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UniProtKB - P39779 (CODY_BACSU)

Entry version 156 (17 Jun 2020)
Sequence version 3 (23 Jan 2007)
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Protein

GTP-sensing transcriptional pleiotropic repressor CodY

Gene

codY

Organism
Bacillus subtilis (strain 168)
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

DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase and sporulation. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor.2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi202 – 221H-T-H motifSequence analysisAdd BLAST20

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionDNA-binding, Repressor
Biological processTranscription, Transcription regulation
LigandGTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU16170-MONOMER

<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%5Fand%5Ftaxonomy%5Fsection">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:
GTP-sensing transcriptional pleiotropic repressor CodY
Alternative name(s):
Vegetative protein 286B
Short name:
VEG286B
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:codY
Ordered Locus Names:BSU16170
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Cytoplasm

<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 <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002132212 – 259GTP-sensing transcriptional pleiotropic repressor CodYAdd BLAST258

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 residuei215Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P39779

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

More...PaxDbi		P39779

PRoteomics IDEntifications database

More...PRIDEi		P39779

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		P39779

<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

Gene expression databases

CollecTF database of bacterial transcription factor binding sites

More...CollecTFi		EXPREG_00000a80

<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%5Fsection%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

Protein-protein interaction databases

Protein interaction database and analysis system

More...IntActi		P39779, 2 interactors

Molecular INTeraction database

More...MINTi		P39779

STRING: functional protein association networks

More...STRINGi		224308.BSU16170

<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

1259
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		P39779

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		P39779

<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

Belongs to the CodY family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG4465 LUCA

KEGG Orthology (KO)

More...KOi		K03706

Identification of Orthologs from Complete Genome Data

More...OMAi		FPEEYNE

Database for complete collections of gene phylogenies

More...PhylomeDBi		P39779

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.10.10, 1 hit
3.30.450.40, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_00621 HTH_type_CodY, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR014154 CodY
IPR029016 GAF-like_dom_sf
IPR010312 GTP_sensing_CodY_N
IPR013198 GTP_sensing_HTH_CodY_C
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf

The PANTHER Classification System

More...PANTHERi		PTHR40062 PTHR40062, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF06018 CodY, 1 hit
PF08222 HTH_CodY, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF011572 GTP_sensing_CodY, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF46785 SSF46785, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR02787 codY_Gpos, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P39779-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MALLQKTRII NSMLQAAAGK PVNFKEMAET LRDVIDSNIF VVSRRGKLLG 
        60         70         80         90        100
YSINQQIEND RMKKMLEDRQ FPEEYTKNLF NVPETSSNLD INSEYTAFPV 
       110        120        130        140        150
ENRDLFQAGL TTIVPIIGGG ERLGTLILSR LQDQFNDDDL ILAEYGATVV 
       160        170        180        190        200
GMEILREKAE EIEEEARSKA VVQMAISSLS YSELEAIEHI FEELDGNEGL 
       210        220        230        240        250
LVASKIADRV GITRSVIVNA LRKLESAGVI ESRSLGMKGT YIKVLNNKFL 

IELENLKSH
Length:259
Mass (Da):29,013
Last modified:January 23, 2007 - v3
<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:i8CC11CCAFCCA43D4
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
U13634 Genomic DNA Translation: AAB03372.1
AL009126 Genomic DNA Translation: CAB13490.1

Protein sequence database of the Protein Information Resource

More...PIRi		S61496

NCBI Reference Sequences

More...RefSeqi		NP_389499.1, NC_000964.3
WP_003220850.1, NZ_JNCM01000035.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB13490; CAB13490; BSU16170

Database of genes from NCBI RefSeq genomes

More...GeneIDi		936491

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU16170

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.1757

<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
U13634 Genomic DNA Translation: AAB03372.1
AL009126 Genomic DNA Translation: CAB13490.1
PIRiS61496
RefSeqiNP_389499.1, NC_000964.3
WP_003220850.1, NZ_JNCM01000035.1

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
2B0LX-ray2.90A/B/C168-259[»]
2B18X-ray1.80A1-155[»]
2GX5X-ray1.74A/B/C/D2-160[»]
2HGVX-ray2.30A1-155[»]
5LNHX-ray3.00A/B/C/D/E/F/G/H/I/K2-259[»]
5LOEX-ray3.00A/B/C/D1-259[»]
5LOJX-ray3.71A/B2-259[»]
5LOOX-ray4.50A/B/C/D/E/F/G/H/I/J/K/L/M/N2-259[»]
SMRiP39779
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

IntActiP39779, 2 interactors
MINTiP39779
STRINGi224308.BSU16170

PTM databases

iPTMnetiP39779

Proteomic databases

jPOSTiP39779
PaxDbiP39779
PRIDEiP39779

Genome annotation databases

EnsemblBacteriaiCAB13490; CAB13490; BSU16170
GeneIDi936491
KEGGibsu:BSU16170
PATRICifig|224308.179.peg.1757

Phylogenomic databases

eggNOGiCOG4465 LUCA
KOiK03706
OMAiFPEEYNE
PhylomeDBiP39779

Enzyme and pathway databases

BioCyciBSUB:BSU16170-MONOMER

Miscellaneous databases

EvolutionaryTraceiP39779

Protein Ontology

More...PROi		PR:P39779

Gene expression databases

CollecTFiEXPREG_00000a80

Family and domain databases

Gene3Di1.10.10.10, 1 hit
3.30.450.40, 1 hit
HAMAPiMF_00621 HTH_type_CodY, 1 hit
InterProiView protein in InterPro
IPR014154 CodY
IPR029016 GAF-like_dom_sf
IPR010312 GTP_sensing_CodY_N
IPR013198 GTP_sensing_HTH_CodY_C
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PANTHERiPTHR40062 PTHR40062, 1 hit
PfamiView protein in Pfam
PF06018 CodY, 1 hit
PF08222 HTH_CodY, 1 hit
PIRSFiPIRSF011572 GTP_sensing_CodY, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
TIGRFAMsiTIGR02787 codY_Gpos, 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 nameiCODY_BACSU
<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: P39779
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: June 17, 2020
This is version 156 of the entry and version 3 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, Reference proteome

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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