RegulonDB RegulonDB 11.1: 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
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.19
External database links:  
ASAP:
 ABE-0001417
CGSC:
 17893
ECHOBASE:
 EB0931
ECOLIHUB:
 secD
OU-MICROARRAY:
 b0408
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 Comment
2 -> 103 LNRYPLWKYVMLIVVIVIGLLYALPNLFGEDPAVQITGARGVAASEQTLIQVQKTLQEEKITAKSVALEEGAILARFDSTDTQLRAREALMGVMGDKYVVAL
10 -> 29 YVMLIVVIVIGLLYALPNLF UniProt: Helical.
78 -> 78 F UniProt: In Ref. 1; CAA39634..
120 -> 140 PMKLGLDLRGGVHFLMEVDMD
155 -> 155 R UniProt: In Ref. 1; CAA39634..

 
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
GO:0031522 - cell envelope Sec protein transport complex
molecular_function GO:0005515 - protein binding
GO:0015450 - protein-transporting ATPase activity
biological_process GO:0015031 - protein transport
GO:0006605 - protein targeting
GO:0006886 - intracellular protein transport
GO:0065002 - intracellular protein transmembrane transport
GO:0032978 - protein insertion into membrane from inner side
GO:0043952 - protein transport by the Sec complex
Note(s): Note(s): ...[more].
Reference(s): [1] Matsuyama S., et al., 1992
[2] Sagara K., et al., 1994
External database links:  
ALPHAFOLD:
 P0AG90
DIP:
 DIP-35837N
ECOCYC:
 SECD
ECOLIWIKI:
 b0408
INTERPRO:
 IPR005791
INTERPRO:
 IPR022813
INTERPRO:
 IPR027398
INTERPRO:
 IPR022646
INTERPRO:
 IPR022645
MINT:
 P0AG90
MODBASE:
 P0AG90
PANTHER:
 PTHR30081
PDB:
 5MG3
PFAM:
 PF13721
PFAM:
 PF07549
PFAM:
 PF02355
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] [3]
  promoter TSS_513 428779 forward nd [RS-EPT-CBR] [3]
  promoter TSS_514 (cluster) 428782 forward nd [RS-EPT-CBR] [3]
  promoter TSS_515 428786 forward nd [RS-EPT-CBR] [3]
  promoter TSS_516 429239 forward nd [RS-EPT-CBR] [3]
  promoter TSS_517 429370 forward nd [RS-EPT-CBR] [3]
  promoter TSS_518 429682 forward nd [RS-EPT-CBR] [3]
  promoter TSS_519 430048 forward nd [RS-EPT-CBR] [3]
  promoter TSS_520 (cluster) 430051 forward nd [RS-EPT-CBR] [3]
  promoter TSS_521 430054 forward nd [RS-EPT-CBR] [3]
  promoter TSS_522 430059 forward nd [RS-EPT-CBR] [3]
  promoter TSS_523 (cluster) 430063 forward nd [RS-EPT-CBR] [3]
  promoter yajDp6 430469 forward nd [COMP-AINF] [4]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Matsuyama S., Fujita Y., Sagara K., Mizushima S., 1992, Overproduction, purification and characterization of SecD and SecF, integral membrane components of the protein translocation machinery of Escherichia coli., Biochim Biophys Acta 1122(1):77-84

 [2] Sagara K., Matsuyama S., Mizushima S., 1994, SecF stabilizes SecD and SecY, components of the protein translocation machinery of the Escherichia coli cytoplasmic membrane., J Bacteriol 176(13):4111-6

 [3] 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.

 [4] 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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