RegulonDB

Gene
Name:	ybjM
Synonym(s):	ECK0839, G6446, b0848
Genome position(nucleotides):	890089 --> 890466 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.74
External database links:

ASAP:	ABE-0002891
ECHOBASE:	EB3446
OU-MICROARRAY:	b0848
PortEco:	ybjM
STRING:	511145.b0848
COLOMBOS:	ybjM

Product

Name:

putative inner membrane protein

Synonym(s):

YbjM

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

14.203

Isoelectric point:

10.774

Motif(s):

Type	Positions	Sequence
	3 -> 117	HKQRWAGAICCFVLFIVVCLFLATHMKGAFRAAGHPEIGLLFFILPGAVASFFSQRREVLKPLFGAMLAAPCSMLIMRLFFSPTRSFWQELAWLLSAVFWCALGALCFLFISSLF
	7 -> 27	WAGAICCFVLFIVVCLFLATH
	35 -> 55	AGHPEIGLLFFILPGAVASFF
	93 -> 113	LAWLLSAVFWCALGALCFLFI
	65 -> 85	LFGAMLAAPCSMLIMRLFFSP

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0016021 - integral component of membrane

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

PRODOM:

REFSEQ:

UNIPROT:

Operon

Name:

ybjM

Operon arrangement:

Transcription unit	Promoter
ybjM

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_992	888924	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_993	888928	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_994 (cluster)	888947	reverse	For this promoter, there is a cluster of 4 transcription start sites,in the interval 888944 to 888947, where the highest frequency is at position 888167. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_995	888953	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_996	889468	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_997 (cluster)	889475	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 889474 to 889475, where the highest frequency is at position 888697. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	ybjMp8	889885	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.926. P-value: 2.845e-6 Read more >	[ICWHO]	[2]
promoter	TSS_998	889888	forward	nd	[RS-EPT-CBR]	[1]
promoter	ybjLp12	889938	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.66. P-value: 2.066e-6 Read more >	[ICWHO]	[2]
promoter	ybjMp4	889940	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.71. P-value: 9.234e-5 Read more >	[ICWHO]	[2]
promoter	ybjLp10	889941	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.153. P-value: 7.264e-5 Read more >	[ICWHO]	[2]
promoter	TSS_999	889945	reverse	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