RegulonDB RegulonDB 10.7: Gene Form
   

ydgD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydgD mdtI ydgU mdtJ TSS_1879 (cluster) TSS_1879 (cluster) ydgDp7 ydgDp7 ydgDp4 ydgDp4 TSS_1878 TSS_1878

Gene      
Name: ydgD    Texpresso search in the literature
Synonym(s): ECK1593, G6856, b1598
Genome position(nucleotides): 1671960 --> 1672781 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.07
External database links:  
ASAP:
ABE-0005340
ECHOBASE:
EB3684
OU-MICROARRAY:
b1598
PORTECO:
ydgD
REGULONDB:
b1598
STRING:
511145.b1598
M3D: ydgD
COLOMBOS: ydgD
PortEco: b1598


Product      
Name: putative serine protease YdgD
Synonym(s): YdgD
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 29.277
Isoelectric point: 6.148
Motif(s):
 
Type Positions Sequence
1 -> 21 MRTTIAVVLGAISLTSAFVFA
22 -> 273 DKPDVARSANDEVSTLFFGHDDRVPVNDTTQSPWDAVGQLETASGNLCTATLIAPNLALTAGHCLLTPPKGKADKAVALRFVSNKGLWRYEIHDIEGRVDPTLGKRLKADGDGWIVPPAAAPWDFGLIVLRNPPSGITPLPLFEGDKAALTAALKAAGRKVTQAGYPEDHLDTLYSHQNCEVTGWAQTSVMSHQCDTLPGDSGSPLMLHTDDGWQLIGVQSSAPAAKDRWRADNRAISVTGFRDKLDQLSQK
50 -> 244 TTQSPWDAVGQLETASGNLCTATLIAPNLALTAGHCLLTPPKGKADKAVALRFVSNKGLWRYEIHDIEGRVDPTLGKRLKADGDGWIVPPAAAPWDFGLIVLRNPPSGITPLPLFEGDKAALTAALKAAGRKVTQAGYPEDHLDTLYSHQNCEVTGWAQTSVMSHQCDTLPGDSGSPLMLHTDDGWQLIGVQSSA

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
molecular_function GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0004252 - serine-type endopeptidase activity
GO:0008236 - serine-type peptidase activity
biological_process GO:0006508 - proteolysis
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11712N
ECOCYC:
G6856-MONOMER
ECOLIWIKI:
b1598
INTERPRO:
IPR033116
INTERPRO:
IPR009003
INTERPRO:
IPR008256
INTERPRO:
IPR001254
INTERPRO:
IPR018114
PFAM:
PF00089
PRIDE:
P76176
PRINTS:
PR00839
PROSITE:
PS00135
PROSITE:
PS00134
PROTEINMODELPORTAL:
P76176
REFSEQ:
NP_416115
SMART:
SM00020
SMR:
P76176
UNIPROT:
P76176


Operon      
Name: ydgD         
Operon arrangement:
Transcription unit        Promoter
 


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_1878 1671916 forward nd [RS-EPT-CBR] [1]
  promoter ydgDp4 1671953 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ydgDp7 1671957 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1879 (cluster) 1671972 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]


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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