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Entry version 107 (18 Sep 2019)
Sequence version 2 (01 Oct 1996)
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Protein

L-methionine gamma-lyase

Gene

mdeA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
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 alpha,gamma-elimination of L-methionine to produce methanethiol, 2-oxobutanoate and ammonia (PubMed:8586629, PubMed:6742420). Is involved in L-methionine catabolism (PubMed:9190812). In fact, shows a multicatalytic function since it also catalyzes gamma-replacement of L-methionine with thiol compounds, alpha,gamma-elimination and gamma-replacement reactions of L-homocysteine and its S-substituted derivatives, O-substituted-L-homoserines and DL-selenomethionine, and, to a lesser extent, alpha,beta-elimination and beta-replacement reactions of L-cysteine, S-methyl-L-cysteine, and O-acetyl-L-serine (PubMed:6742420, PubMed:22785484). Also catalyzes deamination and gamma-addition reactions of L-vinylglycine (PubMed:6742420). Thus, the enzyme is able to cleave C-S, C-Se, and C-O bonds of sulfur, selenium, and oxygen amino acids, respectively (PubMed:6742420, PubMed:22785484).1 Publication3 Publications

<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

pyridoxal 5'-phosphate3 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Irreversibly inactivated by DL-propargylglycine.1 Publication

<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

kcat is 33.4 sec(-1) for the alpha,gamma-elimination of L-methionine. kcat is 71.0 sec(-1) for the alpha,gamma-elimination of DL-homocysteine. kcat is 2.13 sec(-1) for the alpha,beta-elimination of L-cysteine. kcat is 1.58 sec(-1) for the alpha,beta-elimination of S-methyl-L-cysteine. kcat is 2.56 sec(-1) for the alpha,gamma-elimination of O-succinyl-L-homoserine.1 Publication
  1. KM=1.0 mM for L-methionine1 Publication
  2. KM=0.5 mM for L-methionine1 Publication
  3. KM=1.1 mM for DL-homocysteine1 Publication
  4. KM=0.2 mM for L-cysteine1 Publication
  5. KM=0.7 mM for S-methyl-L-cysteine1 Publication
  6. KM=7.2 mM for O-succinyl-L-homoserine1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> 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 sitei114SubstrateCombined sources1 Publication1
    Binding sitei375SubstrateCombined sources1 Publication1

    <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
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:MONOMER-284

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    4.4.1.11 5092

    <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-methionine gamma-lyase2 Publications (EC:4.4.1.112 Publications)
    Short name:
    MGL1 Publication
    Alternative name(s):
    Homocysteine desulfhydrase1 Publication (EC:4.4.1.22 Publications)
    L-methioninase
    <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:mdeAImported
    <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>OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    <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 identifieri303 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    <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

    <p>This subsection of the ‘Pathology and Biotech’ section describes the use of a specific protein in the biotechnological industry.<p><a href='/help/biotechnological_use' target='_top'>More...</a></p>Biotechnological usei

    The recombinant MGL protein cloned form P.putida has been found to have antitumor efficacy in vitro and in vivo. PEGylated MGL is being developed as a cancer drug.1 Publication

    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>Mutagenesisi61R → A, E or F: Loss of elimination activity against L-methionine. 1 Publication1
    Mutagenesisi116C → H: Drastic decrease of the catalytic efficiency of the elimination reaction with L-methionine, by 6700-fold, and increases that with L-cysteine by 7-fold, mainly due to changes in kcat. Loss of ability to catalyze replacement reaction between L-methionine and 2-mercaptoethanol. 1 Publication1
    Mutagenesisi116C → S: 9% of wild-type elimination activity against L-methionine. 1 Publication1
    Mutagenesisi116C → T: 40% of wild-type elimination activity against L-methionine. 1 Publication1
    Mutagenesisi240K → D or E: Marked decrease in elimination activity against both L-methionine and DL-homocysteine. 1 Publication1
    Mutagenesisi240K → M: 50% reduction in alpha,gamma-elimination activity against DL-homocysteine, while retaining elimination activity against L-methionine and L-cysteine. 1 Publication1
    Mutagenesisi241D → H or R: 5 to 14-fold reduction in alpha,gamma-elimination activity against L-methionine, while no change in affinity for L-methionine. 1 Publication1

    Chemistry databases

    Drug and drug target database

    More...
    DrugBanki
    DB04083 N'-Pyridoxyl-Lysine-5'-Monophosphate

    <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_00001147841 – 398L-methionine gamma-lyaseAdd BLAST398

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei211N6-(pyridoxal phosphate)lysineCombined sources5 Publications1

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    <p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

    Is under the control of the positive transcriptional regulator MdeR. Forms part of an operon with mdeB.1 Publication

    <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

    Homotetramer; dimer of active dimers.

    2 Publications

    <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

    1398
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

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

    More...
    SMRi
    P13254

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    P13254

    <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

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni59 – 61Pyridoxal phosphate binding; shared with dimeric partner1 Publication3
    Regioni89 – 90Pyridoxal phosphate binding1 Publication2
    Regioni208 – 210Pyridoxal phosphate binding1 Publication3

    <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

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd00614 CGS_like, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.640.10, 1 hit
    3.90.1150.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR000277 Cys/Met-Metab_PyrdxlP-dep_enz
    IPR006237 L-Met_gamma_lys
    IPR015424 PyrdxlP-dep_Trfase
    IPR015422 PyrdxlP-dep_Trfase_dom1
    IPR015421 PyrdxlP-dep_Trfase_major

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR11808 PTHR11808, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF01053 Cys_Met_Meta_PP, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF001434 CGS, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF53383 SSF53383, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01328 met_gam_lyase, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00868 CYS_MET_METAB_PP, 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>. The information is filed in different subsections. The current subsections and their content are listed below:<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.

    P13254-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MHGSNKLPGF ATRAIHHGYD PQDHGGALVP PVYQTATFTF PTVEYGAACF
    60 70 80 90 100
    AGEQAGHFYS RISNPTLNLL EARMASLEGG EAGLALASGM GAITSTLWTL
    110 120 130 140 150
    LRPGDEVLLG NTLYGCTFAF LHHGIGEFGV KLRHVDMADL QALEAAMTPA
    160 170 180 190 200
    TRVIYFESPA NPNMHMADIA GVAKIARKHG ATVVVDNTYC TPYLQRPLEL
    210 220 230 240 250
    GADLVVHSAT KYLSGHGDIT AGIVVGSQAL VDRIRLQGLK DMTGAVLSPH
    260 270 280 290 300
    DAALLMRGIK TLNLRMDRHC ANAQVLAEFL ARQPQVELIH YPGLASFPQY
    310 320 330 340 350
    TLARQQMSQP GGMIAFELKG GIGAGRRFMN ALQLFSRAVS LGDAESLAQH
    360 370 380 390
    PASMTHSSYT PEERAHYGIS EGLVRLSVGL EDIDDLLADV QQALKASA
    Length:398
    Mass (Da):42,627
    Last modified:October 1, 1996 - 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:iBD50CD1F34CD71E3
    GO

    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
    D88554 Genomic DNA Translation: BAA13642.1
    D89015 Genomic DNA Translation: BAA20553.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    A27691
    JC4174

    <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
    D88554 Genomic DNA Translation: BAA13642.1
    D89015 Genomic DNA Translation: BAA20553.1
    PIRiA27691
    JC4174

    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
    1GC0X-ray1.70A/B/C/D1-398[»]
    1GC2X-ray2.00A/B/C/D1-398[»]
    1PG8X-ray2.68A/B/C/D1-398[»]
    1UKJX-ray1.80A/B/C/D1-398[»]
    2O7CX-ray1.70A/B/C/D1-398[»]
    3VK2X-ray2.30A/B/C/D1-398[»]
    3VK3X-ray2.10A/B/C/D1-398[»]
    3VK4X-ray2.61A/B/C/D1-398[»]
    5X2VX-ray2.40A/B/C/D1-398[»]
    5X2WX-ray2.70A/B/C/D1-398[»]
    5X2XX-ray2.00A/B/C/D1-398[»]
    5X2YX-ray1.79A/B/C/D1-398[»]
    5X2ZX-ray1.80A/B/C/D1-398[»]
    5X30X-ray1.70A/B/C/D1-398[»]
    SMRiP13254
    ModBaseiSearch...
    PDBe-KBiSearch...

    Chemistry databases

    DrugBankiDB04083 N'-Pyridoxyl-Lysine-5'-Monophosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-284
    BRENDAi4.4.1.11 5092

    Miscellaneous databases

    EvolutionaryTraceiP13254

    Family and domain databases

    CDDicd00614 CGS_like, 1 hit
    Gene3Di3.40.640.10, 1 hit
    3.90.1150.10, 1 hit
    InterProiView protein in InterPro
    IPR000277 Cys/Met-Metab_PyrdxlP-dep_enz
    IPR006237 L-Met_gamma_lys
    IPR015424 PyrdxlP-dep_Trfase
    IPR015422 PyrdxlP-dep_Trfase_dom1
    IPR015421 PyrdxlP-dep_Trfase_major
    PANTHERiPTHR11808 PTHR11808, 1 hit
    PfamiView protein in Pfam
    PF01053 Cys_Met_Meta_PP, 1 hit
    PIRSFiPIRSF001434 CGS, 1 hit
    SUPFAMiSSF53383 SSF53383, 1 hit
    TIGRFAMsiTIGR01328 met_gam_lyase, 1 hit
    PROSITEiView protein in PROSITE
    PS00868 CYS_MET_METAB_PP, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    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 nameiMEGL_PSEPU
    <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: P13254
    <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: January 1, 1990
    Last sequence update: October 1, 1996
    Last modified: September 18, 2019
    This is version 107 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, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
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