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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	rfaE
Gene Synonym(s)	ECK3042, b3052, JW3024, hldE, waaE, gmhC, yqiF^[1], yqiF
Product Desc.	fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase^[2]^[3]; Component of fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase^[3] Heptose 7-P kinase/heptose 1-P adenyltransferase; LPS core prescursor synthesis: bifunctional enzyme presumably involved in both D-glycero-D-manno-heptose-1-phosphate and ADP-D-glycero-D-manno-heptose synthesis^[4]
Product Synonyms(s)	fused heptose 7-phosphate kinase^[1], heptose 1-phosphate adenyltransferase^[1], B3052^[2]^[1], HldE^[2]^[1], YqiF^[2]^[1], RfaE^[2]^[1], GmhC^[2]^[1], WaaE^[2]^[1] , ECK3042, gmhC, hldE, JW3024, waaE, yqiF, b3052
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rfaE^[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	rfaE
Mnemonic	Rough
Synonyms	ECK3042, b3052, JW3024, hldE, waaE, gmhC, yqiF^[1], yqiF
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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	68.83 minutes	MG1655: 3194775..3193342 <gbrowseImage> name=NC_000913:3193342..3194775 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3129587..3128154 <gbrowseImage> name=NC_012967:3128154..3129587 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3080490..3081923 <gbrowseImage> name=NC_012759:3080490..3081923 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3195409..3193976 <gbrowseImage> name=NC_007779:3193976..3195409 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3292520..3291087 <gbrowseImage> name=NC_010473:3291087..3292520 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)	Phenotype: Description	Reference	Availability	Comments
ΔrfaE (Keio:JW3024)	deletion	deletion		PMID:16738554	Shigen CGSC10310^[5]
hldEE198D		E198D	Loss of activity			seeded from UniProt:P76658
hldED264E		D264E	Loss of activity			seeded from UniProt:P76658
hldED264N		D264N	Loss of activity			seeded from UniProt:P76658
hldEN195D		N195D	Loss of activity			seeded from UniProt:P76658
ΔrfaE745::kan				PMID:16738554	CGSC:102644
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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
JW3024	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAGTAACGCTGCCAGAGTT Primer 2:CCGCCTTTTTTATCCTGTTGGAT
9F9	Kohara Phage	Genobase	PMID:3038334
tolC210::Tn10	Linked marker	CAG12184 = CGSC7437^[5]	est. P1 cotransduction: 59% ^[6]
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 44% ^[6] Synonyms:zgh-3075::Tn10, zgj-3075::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:G7590	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13416	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004146	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947548	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3192	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010015	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	RfaE
Synonyms	fused heptose 7-phosphate kinase^[1], heptose 1-phosphate adenyltransferase^[1], B3052^[2]^[1], HldE^[2]^[1], YqiF^[2]^[1], RfaE^[2]^[1], GmhC^[2]^[1], WaaE^[2]^[1] , ECK3042, gmhC, hldE, JW3024, waaE, yqiF, b3052
Product description	fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase^[2]^[3]; Component of fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase^[3] Heptose 7-P kinase/heptose 1-P adenyltransferase; LPS core prescursor synthesis: bifunctional enzyme presumably involved in both D-glycero-D-manno-heptose-1-phosphate and ADP-D-glycero-D-manno-heptose synthesis^[4]
EC number (for enzymes)	2.7.1.-^[1] 2.7.7.-^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0016052	carbohydrate catabolic process				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004821	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0511	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01603	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01603	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011913	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011914	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0119	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009058	biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004820	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009058	biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004821	P	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:0016301	kinase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0418	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016773	phosphotransferase activity, alcohol group as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011913	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016773	phosphotransferase activity, alcohol group as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011914	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01603	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004820	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011913	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011914	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0548	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019200	carbohydrate kinase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01603	F	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 fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase	could be indirect
Protein	rplU		PMID:19402753	LCMS(ID Probability):99.6
Protein	secA		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplS		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplJ		PMID:19402753	LCMS(ID Probability):99.5
Protein	rpsM		PMID:19402753	LCMS(ID Probability):99.6
Protein	yniA		PMID:19402753	MALDI(Z-score):36.126628
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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 MKVTLPEFER AGVMVVGDVM LDRYWYGPTS RISPEAPVPV VKVNTIEERP GGAANVAMNI ASLGANARLV GLTGIDDAAR ALSKSLADVN VKCDFVSVPT HPTITKLRVL SRNQQLIRLD FEEGFEGVDP QPLHERINQA LSSIGALVLS DYAKGALASV QQMIQLARKA GVPVLIDPKG TDFERYRGAT LLTPNLSEFE AVVGKCKTEE EIVERGMKLI ADYELSALLV TRSEQGMSLL QPGKAPLHMP TQAQEVYDVT GAGDTVIGVL AATLAAGNSL EEACFFANAA AGVVVGKLGT STVSPIELEN AVRGRADTGF GVMTEEELKL AVAAARKRGE KVVMTNGVFD ILHAGHVSYL ANARKLGDRL IVAVNSDAST KRLKGDSRPV NPLEQRMIVL GALEAVDWVV SFEEDTPQRL IAGILPDLLV KGGDYKPEEI AGSKEVWANG GEVLVLNFED GCSTTNIIKK IQQDKKG
Length	477
Mol. Wt	51.05 kDa
pI	5.2 (calculated)
Extinction coefficient	28,420 - 28,920 (calc based on 8 Y, 3 W, and 4 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	References
Domain	10..307	PF00294 pfkB family carbohydrate kinase	PMID:19920124
Domain	344..470	PF01467 Cytidylyltransferase	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=rfaE 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:16130948	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947548	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010015	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76658	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7590	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13416	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947548	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004146	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3192	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	2803	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	646	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	1508	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)
rfaE
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Figure courtesy of RegulonDB

</protect>

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_000913:3194755..3194795 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b3052 (EcoliWiki Page)	NCBI GEO profiles for rfaE
microarray	GenExpDB:b3052 (EcoliWiki Page)	Summary of data for rfaE 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 rfaE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7590	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3192	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3052
EcoGene	EcoGene:EG13416	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004146	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010015	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
Shigella flexneri	S3298	From SHIGELLACYC
E. coli O157	Z4405	From ECOO157CYC
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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)	PF00294 pfkB family carbohydrate kinase
Pfam (EcoliWiki Page)	PF01467 Cytidylyltransferase
Superfamily (EcoliWiki Page)	SUPERFAMILY:52374
Superfamily (EcoliWiki Page)	SUPERFAMILY:53613
Panther (EcoliWiki Page)	PTHR10584:SF96
EcoCyc	EcoCyc:G7590	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13416	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004146	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3192	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010015	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 ^1.13 ^1.14 ^1.15 ^1.16 ^1.17 ^1.18 ^1.19 ^1.20 ^1.21 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 ^2.13 ^2.14 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).

rfaE: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 rfaE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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