RegulonDB

Gene
Name:	ycfT
Synonym(s):	ECK1101, G6572, b1115
Genome position(nucleotides):	1174092 <-- 1175165 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.53
External database links:

ASAP:	ABE-0003767
ECHOBASE:	EB3212
OU-MICROARRAY:	b1115
PortEco:	ycfT
STRING:	511145.b1115
COLOMBOS:	ycfT

Product

Name:

inner membrane protein YcfT

Synonym(s):

YcfT

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

40.834

Isoelectric point:

9.604

Motif(s):

Type	Positions	Sequence
	136 -> 156	GMITASTSLWYLYALIVYFVV
	232 -> 252	VGAWLFTISLLLSLVSIVVIM
	87 -> 107	IWNIFWVLALWGVVQWLALSA
	311 -> 331	TLLLVYPFVSLFICTVAGLLV
	13 -> 33	GLCICLVVIYHSVITFYPHLT

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		4 - transport --> 4.9.B - Putative uncharacterized transport protein
Gene Ontology Terms (GO)
	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0016021 - integral component of membrane
	molecular_function	GO:0016747 - transferase activity, transferring acyl groups other than amino-acyl groups

Note(s):

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

Evidence:

[AIFS] Automated inference of function from sequence

Reference(s):

[1] Paradis-Bleau C., et al., 2014
[2] Rapp M., et al., 2004

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

ycfT

Operon arrangement:

Transcription unit	Promoter

RNA cis-regulatory element

Attenuation:	Translational

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_1443	1171800	reverse	nd	[RS-EPT-CBR]	[3]
promoter	TSS_1444 (cluster)	1173832	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1173831 to 1173832, where the highest frequency is at position 1173055. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[3]
promoter	TSS_1445	1173978	reverse	nd	[RS-EPT-CBR]	[3]
promoter	TSS_1447	1174023	reverse	nd	[RS-EPT-CBR]	[3]
promoter	ycfTp9	1175325	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.776. P-value: 9.930e-6 Read more >	[ICWHO]	[4]
promoter	ycfTp11	1175329	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.265. P-value: 1.704e-5 Read more >	[ICWHO]	[4]
promoter	TSS_1449	1175350	forward	nd	[RS-EPT-CBR]	[3]
promoter	lolCp6	1175374	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 5.826. P-value: 1.108e-5 Read more >	[ICWHO]	[4]
promoter	lolCp5	1175399	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.096. P-value: 2.781e-5 Read more >	[ICWHO]	[4]
promoter	TSS_1450	1176220	forward	nd	[RS-EPT-CBR]	[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] Rapp M., Drew D., Daley DO., Nilsson J., Carvalho T., Melen K., De Gier JW., Von Heijne G., 2004, Experimentally based topology models for E. coli inner membrane proteins., Protein Sci 13(4):937-45
[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