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Gene |

Product(s) |

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Standard Name	rfbB
Gene Synonym(s)	ECK2035, b2041, JW2026, som, rmlB^[1], rmlB
Product Desc.	RmlB^[2]^[3]; Component of dTDP-glucose 4,6-dehydratase^[2]^[3] TDP-glucose oxidoreductase-4,6 dehydratase^[4]
Product Synonyms(s)	dTDP-glucose 4,6 dehydratase, NAD(P)-binding^[1], B2041^[2]^[1], Som^[2]^[1], RmlB^[2]^[1], RfbB^[2]^[1] , ECK2035, JW2026, rmlB, som, b2041
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rfbBDACX^[2]
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	rfbB
Mnemonic	Rough
Synonyms	ECK2035, b2041, JW2026, som, rmlB^[1], rmlB
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	45.48 minutes, 45.48 minutes	MG1655: 2111085..2110000 <gbrowseImage> name=NC_000913:2110000..2111085 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2046292..2045207 <gbrowseImage> name=NC_012967:2045207..2046292 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2002483..2003568 <gbrowseImage> name=NC_012759:2002483..2003568 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2115198..2114113 <gbrowseImage> name=NC_007779:2114113..2115198 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2202093..2201008 <gbrowseImage> name=NC_010473:2201008..2202093 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
ΔrfbB (Keio:JW2026)	deletion	deletion	PMID:16738554	Shigen CGSC9663^[5]
rfbB::Tn5KAN-2 (FB20591)	Insertion at nt 344 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20591	does not contain pKD46
rfbB::Tn5KAN-2 (FB20592)	Insertion at nt 344 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20592	contains pKD46
ΔrfbB51				CGSC:49547
ΔrfbB739::kan			PMID:16738554	CGSC:102668
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW2026	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAATACTTGTTACTGGTGG Primer 2:CCtTGGCGaCCCTCATAGTTCTGTTCAATC
21H10	Kohara Phage	Genobase	PMID:3038334
1G1	Kohara Phage	Genobase	PMID:3038334
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 36% ^[6] Synonyms:zee-3129::Tn10
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12412	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12412	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002273	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945276	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2311	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006766	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	RfbB
Synonyms	dTDP-glucose 4,6 dehydratase, NAD(P)-binding^[1], B2041^[2]^[1], Som^[2]^[1], RmlB^[2]^[1], RfbB^[2]^[1] , ECK2035, JW2026, rmlB, som, b2041
Product description	RmlB^[2]^[3]; Component of dTDP-glucose 4,6-dehydratase^[2]^[3] TDP-glucose oxidoreductase-4,6 dehydratase^[4]
EC number (for enzymes)	4.2.1.46^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of dTDP-glucose 4,6-dehydratase	could be indirect
Protein	ugpQ		PMID:16606699	Experiment(s):EBI-1141720
Protein	lacZ		PMID:16606699	Experiment(s):EBI-1141720
Protein	nadE		PMID:16606699	Experiment(s):EBI-1141720
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MKILVTGGAG FIGSAVVRHI INNTQDSVVN VDKLTYAGNR ESLADVSDSE RYVFEHADIC DAPAMARIFA QHQPDAVMHL AAESHVDRSI TGPAAFIETN IVGTYVLLEA ARNYWSALDS DKKNSFRFHH ISTDEVYGDL PHPDEVNNTE ELPLFTETTA YAPSSPYSAS KASSDHLVRA WKRTYGLPTI VTNCSNNYGP YHFPEKLIPL VILNALEGKA LPIYGKGDQI RDWLYVEDHA RALYTVVTEG KAGETYNIGG HNEKKNIDVV LTICDLLDEI VPKEKSYREQ ITYVADRPGH DRRYAIDAEK IGRALGWKPQ ETFESGIRKT VEWYLSNTKW VDNVKSGAYQ SWIEQNYEGR Q
Length	361
Mol. Wt	40.558 kDa
pI	5.7 (calculated)
Extinction coefficient	68,300 - 68,675 (calc based on 20 Y, 7 W, and 3 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	3..259	PF01370 NAD dependent epimerase/dehydratase family		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rfbB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129981	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945276	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006766	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37759	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12412	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12412	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945276	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002273	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2311	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	5290	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	1257	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	3631	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
rfbBDACX
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2111065..2111105 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2041 (EcoliWiki Page)	NCBI GEO profiles for rfbB
microarray	GenExpDB:b2041 (EcoliWiki Page)	Summary of data for rfbB from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (2110791..2111276) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:C4^[7]
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Notes

Accessions Related to rfbB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12412	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2311	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2041
EcoGene	EcoGene:EG12412	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002273	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006766	Escherichia coli str. K-12 substr. MG1655
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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Apis mellifera	ENSAPMP00000021860 (score: 1.000; bootstrap: 100%) YP_026255 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	YP_026255 (score: 1.000; bootstrap: 100%) AT1G78570 (score: 1.000; bootstrap: 99%) AT1G53500 (score: 1.000; bootstrap: 99%) AT3G14790 (score: 0.895) AT1G63000 (score: 0.233)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000006984 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.610)	From Inparanoid:20070104
Caenorhabditis briggsae	YP_026255 (score: 0.617) WBGene00034706 (score: 1.000; bootstrap: 100%) WBGene00026470 (score: 0.140)	From Inparanoid:20070104
Caenorhabditis elegans	YP_026255 (score: 0.618) WBGene00018737 (score: 1.000; bootstrap: 100%) WBGene00015298 (score: 0.125)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000007947 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.611)	From Inparanoid:20070104
Danio rerio	YP_026255 (score: 1.000; bootstrap: 99%) ZDB-GENE-030131-5718 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-1388 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-1387 (score: 0.653)	From Inparanoid:20070104
Dictyostelium discoideum	YP_026255 (score: 1.000; bootstrap: 99%) DDB0231748 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000027264 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.608)	From Inparanoid:20070104
Homo sapiens	ENSP00000261296 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.610)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000017161 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.647)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000011711 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.610)	From Inparanoid:20070104
Mus musculus	MGI:1923605 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.604)	From Inparanoid:20070104
Oryza gramene	YP_026255 (score: 1.000; bootstrap: 100%) Q6B6M1 (score: 1.000; bootstrap: 59%) Q6B6L8 (score: 1.000; bootstrap: 52%) Q8W3J1 (score: 0.907) Q5QMG6 (score: 0.903) Q6F3E9 (score: 0.819) Q75PK7 (score: 0.787) Q6B6L9 (score: 0.784) Q6I683 (score: 0.778) Q60E78 (score: 0.756) Q75PK6 (score: 0.720) Q8W3J0 (score: 0.540) Q9FSE2 (score: 0.538) Q6B6M0 (score: 0.532) Q7XY21 (score: 0.531) Q8W2F7 (score: 0.522) Q5QMG5 (score: 0.317)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000010139 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.610)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000012925 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.605)	From Inparanoid:20070104
Schizosaccharomyces pombe	YP_026255 (score: 0.645) SPBPB2B21 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000157727 (score: 1.000; bootstrap: 98%) YP_026255 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00025956001 (score: 1.000; bootstrap: 100%) GSTENP00000105001 (score: 0.057) YP_026255 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000009242 (score: 1.000; bootstrap: 100%) YP_026255 (score: 0.340)	From Inparanoid:20070104
Shigella flexneri	RFBB	From SHIGELLACYC
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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF01370 NAD dependent epimerase/dehydratase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
EcoCyc	EcoCyc:EG12412	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12412	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002273	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2311	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006766	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rfbB:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to rfbB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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