RegulonDB

Gene
Name:	srmB
Synonym(s):	ECK2574, EG10975, b2576, rbaB, rhlA
Genome position(nucleotides):	2712896 --> 2714230 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.76
External database links:

ASAP:	ABE-0008478
CGSC:	32859
ECHOBASE:	EB0968
OU-MICROARRAY:	b2576
PortEco:	srmB
STRING:	511145.b2576
COLOMBOS:	srmB

Gene

Name:

srmB

Synonym(s):

ECK2574, EG10975, b2576, rbaB, rhlA

Genome position(nucleotides):

2712896 --> 2714230 Genome Browser

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.76

External database links:

ASAP:

CGSC:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

28 -> 197

TAIQAAAIPPALDGRDVLGSAPTGTGKTAAYLLPALQHLLDFPRKKSGPPRILILTPTRELAMQVSDHARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATTGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIEHIAGETRWRKQTLLFSATLEGDAIQ

236 -> 343

TALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG

157 -> 160

DEAD

4 -> 32

TTFSELELDESLLEALQDKGFTRPTAIQA

35 -> 209

IPPALDGRDVLGSAPTGTGKTAAYLLPALQHLLDFPRKKSGPPRILILTPTRELAMQVSDHARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATTGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIEHIAGETRWRKQTLLFSATLEGDAIQDFAERLLEDPVE

Type

Positions

Sequence

28 -> 197

TAIQAAAIPPALDGRDVLGSAPTGTGKTAAYLLPALQHLLDFPRKKSGPPRILILTPTRELAMQVSDHARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATTGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIEHIAGETRWRKQTLLFSATLEGDAIQ

236 -> 343

TALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG

157 -> 160

DEAD

4 -> 32

TTFSELELDESLLEALQDKGFTRPTAIQA

35 -> 209

IPPALDGRDVLGSAPTGTGKTAAYLLPALQHLLDFPRKKSGPPRILILTPTRELAMQVSDHARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATTGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIEHIAGETRWRKQTLLFSATLEGDAIQDFAERLLEDPVE

48 -> 55

APTGTGKT

238 -> 387

LLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVIDELRPKTRAPS

Multifun Terms (GenProtEC)

6 - cell structure --> 6.6 - ribosomes

Gene Ontology Terms (GO)

cellular_component

GO:0005737 - cytoplasm
GO:0005829 - cytosol

molecular_function

GO:0003676 - nucleic acid binding
GO:0004386 - helicase activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016887 - ATPase activity
GO:0003723 - RNA binding
GO:0008143 - poly(A) binding
GO:0000166 - nucleotide binding
GO:0003724 - RNA helicase activity
GO:0005524 - ATP binding
GO:0008186 - RNA-dependent ATPase activity
GO:0033592 - RNA strand annealing activity

biological_process

GO:0042254 - ribosome biogenesis
GO:0000027 - ribosomal large subunit assembly

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	yfiCp3	2712805	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.146. P-value: 5.601e-5 Read more >	[ICWHO]	[5]
promoter	srmBp4	2712876	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.116. P-value: 2.060e-5 Read more >	[ICWHO]	[5]
promoter	TSS_2874 (cluster)	2712878	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2712878 to 2712879, where the highest frequency is at position 2710900. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[6]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

yfiCp3

2712805

reverse

Similarity to the consensus
Read more >

[ICWHO]

[5]

promoter

srmBp4

2712876

forward

Similarity to the consensus
Read more >

[ICWHO]

[5]

promoter

TSS_2874 (cluster)

2712878

forward

For this promoter, there
Read more >

[RS-EPT-CBR]

[6]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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] Arunasri K., Adil M., Venu Charan K., Suvro C., Himabindu Reddy S., Shivaji S., 2013, Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression., PLoS One 8(3):e57860
[2] Bizebard T., Ferlenghi I., Iost I., Dreyfus M., 2004, Studies on Three E. coli DEAD-Box Helicases Point to an Unwinding Mechanism Different from that of Model DNA Helicases., Biochemistry 43(24):7857-66
[3] Jain C., 2018, Role of ribosome assembly in Escherichia coli ribosomal RNA degradation., Nucleic Acids Res 46(20):11048-11060
[4] Sharma H., Anand B., 2016, Fluorescence bimolecular complementation enables facile detection of ribosome assembly defects in Escherichia coli., RNA Biol 13(9):872-82
[5] 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
[6] 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] Arunasri K., Adil M., Venu Charan K., Suvro C., Himabindu Reddy S., Shivaji S., 2013, Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression., PLoS One 8(3):e57860

[2] Bizebard T., Ferlenghi I., Iost I., Dreyfus M., 2004, Studies on Three E. coli DEAD-Box Helicases Point to an Unwinding Mechanism Different from that of Model DNA Helicases., Biochemistry 43(24):7857-66

[3] Jain C., 2018, Role of ribosome assembly in Escherichia coli ribosomal RNA degradation., Nucleic Acids Res 46(20):11048-11060

[4] Sharma H., Anand B., 2016, Fluorescence bimolecular complementation enables facile detection of ribosome assembly defects in Escherichia coli., RNA Biol 13(9):872-82

[5] 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

[6] 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.