RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

gyrB gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	gyrB
Synonym(s):	ECK3691, EG10424, acrB, b3699, cou, himB, hisU, hopA, nalC, parA, pcbA, pcpA
Genome position(nucleotides):	3877705 <-- 3880119 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.99
External database links:

ASAP:	ABE-0012093
CGSC:	650
ECHOBASE:	EB0419
ECOLIHUB:	gyrB
OU-MICROARRAY:	b3699
STRING:	511145.b3699
COLOMBOS:	gyrB

Product

Name:

DNA gyrase subunit B

Synonym(s):

AcrB, Cou, GyrB, HimB, HisU, HopA, NalC, ParA, PcbA, PcpA

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

89.95

Isoelectric point:

5.931

Motif(s):

Type	Positions	Sequence
	38 -> 38	H
	136 -> 136	R
	164 -> 164	G
	385 -> 385	A
	419 -> 531	ELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQ

Type	Positions	Sequence
	38 -> 38	H
	136 -> 136	R
	164 -> 164	G
	385 -> 385	A
	419 -> 531	ELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQ
	424 -> 424	E
	564 -> 729	ATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKE
	103 -> 103	K
	447 -> 447	K
	732 -> 793	RGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIE
	5 -> 5	Y
	10 -> 10	I
	42 -> 42	E
	418 -> 533	SELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPP
	426 -> 426	D
	759 -> 760	SR
	221 -> 392	GIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMT
	335 -> 337	QTK
	32 -> 174	DGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLE
	102 -> 103	GK
	115 -> 120	LHGVGV
	436 -> 436	R
	751 -> 751	W
	1 -> 14	MSNSYDSSSIKVLK
	498 -> 498	D
	2 -> 804	SNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI
	502 -> 502	D
	110 -> 110	K
	337 -> 337	K
	500 -> 500	D

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol GO:0005694 - chromosome GO:0009330 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
	molecular_function	GO:0003677 - DNA binding GO:0003916 - DNA topoisomerase activity GO:0005515 - protein binding GO:0008094 - DNA-dependent ATPase activity GO:0016853 - isomerase activity GO:0046872 - metal ion binding GO:0000166 - nucleotide binding GO:0005524 - ATP binding GO:0003918 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity GO:0034335 - DNA negative supercoiling activity
	biological_process	GO:0006261 - DNA-dependent DNA replication GO:0006351 - transcription, DNA-templated GO:0042493 - response to drug GO:0046677 - response to antibiotic GO:0006265 - DNA topological change

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Operon

Name:

gyrB

Operon arrangement:

Transcription unit	Promoter
gyrB	gyrBp
gyrB	gyrBp2

Transcriptional Regulation
	Display Regulation
Repressed by:	Fis

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	yidBp3	3877615	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.463. P-value: 3.830e-5 Read more >	[ICWHO]	[1]
promoter	TSS_4259	3878251	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4260 (cluster)	3878769	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 3878768 to 3878769, where the highest frequency is at position 3876791. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_4261	3878772	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4262	3879127	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4263	3879564	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4264	3880140	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_4265 (cluster)	3880152	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 3880151 to 3880152, where the highest frequency is at position 3878175. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[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.

RegulonDB