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Expression|

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Standard Name	rfbC
Gene Synonym(s)	ECK2032, b2038, JW2023, rmlC^[1], rfbD, rmlC
Product Desc.	DTDPDEHYDRHAMEPIM^[2]^[3]; Component of dTDP-L-rhamnose synthetase^[2]^[3] dTDP-4-deoxyrhamnose-3,5-epimerase^[4]
Product Synonyms(s)	dTDP-4-deoxyrhamnose-3,5-epimerase^[1], B2038^[2]^[1], RfbC^[2]^[1], RmlC^[2]^[1] , ECK2032, JW2023, rfbD, rmlC, b2038
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	rfbC
Mnemonic	Rough
Synonyms	ECK2032, b2038, JW2023, rmlC^[1], rfbD, rmlC
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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	45.43 minutes, 45.43 minutes	MG1655: 2108162..2107605 <gbrowseImage> name=NC_000913:2107605..2108162 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2000088..2000645 <gbrowseImage> name=NC_012759:2000088..2000645 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2112275..2111718 <gbrowseImage> name=NC_007779:2111718..2112275 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2199170..2198613 <gbrowseImage> name=NC_010473:2198613..2199170 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
ΔrfbC (Keio:JW2023)	deletion	deletion	PMID:16738554	Shigen CGSC9660^[5]
rfbC1				CGSC:4502
ΔrfbC736::kan			PMID:16738554	CGSC:102670
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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
JW2023	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATGTGATTAGAACTGAAAT Primer 2:CCTGCAATTAATTTTAATCTGAT
21H10	Kohara Phage	Genobase	PMID:3038334
1G1	Kohara Phage	Genobase	PMID:3038334
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 40% ^[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:EG11979	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11979	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001904	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947482	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1922	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006759	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	RfbC
Synonyms	dTDP-4-deoxyrhamnose-3,5-epimerase^[1], B2038^[2]^[1], RfbC^[2]^[1], RmlC^[2]^[1] , ECK2032, JW2023, rfbD, rmlC, b2038
Product description	DTDPDEHYDRHAMEPIM^[2]^[3]; Component of dTDP-L-rhamnose synthetase^[2]^[3] dTDP-4-deoxyrhamnose-3,5-epimerase^[4]
EC number (for enzymes)	5.1.3.13^[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
	GO:0008830	dTDP-4-dehydrorhamnose 3,5-epimerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000888	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008830	dTDP-4-dehydrorhamnose 3,5-epimerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.1.3.13	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000888	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019305	dTDP-rhamnose biosynthetic process				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0448	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016853	isomerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0413	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042803	protein homodimerization activity				F	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
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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-L-rhamnose synthetase	could be indirect
Protein	groL		PMID:15690043	Experiment(s):EBI-887248
Protein	groL		PMID:16606699	Experiment(s):EBI-1141698
Protein	yhbT		PMID:16606699	Experiment(s):EBI-1141698
Protein	yhjA		PMID:16606699	Experiment(s):EBI-1141698
Protein	groL		PMID:19402753	MALDI(Z-score):17.053160
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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 MNVIRTEIED VLILEPRVFG DDRGFFYESF NQSAFEHILG YPVSFVQDNH SRSSKNVLRG LHFQRGEYAQ DKLVRCTHGA VFDVAVDIRP NSVSFGKWVG VLLSADNKQQ LWIPKGFAHG FLVLSDIAEF QYKTTNYYHP ESDCGICWND ERIAIDWPQT SGLILSPKDE RLFTLDELIR LKLIA
Length	185
Mol. Wt	21.27 kDa
pI	5.7 (calculated)
Extinction coefficient	30,940 - 31,315 (calc based on 6 Y, 4 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..178	PF00908 dTDP-4-dehydrorhamnose 3,5-epimerase		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=rfbC 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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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

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:16129978	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947482	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006759	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37745	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11979	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11979	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947482	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001904	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1922	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 MC4100	2.50E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1965	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	752	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	1537	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_000913:2108142..2108182 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:b2038 (EcoliWiki Page)	NCBI GEO profiles for rfbC
microarray	GenExpDB:b2038 (EcoliWiki Page)	Summary of data for rfbC 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
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Notes

Accessions Related to rfbC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11979	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1922	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2038
EcoGene	EcoGene:EG11979	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001904	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006759	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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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
Anopheles gambiae	ENSANGP00000002008 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00027570 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00015781 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RFBC	From SHIGELLACYC
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Do-It-Yourself Web Tools

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)	PF00908 dTDP-4-dehydrorhamnose 3,5-epimerase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51182
Panther (EcoliWiki Page)	PTHR21047:SF0
EcoCyc	EcoCyc:EG11979	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11979	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001904	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1922	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006759	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 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).

rfbC: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 rfbC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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