RegulonDB

Gene
Name:	ydgD
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
ECOLIHUB:	ydgD
OU-MICROARRAY:	b1598
STRING:	511145.b1598
COLOMBOS:	ydgD

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:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

PRINTS:

PROSITE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ydgD

Operon arrangement:

Transcription unit	Promoter
ydgD

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

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_1878	1671916	forward	nd	[RS-EPT-CBR]	[1]
promoter	ydgDp4	1671953	forward	nd	[ICWHO]	[2]
promoter	ydgDp7	1671957	forward	nd	[ICWHO]	[2]
promoter	TSS_1879 (cluster)	1671972	forward	nd	[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

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