RegulonDB

Gene
Name:	ortT
Synonym(s):	ECK1439, G6756, b1445, ydcX
Genome position(nucleotides):	1517389 --> 1517562 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	44.83
External database links:

ASAP:	ABE-0004818
ECHOBASE:	EB3530
OU-MICROARRAY:	b1445
PortEco:	ydcX
STRING:	511145.b1445
COLOMBOS:	ortT

Product

Name:

orphan toxin OrtT

Synonym(s):

OrtT, YdcX

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

6.646

Isoelectric point:

10.452

Motif(s):

Type	Positions	Sequence
	4 -> 57	YQHMLVFYAVMAAIAFLITWFLSHDKKRIRFLSAFLVGATWPMSFPVALLFSLF
	38 -> 38	F
	6 -> 26	HMLVFYAVMAAIAFLITWFLS
	34 -> 54	FLSAFLVGATWPMSFPVALLF
	1 -> 1	M

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)
	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0005887 - integral component of plasma membrane GO:0016021 - integral component of membrane
	biological_process	GO:0001896 - autolysis

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

ortT

Operon arrangement:

Transcription unit	Promoter

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_1816	1517209	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1817 (cluster)	1517218	reverse	For this promoter, there is a cluster of 3 transcription start sites,in the interval 1517216 to 1517218, where the highest frequency is at position 1515242. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	ydcXp1	1517221	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -2.61. P-value: 4.821e-5 Read more >	[ICWHO]	[2]
promoter	ydcXp7	1517236	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.85. P-value: 7.485e-5 Read more >	[ICWHO]	[2]
promoter	yncLp4	1517246	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.144. P-value: 2.866e-5 Read more >	[ICWHO]	[2]
promoter	ydcXp9	1517354	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.033. P-value: 4.586e-5 Read more >	[ICWHO]	[2]
promoter	ydcYp3	1517610	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.413. P-value: 2.619e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1818 (cluster)	1517612	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1517612 to 1517613, where the highest frequency is at position 1515636. The most upstream position of this cluster is assigned as TSS position in the promoter. 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

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