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Protein

Uncharacterized HTH-type transcriptional regulator YdfD

Gene

ydfD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

Cofactori

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi40 – 5920H-T-H motifPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aminotransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Pyridoxal phosphate

Enzyme and pathway databases

BioCyciBSUB:BSU05370-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Uncharacterized HTH-type transcriptional regulator YdfD
Gene namesi
Name:ydfD
Ordered Locus Names:BSU05370
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 482482Uncharacterized HTH-type transcriptional regulator YdfDPRO_0000360697Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei325 – 3251N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

PaxDbiP96681.

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003023.

Structurei

3D structure databases

ProteinModelPortaliP96681.
SMRiP96681. Positions 7-81, 111-482.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini12 – 8069HTH gntR-typePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

In the C-terminal section; belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family.Curated
Contains 1 HTH gntR-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG1167. LUCA.
HOGENOMiHOG000223054.
InParanoidiP96681.
KOiK18907.
OMAiRQIVDYM.
OrthoDBiEOG6H1Q05.
PhylomeDBiP96681.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR000524. Tscrpt_reg_HTH_GntR.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
PF00392. GntR. 1 hit.
[Graphical view]
PRINTSiPR00035. HTHGNTR.
SMARTiSM00345. HTH_GNTR. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF53383. SSF53383. 1 hit.
PROSITEiPS50949. HTH_GNTR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P96681-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFPEEKKMK KLPKYRQIVH FIKEKIGNGE WPIGSKIPSQ RTLAKDFQVN
60 70 80 90 100
RSTVITALEE LMADGLIEGT MGKGTVVINN TWTLMAKNSA PDWDQYVTSG
110 120 130 140 150
IQMPSRKIVQ EINQSESNTD LIQLSKGELS AEIFPLAVMK EMMGKVSQHM
160 170 180 190 200
EAFGYEEPKG YLPLREALSN YLKTIGINVS SSSILIVSGA LQALQLISMG
210 220 230 240 250
LLQRGSTVYL DQPSYLYSLH VFQSAGMKLT GLPMDNEGLL PENVHLTRGE
260 270 280 290 300
RGRAILYTNP CFHNPTGILM SKKRREEILA VSENTQLPII EDDIYRELWI
310 320 330 340 350
DEIPPYPIKT IDKNGHVLYI GSLSKTLSPG LRIGWIVGPE PVIERLSDIK
360 370 380 390 400
MQTDYGSSSL SQRVAAEWFT SGHYQQHVEK VRQQLKVRRE LALSALETHL
410 420 430 440 450
KEVATWNIPK GGFFVWIKIL PSISMKLLYT KALSKGILIN LGSIYAQEKG
460 470 480
NYIRLSYAYA SLEDLQKGIY ELGLMIKELA SR
Length:482
Mass (Da):54,239
Last modified:May 1, 1997 - v1
Checksum:i63426BF3BC9D5B3A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19371.1.
AL009126 Genomic DNA. Translation: CAB12344.1.
PIRiB69780.
RefSeqiNP_388418.1. NC_000964.3.
WP_003244019.1. NZ_JNCM01000031.1.

Genome annotation databases

EnsemblBacteriaiCAB12344; CAB12344; BSU05370.
GeneIDi939903.
KEGGibsu:BSU05370.
PATRICi18972678. VBIBacSub10457_0560.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19371.1.
AL009126 Genomic DNA. Translation: CAB12344.1.
PIRiB69780.
RefSeqiNP_388418.1. NC_000964.3.
WP_003244019.1. NZ_JNCM01000031.1.

3D structure databases

ProteinModelPortaliP96681.
SMRiP96681. Positions 7-81, 111-482.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003023.

Proteomic databases

PaxDbiP96681.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12344; CAB12344; BSU05370.
GeneIDi939903.
KEGGibsu:BSU05370.
PATRICi18972678. VBIBacSub10457_0560.

Phylogenomic databases

eggNOGiCOG1167. LUCA.
HOGENOMiHOG000223054.
InParanoidiP96681.
KOiK18907.
OMAiRQIVDYM.
OrthoDBiEOG6H1Q05.
PhylomeDBiP96681.

Enzyme and pathway databases

BioCyciBSUB:BSU05370-MONOMER.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR000524. Tscrpt_reg_HTH_GntR.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
PF00392. GntR. 1 hit.
[Graphical view]
PRINTSiPR00035. HTHGNTR.
SMARTiSM00345. HTH_GNTR. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF53383. SSF53383. 1 hit.
PROSITEiPS50949. HTH_GNTR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A 148 kbp sequence of the region between 35 and 47 degree of the Bacillus subtilis genome."
    Kasahara Y., Nakai S., Lee S., Sadaie Y., Ogasawara N.
    Submitted (MAR-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "GabR, a member of a novel protein family, regulates the utilization of gamma-aminobutyrate in Bacillus subtilis."
    Belitsky B.R., Sonenshein A.L.
    Mol. Microbiol. 45:569-583(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY.

Entry informationi

Entry nameiYDFD_BACSU
AccessioniPrimary (citable) accession number: P96681
Secondary accession number(s): Q797H0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: May 1, 1997
Last modified: February 17, 2016
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.