RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

frdB gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	frdB
Synonym(s):	ECK4149, EG10331, b4153
Genome position(nucleotides):	4379783 <-- 4380517 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.61
External database links:

ASAP:	ABE-0013602
CGSC:	741
ECHOBASE:	EB0327
ECOLIHUB:	frdB
OU-MICROARRAY:	b4153
STRING:	511145.b4153
COLOMBOS:	frdB

Product

Name:

fumarate reductase iron-sulfur protein

Synonym(s):

FrdB

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane,cytosol

Molecular weight:

27.123

Isoelectric point:

6.491

Motif(s):

Type	Positions	Sequence
	2 -> 244	AEMKNLKIEVVRYNPEVDTAPHSAFYEVPYDATTSLLDALGYIKDNLAPDLSYRWSCRMAICGSCGMMVNNVPKLACKTFLRDYTDGMKVEALANFPIERDLVVDMTHFIESLEAIKPYIIGNSRTADQGTNIQTPAQMAKYHQFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHVDPAAAIQQGKVESSKDFLIATLKPR
	63 -> 63	C
	66 -> 66	C
	146 -> 219	FSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHV
	58 -> 58	C

Classification:

Multifun Terms (GenProtEC)
		1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.5 - fermentation
		1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
		1 - metabolism --> 1.4 - energy production/transport --> 1.4.2 - electron acceptors
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol GO:0016020 - membrane GO:0005886 - plasma membrane GO:0045284 - plasma membrane fumarate reductase complex
	molecular_function	GO:0102040 - fumarate reductase (menaquinone) GO:0005515 - protein binding GO:0009055 - electron transfer activity GO:0046872 - metal ion binding GO:0016491 - oxidoreductase activity GO:0051536 - iron-sulfur cluster binding GO:0051539 - 4 iron, 4 sulfur cluster binding GO:0051537 - 2 iron, 2 sulfur cluster binding GO:0051538 - 3 iron, 4 sulfur cluster binding
	biological_process	GO:0006099 - tricarboxylic acid cycle GO:0006113 - fermentation GO:0009061 - anaerobic respiration GO:0001539 - cilium or flagellum-dependent cell motility GO:0022900 - electron transport chain GO:0055114 - oxidation-reduction process GO:0044780 - bacterial-type flagellum assembly

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PFAM:

PFAM:

PRIDE:

PRODB:

PROSITE:

PROSITE:

PROSITE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

frdABCD

Operon arrangement:

Transcription unit	Promoter
frdABCD	frdAp
frdABCD	frdAp2

Transcriptional Regulation
	Display Regulation
Activated by:	FNR, DcuR
Repressed by:	NarL

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	frdDp2	4379433	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -1.01. P-value: 4.373e-6 Read more >	[ICWHO]	[1]
promoter	TSS_4971	4379467	reverse	nd	[RS-EPT-CBR]	[2]
promoter	frdDp1	4379473	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -1.49. P-value: 1.738e-5 Read more >	[ICWHO]	[1]
promoter	frdDp7	4379474	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.28. P-value: 3.167e-5 Read more >	[ICWHO]	[1]
promoter	TSS_4972	4379642	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4973	4380402	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4974	4380562	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4975 (cluster)	4380608	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 4380607 to 4380608, where the highest frequency is at position 4378630. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4976	4380764	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4977	4380768	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4978	4380783	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4979	4380790	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4980 (cluster)	4380795	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 4380794 to 4380795, where the highest frequency is at position 4378818. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4981	4380800	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4982	4380895	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4983	4381317	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4984	4381338	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4985	4381346	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4986	4381467	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4987	4381476	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4988	4381624	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4989	4382039	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4990 (cluster)	4382309	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 4382308 to 4382309, where the highest frequency is at position 4380332. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4991 (cluster)	4382324	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 4382323 to 4382324, where the highest frequency is at position 4380346. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4992	4382327	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4993 (cluster)	4382334	reverse	For this promoter, there is a cluster of 4 transcription start sites,in the interval 4382331 to 4382334, where the highest frequency is at position 4380356. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4994	4382336	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4995 (cluster)	4382398	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 4382397 to 4382398, where the highest frequency is at position 4380421. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4996 (cluster)	4382418	reverse	For this promoter, there is a cluster of 6 transcription start sites,in the interval 4382413 to 4382418, where the highest frequency is at position 4380437. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4998	4383369	forward	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.

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