RegulonDB

Gene
Name:	ycaL
Synonym(s):	ECK0900, G6470, b0909
Genome position(nucleotides):	960264 --> 961028 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.93
External database links:

ASAP:	ABE-0003098
ECHOBASE:	EB2932
OU-MICROARRAY:	b0909
PortEco:	ycaL
STRING:	511145.b0909
COLOMBOS:	ycaL

Product

Name:

periplasmic protease YcaL

Synonym(s):

YcaL

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane,periplasmic space,extracellular space

Molecular weight:

26.74

Isoelectric point:

7.6

Motif(s):

Type	Positions	Sequence
	20 -> 254	CQNTHGIDTNMAISSGLNAYKAATLSDADAKAIANQGCAEMDSGNQVASKSSKYGKRLAKIAKALGNNINGTPVNYKVYMTSDVNAWAMANGCVRVYSGLMDMMNDNEIEGVLGHELGHVALGHSLAEMKASYAIVAARDAISATSGVASQLSRSQLGDIAEGAINAKYSRDKESEADDFSFDLLKKRGISTQGLVGSFETLASLDGGRTQSMFDSHPPSTERAQHIRDRIASGK
	1 -> 19	MKNTKLLLAIATSAALLTG
	77 -> 249	LAKIAKALGNNINGTPVNYKVYMTSDVNAWAMANGCVRVYSGLMDMMNDNEIEGVLGHELGHVALGHSLAEMKASYAIVAARDAISATSGVASQLSRSQLGDIAEGAINAKYSRDKESEADDFSFDLLKKRGISTQGLVGSFETLASLDGGRTQSMFDSHPPSTERAQHIRDR
	241 -> 254	ERAQHIRDRIASGK

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides
Gene Ontology Terms (GO)
	cellular_component	GO:0016020 - membrane GO:0030288 - outer membrane-bounded periplasmic space GO:0005886 - plasma membrane GO:0005576 - extracellular region
	molecular_function	GO:0005515 - protein binding GO:0008233 - peptidase activity GO:0016787 - hydrolase activity GO:0046872 - metal ion binding GO:0004222 - metalloendopeptidase activity GO:0008237 - metallopeptidase activity
	biological_process	GO:0006508 - proteolysis GO:0051603 - proteolysis involved in cellular protein catabolic process

Note(s):

Note(s): ...[more].

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ycaL

Operon arrangement:

Transcription unit	Promoter

RNA cis-regulatory element

Attenuation:	Transcriptional

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	ycaLp1	960132	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -2.89. P-value: 3.717e-5 Read more >	[ICWHO]	[1]
promoter	ycaLp8	960143	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.616. P-value: 4.373e-6 Read more >	[ICWHO]	[1]
promoter	ycaLp9	960238	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.908. P-value: 2.517e-5 Read more >	[ICWHO]	[1]
promoter	ycaLp6	960255	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.51. P-value: 5.068e-5 Read more >	[ICWHO]	[1]
promoter	TSS_1178	961718	forward	nd	[RS-EPT-CBR]	[2]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] 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
[2] 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.

Reference(s)

[1] 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

[2] 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.