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UniProtKB - P96669 (YDEL_BACSU)

Entry version 123 (16 Oct 2019)
Sequence version 1 (01 May 1997)
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Protein

Uncharacterized HTH-type transcriptional regulator YdeL

Gene

ydeL

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:2 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>-Protein inferred from homologyi <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

<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'-phosphateBy similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 bindingi41 – 60H-T-H motifPROSITE-ProRule annotationAdd 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 functionAminotransferase, DNA-binding, Transferase
Biological processTranscription, Transcription regulation
LigandPyridoxal phosphate

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU05240-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_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:
Uncharacterized HTH-type transcriptional regulator YdeL
<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:ydeL
Ordered Locus Names:BSU05240
<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>OrganismiBacillus subtilis (strain 168)
<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 identifieri224308 [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 lineageiBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<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
  • UP000001570 <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

<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_00003606961 – 463Uncharacterized HTH-type transcriptional regulator YdeLAdd BLAST463

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 residuei308N6-(pyridoxal phosphate)lysineBy similarity1

Proteomic databases

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

More...PaxDbi		P96669

PRoteomics IDEntifications database

More...PRIDEi		P96669

<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

Protein-protein interaction databases

Protein interaction database and analysis system

More...IntActi		P96669, 17 interactors

STRING: functional protein association networks

More...STRINGi		224308.BSU05240

<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

3D structure databases

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

More...SMRi		P96669

Database of comparative protein structure models

More...ModBasei		Search...

<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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini13 – 81HTH gntR-typePROSITE-ProRule annotationAdd BLAST69

<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

In the C-terminal section; belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105C1I Bacteria
COG1167 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000223052

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P96669

KEGG Orthology (KO)

More...KOi		K00375

Identification of Orthologs from Complete Genome Data

More...OMAi		DSEFRHT

Database for complete collections of gene phylogenies

More...PhylomeDBi		P96669

Family and domain databases

Conserved Domains Database

More...CDDi		cd07377 WHTH_GntR, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.10.10, 1 hit
3.40.640.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR004839 Aminotransferase_I/II
IPR015424 PyrdxlP-dep_Trfase
IPR015421 PyrdxlP-dep_Trfase_major
IPR000524 Tscrpt_reg_HTH_GntR
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00155 Aminotran_1_2, 1 hit
PF00392 GntR, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00035 HTHGNTR

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00345 HTH_GNTR, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF46785 SSF46785, 1 hit
SSF53383 SSF53383, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50949 HTH_GNTR, 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.

P96669-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDITPFLNRT LDIPLYQQLY RYFKENMHRG RIQKGMKLPS KRLLANQLSI 
        60         70         80         90        100
SQTTVERAYE QLAAEGYIVS KPRSGWFADY HDSDFAYDRM PSTTPIQQEA 
       110        120        130        140        150
EENKQWIDFH YGNVDSSYFP FSAWRKSMVN SLDQYGHELY RPGHVLGEFE 
       160        170        180        190        200
LRTLIAEYLY QSRGVHCGPE QVIIGAGNPI LLQILCQVFE PNISIGYEDP 
       210        220        230        240        250
GYPRARKIFE ANRMNIVPIP VDDEGICIQK IKEQQPNLVY VTPSHQFTLG 
       260        270        280        290        300
TIMTINRRIQ LLKWAAENQS FIIEDDYDGE FRYTGQPVPS LQGLDQHNRV 
       310        320        330        340        350
IYMGTFSKSL LPSLRISYMI LPSPLLKKGH EITSLYKQTV SCHSQLTLAE 
       360        370        380        390        400
FIKNGEWQKH INRMRKLYRK KRAIVLEAVQ RELGEHVRIR GENSGLRILL 
       410        420        430        440        450
DVYLPFGEKE LIEKAKKHGV KIYPVSLSYQ HHPPTKTVSL GFAGVSESDI 
       460 
REGIKKLKAA WKI
Length:463
Mass (Da):53,525
Last modified:May 1, 1997 - v1
<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:iDBB7BA2C5D2EF8B7
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
AB001488 Genomic DNA Translation: BAA19359.1
AL009126 Genomic DNA Translation: CAB12331.1

Protein sequence database of the Protein Information Resource

More...PIRi		F69778

NCBI Reference Sequences

More...RefSeqi		NP_388405.1, NC_000964.3
WP_003234223.1, NZ_JNCM01000031.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB12331; CAB12331; BSU05240

Database of genes from NCBI RefSeq genomes

More...GeneIDi		939904

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU05240

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.559

<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
AB001488 Genomic DNA Translation: BAA19359.1
AL009126 Genomic DNA Translation: CAB12331.1
PIRiF69778
RefSeqiNP_388405.1, NC_000964.3
WP_003234223.1, NZ_JNCM01000031.1

3D structure databases

SMRiP96669
ModBaseiSearch...

Protein-protein interaction databases

IntActiP96669, 17 interactors
STRINGi224308.BSU05240

Proteomic databases

PaxDbiP96669
PRIDEiP96669

Genome annotation databases

EnsemblBacteriaiCAB12331; CAB12331; BSU05240
GeneIDi939904
KEGGibsu:BSU05240
PATRICifig|224308.179.peg.559

Phylogenomic databases

eggNOGiENOG4105C1I Bacteria
COG1167 LUCA
HOGENOMiHOG000223052
InParanoidiP96669
KOiK00375
OMAiDSEFRHT
PhylomeDBiP96669

Enzyme and pathway databases

BioCyciBSUB:BSU05240-MONOMER

Family and domain databases

CDDicd07377 WHTH_GntR, 1 hit
Gene3Di1.10.10.10, 1 hit
3.40.640.10, 1 hit
InterProiView protein in InterPro
IPR004839 Aminotransferase_I/II
IPR015424 PyrdxlP-dep_Trfase
IPR015421 PyrdxlP-dep_Trfase_major
IPR000524 Tscrpt_reg_HTH_GntR
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PfamiView protein in Pfam
PF00155 Aminotran_1_2, 1 hit
PF00392 GntR, 1 hit
PRINTSiPR00035 HTHGNTR
SMARTiView protein in SMART
SM00345 HTH_GNTR, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
SSF53383 SSF53383, 1 hit
PROSITEiView protein in PROSITE
PS50949 HTH_GNTR, 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 nameiYDEL_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: P96669
Secondary accession number(s): Q797H9
<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 20, 2009
Last sequence update: May 1, 1997
Last modified: October 16, 2019
This is version 123 of the entry and version 1 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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