RegulonDB

Gene
Name:	epmC
Synonym(s):	ECK2320, G7201, b2326, yfcM
Genome position(nucleotides):	2444203 <-- 2444751 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.27
External database links:

ASAP:	ABE-0007686
ECHOBASE:	EB3869
OU-MICROARRAY:	b2326
PortEco:	yfcM
STRING:	511145.b2326
COLOMBOS:	epmC

Product

Name:

EF-P-Lys34 hydroxylase

Synonym(s):

EpmC, YfcM

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

21.146

Isoelectric point:

4.482

Motif(s):

Type	Positions	Sequence
	13 -> 175	IFNSCFADDFNTRLIKGDDEPIYLPADAEVPYNRIVFAHGFYASAIHEISHWCIAGKARRELVDFGYWYCPDGRDAQTQSQFEDVEVKPQALDWLFCVAAGYPFNVSCDNLEGDFEPDRVVFQRRVHAQVMDYLTNGIPERPARFIKALQNYYHTPELTAEQF

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0046872 - metal ion binding GO:0016491 - oxidoreductase activity GO:0004497 - monooxygenase activity GO:0016709 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
	biological_process	GO:0043687 - post-translational protein modification GO:0055114 - oxidation-reduction process GO:1901260 - peptidyl-lysine hydroxylation involved in bacterial-type EF-P lysine modification

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PDB:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

prmB-aroC-mepA-yfcA-epmC-yfcL

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	yfcLp5	2444251	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.23. P-value: 5.275e-5 Read more >	[ICWHO]	[1]
promoter	TSS_2637	2444742	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2638	2444784	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2639 (cluster)	2444800	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2444799 to 2444800, where the highest frequency is at position 2442821. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_2640 (cluster)	2444805	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2444804 to 2444805, where the highest frequency is at position 2442827. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_2641 (cluster)	2444859	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2444858 to 2444859, where the highest frequency is at position 2442881. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_2642	2444872	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2643	2444876	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2644 (cluster)	2444884	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2444883 to 2444884, where the highest frequency is at position 2442906. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_2645	2445745	reverse	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.