RegulonDB RegulonDB 10.8: Gene Form
   

secD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

secD secF yajC anti-terminator anti-anti-terminator yajDp6 yajDp6 TSS_523 (cluster) TSS_523 (cluster) TSS_522 TSS_522 TSS_521 TSS_521 TSS_520 (cluster) TSS_520 (cluster) TSS_519 TSS_519 TSS_518 TSS_518 TSS_517 TSS_517 TSS_516 TSS_516 TSS_515 TSS_515 TSS_514 (cluster) TSS_514 (cluster) TSS_513 TSS_513 TSS_512 TSS_512

Gene      
Name: secD    Texpresso search in the literature
Synonym(s): ECK0402, EG10938, b0408
Genome position(nucleotides): 427647 --> 429494 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.19
External database links:  
ASAP:
ABE-0001417
CGSC:
17893
ECHOBASE:
EB0931
OU-MICROARRAY:
b0408
PortEco:
secD
STRING:
511145.b0408
COLOMBOS: secD


Product      
Name: Sec translocon accessory complex subunit SecD
Synonym(s): SecD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 66.632
Isoelectric point: 8.99
Motif(s):
 
Type Positions Sequence
279 -> 426 LEFRLVNTNVDQAAAASGRVPGDSEVKQTREGQPVVLYKRVILTGDHITDSTSSQDEYNQPQVNISLDSAGGNIMSNFTKDNIGKPMATLFVEYKDSGKKDANGRAVLVKQEEVINIANIQSRLGNSFRITGINNPNEARQLSLLLRA
2 -> 103 LNRYPLWKYVMLIVVIVIGLLYALPNLFGEDPAVQITGARGVAASEQTLIQVQKTLQEEKITAKSVALEEGAILARFDSTDTQLRAREALMGVMGDKYVVAL
78 -> 78 F
586 -> 605 VATSMFTAIVGTRAIVNLLY
10 -> 29 YVMLIVVIVIGLLYALPNLF

 

Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.5 - The Type II (General) Secretory Pathway (IISP) Family
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
GO:0015450 - P-P-bond-hydrolysis-driven protein transmembrane transporter activity
biological_process GO:0015031 - protein transport
GO:0006605 - protein targeting
GO:0006886 - intracellular protein transport
GO:0065002 - intracellular protein transmembrane transport
GO:0043952 - protein transport by the Sec complex
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-35837N
ECOCYC:
SECD
ECOLIWIKI:
b0408
INTERPRO:
IPR005791
INTERPRO:
IPR027398
INTERPRO:
IPR022813
INTERPRO:
IPR022646
INTERPRO:
IPR022645
MINT:
P0AG90
MODBASE:
P0AG90
PANTHER:
PTHR30081
PDB:
5MG3
PFAM:
PF13721
PFAM:
PF02355
PFAM:
PF07549
PRIDE:
P0AG90
PRODB:
PRO_000023925
REFSEQ:
NP_414942
SMR:
P0AG90
UNIPROT:
P0AG90


Operon      
Name: tgt-yajC-secDF         
Operon arrangement:
Transcription unit        Promoter
tgt-yajC
yajC-secDF


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_512 427649 forward nd [RS-EPT-CBR] [1]
  promoter TSS_513 428779 forward nd [RS-EPT-CBR] [1]
  promoter TSS_514 (cluster) 428782 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_515 428786 forward nd [RS-EPT-CBR] [1]
  promoter TSS_516 429239 forward nd [RS-EPT-CBR] [1]
  promoter TSS_517 429370 forward nd [RS-EPT-CBR] [1]
  promoter TSS_518 429682 forward nd [RS-EPT-CBR] [1]
  promoter TSS_519 430048 forward nd [RS-EPT-CBR] [1]
  promoter TSS_520 (cluster) 430051 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_521 430054 forward nd [RS-EPT-CBR] [1]
  promoter TSS_522 430059 forward nd [RS-EPT-CBR] [1]
  promoter TSS_523 (cluster) 430063 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter yajDp6 430469 forward Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78


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