620 and TKV_c19530 or one predicted [4Fe4S] cluster in TKV_c16450 and TKV_c10420 respectively. The reduction potential (Em ) for TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530 was determined to be -386 4...”
CD630_11420, CDIF630erm_01289 RnfABCDGE type electron transport complex subunit B from Clostridioides difficile
47% identity, 15% coverage
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...RnfE 1.17 OFF 3.47 OFF CD630_11410 CDIF630erm_01288 rnfA Electron transport complex protein RnfA 1.88 3.55 CD630_11420 CDIF630erm_01289 rnfB Electron transport complex protein RnfB 1.61 -1.38 2.47 -0.91 CD630_11700 CDIF630erm_01318 larA Lactate racemase 1.41 2.86 CD630_11710 CDIF630erm_01319 etfB Lactate dehydrogenase, electron transfer flavoprotein beta subunit 0.67 OFF...”
- “...1.17 OFF 3.47 OFF CD630_11410 CDIF630erm_01288 rnfA Electron transport complex protein RnfA 1.88 3.55 CD630_11420 CDIF630erm_01289 rnfB Electron transport complex protein RnfB 1.61 -1.38 2.47 -0.91 CD630_11700 CDIF630erm_01318 larA Lactate racemase 1.41 2.86 CD630_11710 CDIF630erm_01319 etfB Lactate dehydrogenase, electron transfer flavoprotein beta subunit 0.67 OFF 2.43...”
Gmet_1033 4Fe-4S ferredoxin, iron-sulfur binding protein from Geobacter metallireducens GS-15
48% identity, 66% coverage
TK0290 pyruvate-formate lyase-activating enzyme from Thermococcus kodakaraensis KOD1
44% identity, 15% coverage
Q9P9E6 pyruvate synthase (subunit 3/5) (EC 1.2.7.1) from Methanococcus maripaludis (see paper)
48% identity, 55% coverage
PIN17_RS06895, PIOMA14_I_1049, PIOMA14_RS05315 4Fe-4S binding protein from Prevotella intermedia
45% identity, 89% coverage
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...locus of P. gingivalis W83 (PG_RS10480, PG1421), B. thetaiotaomicron VPI-5482 (BT_2414), and P. intermedia 17 (PIN17_RS06895). The conclusion from the above-described regulated genes is that iron/hemin uptake and iron-independent metabolism mechanisms are drastically upregulated while the iron-dependent metabolism and oxidative stress defense mechanisms are downregulated under...”
- “...0.00040257 PIOMA14_RS04855 to 60 PIOMA14_I_0955 to 56 YitT family protein and porin 8.9 0.003 PIOMA14_RS05315 PIOMA14_I_1049 4Fe-4S binding protein 2.4 0.013 PIOMA14_RS05915 PIOMA14_I_1159 Acyltransferase family protein 3.2 0.095 PIOMA14_RS06410 PIOMA14_I_1256 Site-specific integrase 3.2 0.027 PIOMA14_RS06655 PIOMA14_I_1304 GntR family transcriptional regulator 9.3 to 8.6 2.933E-12 to 1.7193E-11...”
- “...operon PIOMA14_I_1410 to PIOMA14_I_1412 encoding the fumarate reductase/succinate dehydrogenase system (8.5-, 9.2-, and 9.3-fold, respectively). PIOMA14_I_1049 (PIOMA14_RS05315) coding for the 4Fe-4S binding protein (ferredoxin, similar to PG1421 and BT2414) was also downregulated by 8.9-fold ( Fig.2E ; see Fig. S1 in the supplemental material). The major...”
- “...2.0 0.00040257 PIOMA14_RS04855 to 60 PIOMA14_I_0955 to 56 YitT family protein and porin 8.9 0.003 PIOMA14_RS05315 PIOMA14_I_1049 4Fe-4S binding protein 2.4 0.013 PIOMA14_RS05915 PIOMA14_I_1159 Acyltransferase family protein 3.2 0.095 PIOMA14_RS06410 PIOMA14_I_1256 Site-specific integrase 3.2 0.027 PIOMA14_RS06655 PIOMA14_I_1304 GntR family transcriptional regulator 9.3 to 8.6 2.933E-12 to...”
- “...PIOMA14_I_1410 to PIOMA14_I_1412 encoding the fumarate reductase/succinate dehydrogenase system (8.5-, 9.2-, and 9.3-fold, respectively). PIOMA14_I_1049 (PIOMA14_RS05315) coding for the 4Fe-4S binding protein (ferredoxin, similar to PG1421 and BT2414) was also downregulated by 8.9-fold ( Fig.2E ; see Fig. S1 in the supplemental material). The major iron-dependent...”
MMP1506 pyruvate oxidoreductase (synthase) subunit delta from Methanococcus maripaludis S2
48% identity, 55% coverage
Halsa_1863 NADH-quinone oxidoreductase subunit NuoF from Halanaerobium hydrogeniformans
46% identity, 8% coverage
MMP0824 coenzyme F420-non-reducing hydrogenase subunit beta from Methanococcus maripaludis S2
43% identity, 13% 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