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Standard Name	rfbD
Gene Synonym(s)	ECK2034, b2040, JW2025, rmlD^[1], rmlD
Product Desc.	DTDPDEHYRHAMREDUCT^[2]^[3]; Component of dTDP-L-rhamnose synthetase^[2]^[3] dTDP-L-rhamnose synthase^[4]
Product Synonyms(s)	dTDP-4-dehydrorhamnose reductase subunit, NAD(P)-binding, of dTDP-L-rhamnose synthase^[1], B2040^[2]^[1], RfbD^[2]^[1], RmlD^[2]^[1] , ECK2034, JW2025, rmlD, b2040
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	rfbD
Mnemonic	Rough
Synonyms	ECK2034, b2040, JW2025, rmlD^[1], rmlD
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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	45.46 minutes, 45.46 minutes	MG1655: 2110000..2109101 <gbrowseImage> name=NC_000913:2109101..2110000 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2001584..2002483 <gbrowseImage> name=NC_012759:2001584..2002483 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2114113..2113214 <gbrowseImage> name=NC_007779:2113214..2114113 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2201008..2200109 <gbrowseImage> name=NC_010473:2200109..2201008 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
ΔrfbD (Keio:JW2025)	deletion	deletion	PMID:16738554	Shigen CGSC9662^[5]
ΔrfbD738::kan			PMID:16738554	CGSC:102672
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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
JW2025	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATATCCTCCTTTTTGGCAA Primer 2:CCAATTGCTGTAGTCGTAAATAA
21H10	Kohara Phage	Genobase	PMID:3038334
1G1	Kohara Phage	Genobase	PMID:3038334
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 37% ^[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:EG12411	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12411	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002272	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947117	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2310	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006764	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	RfbD
Synonyms	dTDP-4-dehydrorhamnose reductase subunit, NAD(P)-binding, of dTDP-L-rhamnose synthase^[1], B2040^[2]^[1], RfbD^[2]^[1], RmlD^[2]^[1] , ECK2034, JW2025, rmlD, b2040
Product description	DTDPDEHYRHAMREDUCT^[2]^[3]; Component of dTDP-L-rhamnose synthetase^[2]^[3] dTDP-L-rhamnose synthase^[4]
EC number (for enzymes)	1.1.1.133^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008831	dTDP-4-dehydrorhamnose reductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005913	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008831	dTDP-4-dehydrorhamnose reductase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.133	F	Seeded from EcoCyc (v14.0)	complete
	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:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0045226	extracellular polysaccharide biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005913	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
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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	rmlA1		PMID:16606699	Experiment(s):EBI-1141711
Protein	rpiR		PMID:16606699	Experiment(s):EBI-1141711
Protein	prs		PMID:16606699	Experiment(s):EBI-1141711
Protein	exuR		PMID:16606699	Experiment(s):EBI-1141711
Protein	groL		PMID:16606699	Experiment(s):EBI-1141711
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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 MNILLFGKTG QVGWELQRAL APLGNLIAFD VHSTDYCGDF SNPEGVAETV RSIRPDIIVN AAAHTAVDKA ESEPEFAQLI NATSVEAIAK AANEVGAWVI HYSTDYVFPG NGDMPWLETD ATAPLNVYGE TKLAGEKALQ EYCAKHLIFR TSWVYAGKGN NFAKTMLRLA KEREELAVIN DQFGAPTGAE LLADCTAHAI RVALNKPDVA GLYHLVASGT TTWYDYAALV FEEARKAGIP LALNKLNAVP TTAYPTPARR PHNSRLNTEK FQQNFALVLP DWQVGVKRML NELFTTTAI
Length	299
Mol. Wt	32.694 kDa
pI	5.7 (calculated)
Extinction coefficient	47,900 - 48,275 (calc based on 10 Y, 6 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	1..295	PF04321 RmlD substrate binding domain		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=rfbD 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:16129980	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947117	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006764	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37760	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12411	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12411	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947117	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002272	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2310	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	Notes	Reference(s)
Protein	Ecoli K-12	50.046+/-0.387	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.107341491	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	2876	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	821	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	2267	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_000913:2109980..2110020 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:b2040 (EcoliWiki Page)	NCBI GEO profiles for rfbD
microarray	GenExpDB:b2040 (EcoliWiki Page)	Summary of data for rfbD 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 rfbD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12411	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2310	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2040
EcoGene	EcoGene:EG12411	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002272	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006764	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
Arabidopsis thaliana	AT4G00560 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000009891 (score: 1.000; bootstrap: 100%) ENSBTAP00000016399 (score: 0.975)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000025303 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050320-38 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050320-38 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231749 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000002680 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000325425 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000018374 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000009445 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1913667 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6K7R8 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000029903 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000004269 (score: 1.000; bootstrap: 100%) ENSRNOP00000044920 (score: 0.400)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000150935 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000032976 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RFBD	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Panther (EcoliWiki Page)	PTHR10491:SF0
Pfam (EcoliWiki Page)	PF04321 RmlD substrate binding domain
EcoCyc	EcoCyc:EG12411	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12411	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002272	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2310	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006764	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 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).

rfbD: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 rfbD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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