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UniProtKB - P96663 (YDEF_BACSU)

Entry version 137 (25 May 2022)
Sequence version 2 (20 Jan 2009)
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Protein

Uncharacterized HTH-type transcriptional regulator YdeF

Gene

ydeF

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%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 bindingi50 – 69H-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:BSU05180-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:
Uncharacterized HTH-type transcriptional regulator YdeF
<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:ydeF
Ordered Locus Names:BSU05180
<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 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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003606951 – 462Uncharacterized HTH-type transcriptional regulator YdeFAdd BLAST462

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		P96663

<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

STRING: functional protein association networks

More...STRINGi		224308.BSU05180

<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

AlphaFold Protein Structure Database

More...AlphaFoldDBi		P96663

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

More...SMRi		P96663

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%5Fand%5Fdomains%5Fsection">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>Domaini22 – 90HTH 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		COG1167, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P96663

Identification of Orthologs from Complete Genome Data

More...OMAi		NMVFPRH

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
3.90.1150.10, 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
IPR015422, PyrdxlP-dep_Trfase_small
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

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%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.

P96663-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MPINSFENYP MSWKPSIDKA EKPIYKALAG QLEQDILNGV LLPGTKLPPQ 
        60         70         80         90        100
RELADYLDLN VSTISKAFKV CELKGLLSAT VGSGTFVSYD ALSNAYLLED 
       110        120        130        140        150
TKPTHLIEMG AILPDHASYE PLLYQLKNMV HEEDYEKWFS YGRAGESLWQ 
       160        170        180        190        200
KDAAVKLIQR GGFETSVDHI LFANGGQNAI AATLASLCKP GDRIGVDHHT 
       210        220        230        240        250
YPGLKTVASL LSVQIVPIKS ENDEMSPESL EYACKNENIK GLYLIPDYHN 
       260        270        280        290        300
PTTSFMSVEN RRMVADIVKK YNLFVIEDAS YHLLNKNPLP ALASFAPQQV 
       310        320        330        340        350
IHIASLSKSL APGLRLAYVA VPRQYKEPIS KALYNLNITV SPLLAELTAR 
       360        370        380        390        400
TIVSNQFEVL IESHREQTIR RNQLVNRYVA GYTCLGVETG IFRWLLLPGK 
       410        420        430        440        450
MSGAEFEELA ARLGVQVYAA ERFVVGNSCP ERAVRVSVCA PKTLEELEQG 
       460 
LMILRRLLDD LT
Length:462
Mass (Da):51,403
Last modified:January 20, 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:i5ACA85287ACD75F5
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 BAA19353 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.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
AB001488 Genomic DNA Translation: BAA19353.1 Different initiation.
AL009126 Genomic DNA Translation: CAB12325.2

Protein sequence database of the Protein Information Resource

More...PIRi		H69777

NCBI Reference Sequences

More...RefSeqi		NP_388399.1, NC_000964.3
WP_003244576.1, NZ_JNCM01000031.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB12325; CAB12325; BSU_05180

Database of genes from NCBI RefSeq genomes

More...GeneIDi		939911

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU05180

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.553

<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: BAA19353.1 Different initiation.
AL009126 Genomic DNA Translation: CAB12325.2
PIRiH69777
RefSeqiNP_388399.1, NC_000964.3
WP_003244576.1, NZ_JNCM01000031.1

3D structure databases

AlphaFoldDBiP96663
SMRiP96663
ModBaseiSearch...

Protein-protein interaction databases

STRINGi224308.BSU05180

Proteomic databases

PaxDbiP96663

Genome annotation databases

EnsemblBacteriaiCAB12325; CAB12325; BSU_05180
GeneIDi939911
KEGGibsu:BSU05180
PATRICifig|224308.179.peg.553

Phylogenomic databases

eggNOGiCOG1167, Bacteria
InParanoidiP96663
OMAiNMVFPRH

Enzyme and pathway databases

BioCyciBSUB:BSU05180-MONOMER

Family and domain databases

CDDicd07377, WHTH_GntR, 1 hit
Gene3Di1.10.10.10, 1 hit
3.40.640.10, 1 hit
3.90.1150.10, 1 hit
InterProiView protein in InterPro
IPR004839, Aminotransferase_I/II
IPR015424, PyrdxlP-dep_Trfase
IPR015421, PyrdxlP-dep_Trfase_major
IPR015422, PyrdxlP-dep_Trfase_small
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
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

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 nameiYDEF_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: P96663
Secondary accession number(s): Q797I5
<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: January 20, 2009
Last sequence update: January 20, 2009
Last modified: May 25, 2022
This is version 137 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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