RegulonDB

Gene
Name:	fumD
Synonym(s):	ECK1671, G6903, b1675, ydhZ
Genome position(nucleotides):	1754932 <-- 1755141 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	46.67
External database links:

ASAP:	ABE-0005591
ECHOBASE:	EB3718
OU-MICROARRAY:	b1675
PortEco:	ydhZ
STRING:	511145.b1675
COLOMBOS:	fumD

Product

Name:

fumarase D

Synonym(s):

FumD, YdhZ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

7.907

Isoelectric point:

9.911

Motif(s):

Type	Positions	Sequence
	1 -> 67	MGNRTKEDELYREMCRVVGKVVLEMRDLGQEPKHIVIAGVLRTALANKRIQRSELEKQAMETVINAL

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		1 - metabolism --> 1.3 - energy metabolism, carbon
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0016829 - lyase activity GO:0004333 - fumarate hydratase activity

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

fumD

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_1959 (cluster)	1755165	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1755164 to 1755165, where the highest frequency is at position 1753189. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	fumDp5	1755167	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.926. P-value: 7.636e-5 Read more >	[ICWHO]	[2]
promoter	fumDp6	1755209	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.746. P-value: 1.438e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1960 (cluster)	1755468	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1755468 to 1755469, where the highest frequency is at position 1753493. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1961	1755475	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1962	1755528	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1963	1755559	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1965 (cluster)	1755619	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1755619 to 1755620, where the highest frequency is at position 1753644. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1966	1755627	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1967	1755661	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1968	1755668	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1969	1755671	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1970	1755674	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1971	1755742	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1972	1755764	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1973 (cluster)	1756032	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1756032 to 1756033, where the highest frequency is at position 1754057. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1974	1756122	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1975	1756213	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1976	1756218	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1977	1756232	forward	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