RegulonDB

Gene
Name:	yafL
Synonym(s):	ECK0228, G6111, b0227
Genome position(nucleotides):	246712 --> 247461 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.4
External database links:

ASAP:	ABE-0000775
ECHOBASE:	EB2943
ECOLIHUB:	yafL
OU-MICROARRAY:	b0227
STRING:	511145.b0227
COLOMBOS:	yafL

Product

Name:

NlpC/P60 family protein YafL

Synonym(s):

C40 family non-peptidase homologue, YafL

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

28.785

Isoelectric point:

9.955

Motif(s):

Type	Positions	Sequence
	131 -> 241	GKPYVWGGTRPDKGFDCSGLVFYAYNKILEAKLPRTANEMYHYRRATIVANNDLRRGDLLFFHIHSREIADHMGVYLGDGQFIESPRTGETIRISRLAEPFWQDHFLGARR
	18 -> 249	CLPFSSFASATTSHISFSYAARQRMQNRARLLKQYQTHLKKQASYIVEGNAESKRALRQHNREQIKQHPEWFPAPLKASDRRWQALAENNHFLSSDHLHNITEVAIHRLEQQLGKPYVWGGTRPDKGFDCSGLVFYAYNKILEAKLPRTANEMYHYRRATIVANNDLRRGDLLFFHIHSREIADHMGVYLGDGQFIESPRTGETIRISRLAEPFWQDHFLGARRILTEETIL
	1 -> 17	MSLPSIPSFVLSGLLLI

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane
	molecular_function	GO:0008233 - peptidase activity GO:0016787 - hydrolase activity GO:0008234 - cysteine-type peptidase activity
	biological_process	GO:0006508 - proteolysis

Note(s):

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

Reference(s):

[1] Paradis-Bleau C., et al., 2014

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

yafL

Operon arrangement:

Transcription unit	Promoter
yafL

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_445 (cluster)	246533	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 246532 to 246533, where the highest frequency is at position 246533. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	yafLp6	246641	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.86. P-value: 6.928e-6 Read more >	[ICWHO]	[3]
promoter	rayTp1	247544	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 0.54. P-value: 2.679e-6 Read more >	[ICWHO]	[3]
promoter	TSS_446	247622	forward	nd	[RS-EPT-CBR]	[2]
promoter	rayTp8	247624	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.686. P-value: 5.435e-5 Read more >	[ICWHO]	[3]

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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056
[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.
[3] 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