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Protein

L-rhamnonate dehydratase

Gene

rhmD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate, L-mannonate and D-gulonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.1 Publication

Miscellaneous

Reaction proceeds via a syn dehydration.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

The catalytic efficiency observed with L-rhamnonate as substrate is 70- and 16-fold higher than that observed with L-lyxonate and L-mannonate, respectively.
  1. KM=0.15 mM for L-rhamnonate1 Publication
  2. KM=2.0 mM for L-lyxonate1 Publication
  3. KM=0.15 mM for L-mannonate1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei29Substrate1
    Binding sitei55SubstrateBy similarity1
    <p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi222MagnesiumBy similarity1
    Metal bindingi248MagnesiumBy similarity1
    Metal bindingi276MagnesiumBy similarity1
    <p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei298Increases basicity of active site HisBy similarity1
    <p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei325Proton acceptor1
    Binding sitei345SubstrateBy similarity1
    Sitei345Transition state stabilizerBy similarity1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionLyase
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:G7160-MONOMER
    MetaCyc:G7160-MONOMER

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    4.2.1.90 2165

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    L-rhamnonate dehydratase (EC:4.2.1.90)
    Short name:
    RhamD
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:rhmD
    Synonyms:yfaW
    Ordered Locus Names:b2247, JW2241
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    Escherichia coli strain K12 genome database

    More...
    EcoGenei
    EG14085 rhmD

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi29H → N: Loss of activity due to absence of substrate binding. 1 Publication1
    Mutagenesisi277H → N: 35-fold decrease in activity. 59-fold decrease in substrate affinity. 1 Publication1
    Mutagenesisi325H → N: Loss of activity. 2-fold decrease in substrate affinity. 1 Publication1

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001712621 – 401L-rhamnonate dehydrataseAdd BLAST401

    Proteomic databases

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    P77215

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P77215

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homooctamer; tetramer of dimers.1 Publication

    GO - Molecular functioni

    Protein-protein interaction databases

    The Biological General Repository for Interaction Datasets (BioGrid)

    More...
    BioGridi
    4261221, 144 interactors

    Database of interacting proteins

    More...
    DIPi
    DIP-11955N

    Protein interaction database and analysis system

    More...
    IntActi
    P77215, 11 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    316385.ECDH10B_2407

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1401
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    P77215

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    P77215

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    P77215

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4105CXK Bacteria
    COG4948 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000113755

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P77215

    KEGG Orthology (KO)

    More...
    KOi
    K12661

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P77215

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.20.20.120, 1 hit
    3.30.390.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_01288 Rhamnon_dehydrat, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR036849 Enolase-like_C_sf
    IPR029017 Enolase-like_N
    IPR029065 Enolase_C-like
    IPR023444 L-Rhamnon_dehydrat
    IPR018110 Mandel_Rmase/mucon_lact_enz_CS
    IPR013342 Mandelate_racemase_C
    IPR013341 Mandelate_racemase_N_dom

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR13794:SF59 PTHR13794:SF59, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF13378 MR_MLE_C, 1 hit
    PF02746 MR_MLE_N, 1 hit

    Structure-Function Linkage Database

    More...
    SFLDi
    SFLDF00006 rhamnonate_dehydratase, 1 hit

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM00922 MR_MLE, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51604 SSF51604, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00908 MR_MLE_1, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    P77215-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MTLPKIKQVR AWFTGGATAE KGAGGGDYHD QGANHWIDDH IATPMSKYRD
    60 70 80 90 100
    YEQSRQSFGI NVLGTLVVEV EAENGQTGFA VSTAGEMGCF IVEKHLNRFI
    110 120 130 140 150
    EGKCVSDIKL IHDQMLSATL YYSGSGGLVM NTISCVDLAL WDLFGKVVGL
    160 170 180 190 200
    PVYKLLGGAV RDEIQFYATG ARPDLAKEMG FIGGKMPTHW GPHDGDAGIR
    210 220 230 240 250
    KDAAMVADMR EKCGEDFWLM LDCWMSQDVN YATKLAHACA PYNLKWIEEC
    260 270 280 290 300
    LPPQQYESYR ELKRNAPVGM MVTSGEHHGT LQSFRTLSET GIDIMQPDVG
    310 320 330 340 350
    WCGGLTTLVE IAAIAKSRGQ LVVPHGSSVY SHHAVITFTN TPFSEFLMTS
    360 370 380 390 400
    PDCSTMRPQF DPILLNEPVP VNGRIHKSVL DKPGFGVELN RDCNLKRPYS

    H
    Length:401
    Mass (Da):44,226
    Last modified:November 24, 2009 - v2
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i4622CE539229AD58
    GO

    <p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

    The sequence BAA16071 differs from that shown. Reason: Erroneous initiation.Curated

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    U00096 Genomic DNA Translation: AAC75307.2
    AP009048 Genomic DNA Translation: BAA16071.1 Different initiation.

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    E64995

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_416750.2, NC_000913.3
    WP_001319848.1, NZ_LN832404.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC75307; AAC75307; b2247
    BAA16071; BAA16071; BAA16071

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    945881

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW2241
    eco:b2247

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|511145.12.peg.2338

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA Translation: AAC75307.2
    AP009048 Genomic DNA Translation: BAA16071.1 Different initiation.
    PIRiE64995
    RefSeqiNP_416750.2, NC_000913.3
    WP_001319848.1, NZ_LN832404.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2I5QX-ray2.10A/B1-401[»]
    ProteinModelPortaliP77215
    SMRiP77215
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261221, 144 interactors
    DIPiDIP-11955N
    IntActiP77215, 11 interactors
    STRINGi316385.ECDH10B_2407

    Proteomic databases

    PaxDbiP77215
    PRIDEiP77215

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75307; AAC75307; b2247
    BAA16071; BAA16071; BAA16071
    GeneIDi945881
    KEGGiecj:JW2241
    eco:b2247
    PATRICifig|511145.12.peg.2338

    Organism-specific databases

    EchoBASE - an integrated post-genomic database for E. coli

    More...
    EchoBASEi
    EB3838
    EcoGeneiEG14085 rhmD

    Phylogenomic databases

    eggNOGiENOG4105CXK Bacteria
    COG4948 LUCA
    HOGENOMiHOG000113755
    InParanoidiP77215
    KOiK12661
    PhylomeDBiP77215

    Enzyme and pathway databases

    BioCyciEcoCyc:G7160-MONOMER
    MetaCyc:G7160-MONOMER
    BRENDAi4.2.1.90 2165

    Miscellaneous databases

    EvolutionaryTraceiP77215

    Protein Ontology

    More...
    PROi
    PR:P77215

    Family and domain databases

    Gene3Di3.20.20.120, 1 hit
    3.30.390.10, 1 hit
    HAMAPiMF_01288 Rhamnon_dehydrat, 1 hit
    InterProiView protein in InterPro
    IPR036849 Enolase-like_C_sf
    IPR029017 Enolase-like_N
    IPR029065 Enolase_C-like
    IPR023444 L-Rhamnon_dehydrat
    IPR018110 Mandel_Rmase/mucon_lact_enz_CS
    IPR013342 Mandelate_racemase_C
    IPR013341 Mandelate_racemase_N_dom
    PANTHERiPTHR13794:SF59 PTHR13794:SF59, 1 hit
    PfamiView protein in Pfam
    PF13378 MR_MLE_C, 1 hit
    PF02746 MR_MLE_N, 1 hit
    SFLDiSFLDF00006 rhamnonate_dehydratase, 1 hit
    SMARTiView protein in SMART
    SM00922 MR_MLE, 1 hit
    SUPFAMiSSF51604 SSF51604, 1 hit
    PROSITEiView protein in PROSITE
    PS00908 MR_MLE_1, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRHMD_ECOLI
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P77215
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 24, 2009
    Last modified: December 5, 2018
    This is version 140 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
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