PaperBLAST
Full List of Papers Linked to P96404
P96404 Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
L7N5S5 Enoyl-CoA hydratase/isomerase family protein from Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
NP_214736 enoyl-CoA hydratase EchA1 from Mycobacterium tuberculosis H37Rv
Rv0222 enoyl-CoA hydratase from Mycobacterium tuberculosis H37Rv
- Mycobacterium tuberculosis peptides presented by HLA-E molecules are targets for human CD8 T-cells with cytotoxic as well as regulatory activity
Joosten, PLoS pathogens 2010 - “...29 LMHYRGELL Rv1965 O53966 201 20 30 NMMARGMDL Rv0221 P96403 201 >50 31 LPAERAHEL Rv0222 P96404 202 >50 32 VMMSEIAGL Rv1813c P64889 348 13 33 TMITFRLRL Rv1733c P71991 373 2,4 34 VMTTVLATL Rv1734c P71992 348 1,8 35 GMGMVGTAL Rv1737c P71995 348 >50 36 AMAGSIDLL Rv2006 Q10850...”
- Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases
Lopez, Frontiers in microbiology 2020 - “...Q7D7S1 Rv1925 fadD31 No PP: acyl-CoA synthase Q50824 Rv0685 desA1 Yes PP: putative acyl-[acyl-carrier-protein] desaturase L7N5S5 Rv0222 echA1 No SF: probable enoyl-CoA hydratase; crotonase P0A4W6 Rv2244 AcpM Yes SF: meromycolate extension acyl carrier protein Q11198 Rv3389c htdY No SF: 3-hydroxy acyl thioester dehydratase Ribosomal/transcriptional function P66044...”
- Host-mediated ubiquitination of a mycobacterial protein suppresses immunity.
Wang, Nature 2020 (PubMed)- GeneRIF: host E3 ubiquitin ligase ANAPC2 interacts with the mycobacterial protein Rv0222 and promotes the attachment of lysine-11-linked ubiquitin chains to lysine 76 of Rv0222 in order to suppress the expression of proinflammatory cytokines; identification of mechanism that M. tuberculosis uses to suppress host immunity, and provide insights relevant to the development of effective immunomodulators that target M. tuberculosis
- Identification of new diagnostic biomarkers for Mycobacterium tuberculosis and the potential application in the serodiagnosis of human tuberculosis
Ren, Microbial biotechnology 2018 - “...2010b ). Rv0222, a 263amino acid protein, is possibly an enoylCoA hydratase (GenBank accession no: NP_214736 ), which is conserved in most mycobacterial species. Although Rv0222 was previously used to detect TB, with a sensitivity of 82% in 38TB cases, including 29 PTB and 9 EPTB...”
- Improving sensitivity for serodiagnosis of tuberculosis using TB16.3-echA1 fusion protein.
Khurshid, Tuberculosis (Edinburgh, Scotland) 2014 (PubMed)- GeneRIF: Novel fusion protein TB16.3-echA1 has a potential in serodiagnosis of tuberculosis with improved sensitivity and reliability.
- Development and evaluation of a triplex droplet digital PCR method for differentiation of M. tuberculosis, M. bovis and BCG
Qu, Frontiers in microbiology 2024 (PubMed)- “...(targeting CFP-10-ESAT-6 gene of RD1 and Rv0222 genes of RD4), <italic>M. bovis</italic> (targeting CFP-10-ESATs-6 gene of RD1), and...”
- “...<i>M. tuberculosis</i> (targeting CFP-10-ESAT-6 gene of RD1 and Rv0222 genes of RD4), <i>M. bovis</i> (targeting CFP-10-ESATs-6 gene of RD1), and BCG (targeting...”
- Mycobacterium tuberculosis protein Rv2652c enhances intracellular survival by inhibiting host immune responses
Li, Immunity, inflammation and disease 2024 - “...through the inhibition of p38 MAPK and NFB signaling cascades. 24 On the other hand, Rv0222 has been demonstrated to subvert innate immune responses by targeting the JNK, p38 MAPK, and NFB signaling pathways. 25 Furthermore, Mce3E effectively inhibits the ERK1/2 signaling cascade, consequently suppressing the...”
- In silico design of Mycobacterium tuberculosis multi-epitope adhesin protein vaccines
Pillay, Heliyon 2024 - “...interaction. The authors further showed that the fusion of the truncated PstS1 to the EchA1 (Rv0222) proteins displayed an improved serodiagnosis of TB [ 112 ]. 4.2 Two trifusion protein constructs with multi-epitope regions lacking a signal peptide with good population coverage Common B-cell epitope regions...”
- From pathogenesis to antigens: the key to shaping the future of TB vaccines
Yang, Frontiers in immunology 2024 - “...of TNF-, IL-6, and NO via interacting with macrophage ubiquitin ligase (E3) ( 44 ) Rv0222 Through interaction with the host E3 ubiquitin ligase ANAPC2, Rv0222 prevents ubiquitination and activation of TRAF6 by facilitating the binding of the protein tyrosine phosphatase SHP1 to the adaptor protein...”
- Mycobacterial Rv1804c binds to the PEST domain of IκBα and activates macrophage-mediated proinflammatory responses
Zheng, iScience 2024 - “...NF-B and AP-1 signaling pathways by interacting with makorin ring finger protein 1. 13 Mtb Rv0222 suppresses the expression of proinflammatory cytokines by interacting with anaphase-promoting complex subunit 2, an E3 ubiquitin ligase, in the host. 14 Mtb PPE36 inhibits host inflammatory responses and increases bacterial...”
- Research progress of single-cell sequencing in tuberculosis
Pan, Frontiers in immunology 2023 - “...residues on the bacterial cell surface ( 8 ), Mtb can secrete the virulence factor Rv0222 to escape the immune response after infecting the human body ( 9 ). However, after infection, a comprehensive panorama of the intricate host immune regulatory processes and dynamic evolution still...”
- The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection
Shariq, Autophagy 2023 (secret) - Mycobacterium tuberculosis-macrophage interaction: Molecular updates
Bo, Frontiers in cellular and infection microbiology 2023 - “...etal., 2022 ). This inhibition of host immunity was also reported following lysine-11-linked ubiquitination of Rv0222 by the host E3 ubiquitin ligase ANAPC2 involving SHP1 and TRAF6, or deubiquitination of TRAF6 by HAUSP after PE_PGRS38 ectopic expression in M. smegmatis in murine bone marrow-derived macrophages (...”
- Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system
Roberts, The EMBO journal 2023 (secret) - Uncovering new insights into the role of the ubiquitin ligase Smurf1 on the regulation of innate immune signaling and resistance to infection
Souza-Costa, Frontiers in immunology 2023 - “...response and increased susceptibility to M. tuberculosis infection. Likewise, M. tuberculosis also secretes PtpA and Rv0222, two virulence factors capable to subvert the function and enzymatic activity of other host E3 ubiquitin ligases to favor its survival ( 59 61 ). These findings raise the possibility...”
- Virulence-Associated Secretion in Mycobacterium abscessus
Bar-Oz, Frontiers in immunology 2022 - “...following are mechanism of such immune-response and cytokine release modulation. Enoyl coA hydratase A1 (EchA1, Rv0222) is secreted by Mtb through an unknown mechanism and reaches the host cell cytosol. Wang etal. found that EchA1 is subjected to ubiquitination by the host cell ubiquitin ligase ANAPC2...”
- “...probable enoyl coA hydratase gene in Mabs genome ( MAB_0606c ) with 44% similarity to Rv0222. One should note, though, that a 44% similarity is quite low, and take this homology with caution. No other information regarding this protein in Mabs is currently known. Disulfide bond...”
- PE_PGRS38 Interaction With HAUSP Downregulates Antimycobacterial Host Defense via TRAF6
Kim, Frontiers in immunology 2022 - “...several mycobacteria antigens interacted with TRAF6 and regulated the activation of inflammation in the host. Rv0222, which is a serodiagnostic protein for tuberculosis, was associated with anaphase promoting complex subunit 2 (ANAPC2) and promoted K11-linked-ubiquitination in K76 of Rv0222. This ubiquitination in Rv0222 reduced TRAF6 activation...”
- “...the level of inflammatory cytokines with increase the survival of Mtb. Deletion of K76 in Rv0222 or knockdown of ANAPC2 impaired the function of Rv0222 and attenuated the virulence of Mtb ( 44 ). Furthermore, Rv2626c, a promising vaccine candidate of tuberculosis, directly bound to TRAF6...”
- Bag it, tag it: ubiquitin ligases and host resistance to Mycobacterium tuberculosis
Campos, Trends in microbiology 2022 - “...immune inflammation during Mtb infection by facilitating the attachment of K11-linked polyubiquitin to Mtb protein Rv0222 (an enoyl-CoA hydratase) [ 39 ]. ANAPC2-mediated ubiquitination of Mtb Rv0222 mediates recruitment of SHP1 (Src homology region 2 domain-containing phosphatase-1) (a tyrosine phosphatase) to the adaptor protein TRAF6 (Tumor...”
- “...inhibits inflammation during Mtb infection. Host ANAPC2 mediates K11-linked polyubiquitination of the Mtb secreted protein Rv0222 (1), which is required for the recruitment of the tyrosine phosphatase SHP1 to TRAF6 adaptor (2). Interaction between SHP1 and TRAF6 leads to decreased activation of NF-B and AP-1 transcription...”
- Host MKRN1-Mediated Mycobacterial PPE Protein Ubiquitination Suppresses Innate Immune Response
Dou, Frontiers in immunology 2022 - “...(e.g., RD1: ESAT-6 (Rv3874) and CFP-10 (Rv3875); RD2: MPT64 (Rv1980c); RD3: EST12 (Rv1579) and RD4: Rv0222) have been characterized and analyzed thus far ( 8 11 ). ESAT-6 and CFP-10 contain multiple T cell and B cell epitopes and are widely used in TB diagnosis and...”
- “...the expression of genes encoding a variety of inflammatory mediators ( 22 ). Mtb protein Rv0222 can bind to TRAF6 protein and inhibit TLR-mediated macrophage inflammation ( 10 ). Rv2626c interacts with TRAF6 and inhibits K63-linked polyubiquitination of TRAF6, which leads to suppression of TLR4 inflammatory...”
- Use of Rv0222-Rv2657c-Rv1509 Fusion Protein to Improve the Accuracy of an Antibody ELISA for Extra-Pulmonary Tuberculosis in Humans
Chen, Pathogens (Basel, Switzerland) 2021 - “...the sensitivity and specificity of an antibody ELISA for TB and EPTB. Here we found Rv0222, Rv1509 and Rv2657 C were with highly immunogenic and had potential use for TB diagnosis. 2. Results 2.1. Generation of Fusion Antigens The similarity of cloned sequences and those in...”
- “...diagnosis of TB [ 8 , 21 , 22 , 23 ]. The presence of Rv0222, Rv2657c and Rv1509 have previously been reported to be strongly associated with PTB [ 6 , 21 ], although their use in the diagnosis of EPTB has rarely been reported...”
- Post translational modifications in tuberculosis: ubiquitination paradox
Shariq, Autophagy 2021 (secret) - In silico comparisons of lipid-related genes between Mycobacterium tuberculosis and BCG vaccine strains
Sarno, Genetics and molecular biology 2021 - “...proteins Virulence, detoxification, adaptation Rv1965-Rv1969 YrbE3B, Mce3A, Mce3B, Mce3C and Mce3D Rv1971 Mce3F Lipid Metabolism Rv0222 Enoyl-CoA hydratase (EchA1) Intermediary metabolism and respiration Rv2349c-Rv2351c Phospholipases C (PlcC, PlcB and PlcA) Ten of these 14 genes belonged to the mce3 operon: four were in the cell wall...”
- “...to Rv1969 and Rv1971) in the virulence, detoxification, adaptation category. The gene encoding enoyl-CoA hydratase (Rv0222), which is part of the fatty acid degradation metabolism, was categorized as lipid metabolism. Finally, three genes encoding phospholipases PlcC, PlcB and PlcA (Rv2349c to Rv2351c, respectively), related to lipid...”
- Mycobacterium tuberculosis Rv0927c Inhibits NF-κB Pathway by Downregulating the Phosphorylation Level of IκBα and Enhances Mycobacterial Survival
Xia, Frontiers in immunology 2021 - “...of proinflammatory cytokines by interfering with a range of processes in NF-B and MAPKs pathways. Rv0222 utilizes E3 ubiquitin ligase anaphase promoting complex (APC) subunit 2 (ANAPC2) to induce K11-linked ubiquitination. K11-linked ubiquitination ofRv0222 promotes the recruitment of protein tyrosine phosphatase SHP1 to TRAF6, which prevents...”
- Host-mediated ubiquitination of a mycobacterial protein suppresses immunity
Wang, Nature 2020 (PubMed)- “...anaphase-promoting complex/cyclosome--interacts with the mycobacterial protein Rv0222 and promotes the attachment of lysine-11linked ubiquitin chains to lysine...”
- “...short hairpin RNA abolishes the inhibitory effect of Rv0222 on proinflammatory responses. Moreover, mutation of the ubiquitination site on Rv0222 impairs the...”
- Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases
Lopez, Frontiers in microbiology 2020 - “...Rv1925 fadD31 No PP: acyl-CoA synthase Q50824 Rv0685 desA1 Yes PP: putative acyl-[acyl-carrier-protein] desaturase L7N5S5 Rv0222 echA1 No SF: probable enoyl-CoA hydratase; crotonase P0A4W6 Rv2244 AcpM Yes SF: meromycolate extension acyl carrier protein Q11198 Rv3389c htdY No SF: 3-hydroxy acyl thioester dehydratase Ribosomal/transcriptional function P66044 Rv0651...”
- “...data not shown), known or potential fatty acid metabolism enzymes Rv3224 (possible short chain dehydrogenase), Rv0222 (EchA1), and Rv3389 (putative HtdY) ( Figure 6A and Supplementary Figures S3A,B ), LldD (possible L -lactate dehydrogenase), and PdxH, pyridoxine 5-oxidase ( Supplementary Figures S3A,B ). FIGURE 6 Effects...”
- New insights into the evasion of host innate immunity by Mycobacterium tuberculosis
Chai, Cellular & molecular immunology 2020 - “...xenophagy to restrict host inflammatory responses. 81 More recently, we identified a Mtb-secreted protein effector, Rv0222, as a key suppressor of host NF-B activation, showing that it undergoes K11-linked ubiquitination mediated by the host E3 ubiquitin ligase anaphase promoting complex (APC) subunit 2 (ANAPC2). 165 Interestingly,...”
- Identification of new diagnostic biomarkers for Mycobacterium tuberculosis and the potential application in the serodiagnosis of human tuberculosis
Ren, Microbial biotechnology 2018 - “...indirect ELISA . With respect to the PTB diagnosis, receiver operating characteristic analysis showed that Rv0222 [area under the curve ( AUC ), 0.8129; 95% confidence interval ( CI ), 0.72800.8979] and Rv3403c ( AUC , 0.8537; 95% CI , 0.77790.9294) performed better than ESAT 6/...”
- “...in the PTB SN group (sensitivity, 70%; specificity, 80%). With respect to the EPTB diagnosis, Rv0222 exhibited the highest diagnostic value ( AUC , 0.7523; sensitivity, 68.8%; specificity, 87.5%). In addition, the combination of Rv0222 and Rv3403c improved the test for PTB SN . These results...”
- Evaluation of panels of Mycobacterium tuberculosis antigens for serodiagnosis of tuberculosis
Yan, The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2018 (PubMed)- “...proteins 38KD, MPT32 (M. tuberculosis protein 32), MPT64, EspC (ESX-1 secretion-associated protein), Mtb81, Rv3881, Rv3425, Rv0222, Rv3872 and CFP21 (culture filtrate protein 21), and obtained lipoarabinomannan (LAM) polysaccharide antigen from BEI Resources. The plasma immunoglobulin (Ig)G titre responses to the 11 antigens based on 45 patients...”
- Identification of Antibody Targets for Tuberculosis Serology using High-Density Nucleic Acid Programmable Protein Arrays
Song, Molecular & cellular proteomics : MCP 2017 - “...TB biomarker value; four (Rv0054, Rv0831c, Rv2031c and Rv0222) of these were previously identified in serology studies, and four (Rv0948c, Rv2853, Rv3405c,...”
- “...Rv0831c (60.0%, US/HIV-), Rv0054 (52.4%, US/HIV), Rv0831c/ Rv0222 (76.9%, SA/HIV-) and Rv3405c (57.3%, SA/HIV). The proteins with the highest specificity at...”
- Human Immunology of Tuberculosis
, Microbiology spectrum
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