RegulonDB

Gene
Name:	panB
Synonym(s):	ECK0133, EG11675, b0134
Genome position(nucleotides):	148807 <-- 149601 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.59
External database links:

ASAP:	ABE-0000467
CGSC:	427
ECHOBASE:	EB1626
OU-MICROARRAY:	b0134
PortEco:	panB
STRING:	511145.b0134
COLOMBOS:	panB

Gene

Name:

panB

Synonym(s):

ECK0133, EG11675, b0134

Genome position(nucleotides):

148807 <-- 149601 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.59

External database links:

ASAP:

CGSC:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

7 -> 8

124 -> 124

4 -> 258

TTISLLQKYKQEKKRFATITAYDYSFAKLFADEGLNVMLVGDSLGMTVQGHDSTLPVTVADIAYHTAAVRRGAPNCLLLADLPFMAYATPEQAFENAATVMRAGANMVKIEGGEWLVETVQMLTERAVPVCGHLGLTPQSVNIFGGYKVQGRGDEAGDQLLSDALALEAAGAQLLVLECVPVELAKRITEALAIPVIGIGAGNVTDGQILVMHDAFGITGGHIPKFAKNFLAETGDIRAAVRQYMAEVESGVYPG

15 -> 15

12 -> 12

Type

Positions

Sequence

7 -> 8

124 -> 124

4 -> 258

15 -> 15

12 -> 12

45 -> 46

63 -> 63

Multifun Terms (GenProtEC)

1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.5 - Coenzyme A and its modification

Gene Ontology Terms (GO)

cellular_component

GO:0005737 - cytoplasm
GO:0005829 - cytosol

molecular_function

GO:0003824 - catalytic activity
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity
GO:0000287 - magnesium ion binding
GO:0042802 - identical protein binding

biological_process

GO:0015940 - pantothenate biosynthetic process

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	panCp4	148910	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.1. P-value: 5.275e-5 Read more >	[ICWHO]	[4]
promoter	panCp2	148920	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.72. P-value: 4.149e-5 Read more >	[ICWHO]	[4]
promoter	TSS_272	149617	reverse	nd	[RS-EPT-CBR]	[5]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

panCp4

148910

reverse

Similarity to the consensus
Read more >

[ICWHO]

[4]

promoter

panCp2

148920

reverse

Similarity to the consensus
Read more >

[ICWHO]

[4]

promoter

TSS_272

149617

reverse

[RS-EPT-CBR]

[5]

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] Lobley CM., Schmitzberger F., Kilkenny ML., Whitney H., Ottenhof HH., Chakauya E., Webb ME., Birch LM., Tuck KL., Abell C., Smith AG., Blundell TL., 2003, Structural insights into the evolution of the pantothenate-biosynthesis pathway., Biochem Soc Trans 31(Pt 3):563-71
[2] Merkel WK., Nichols BP., 1996, Characterization and sequence of the Escherichia coli panBCD gene cluster., FEMS Microbiol Lett 143(2-3):247-52
[3] Vallari DS., Rock CO., 1985, Isolation and characterization of Escherichia coli pantothenate permease (panF) mutants., J Bacteriol 164(1):136-42
[4] 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
[5] 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] Lobley CM., Schmitzberger F., Kilkenny ML., Whitney H., Ottenhof HH., Chakauya E., Webb ME., Birch LM., Tuck KL., Abell C., Smith AG., Blundell TL., 2003, Structural insights into the evolution of the pantothenate-biosynthesis pathway., Biochem Soc Trans 31(Pt 3):563-71

[2] Merkel WK., Nichols BP., 1996, Characterization and sequence of the Escherichia coli panBCD gene cluster., FEMS Microbiol Lett 143(2-3):247-52

[3] Vallari DS., Rock CO., 1985, Isolation and characterization of Escherichia coli pantothenate permease (panF) mutants., J Bacteriol 164(1):136-42

[4] 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

[5] 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.