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Gene |

Product(s) |

Expression|

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Standard Name	rfaH
Gene Synonym(s)	ECK3834, b3842, JW3818, sfrB, hlyT^[1], hlyT
Product Desc.	DNA-binding transcriptional antiterminator^[2]; Transcriptional regulatory protein RfaH^[3] Transcription antitermination factor, LPS biosynthesis genes; negatively controls expression and surface presentation of Ag43 (Flu), reducing adhesion and biofilm; also regulates F-factor sex pilus and hemolysin genes^[4]
Product Synonyms(s)	DNA-binding transcriptional antiterminator^[1], B3842^[2]^[1], SfrB^[2]^[1], HlyT^[2]^[1], RfaH^[2]^[1] , ECK3834, hlyT, JW3818, sfrB, b3842
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rfaH^[2]
Regulation/Activity
Quick Links
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Notes

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RfaH is recruited by JUMPstart/ops sequence elements.^[4]

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	rfaH
Mnemonic	Rough
Synonyms	ECK3834, b3842, JW3818, sfrB, hlyT^[1], hlyT
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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	86.69 minutes	MG1655: 4022844..4022356 <gbrowseImage> name=NC_000913:4022356..4022844 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4003292..4002804 <gbrowseImage> name=NC_012967:4002804..4003292 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3912025..3912513 <gbrowseImage> name=NC_012759:3912025..3912513 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3611860..3612348 <gbrowseImage> name=NC_007779:3611860..3612348 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4121764..4121276 <gbrowseImage> name=NC_010473:4121276..4121764 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
ΔrfaH (Keio:JW3818)	deletion	deletion	PMID:16738554	Shigen CGSC10762^[5]
rfaH565				CGSC:9024
rfaH564::Tn5				CGSC:64598
ΔrfaH783::kan			PMID:16738554	CGSC:102650
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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
JW3818	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAATCCTGGTATTTACTGTA Primer 2:CCGAGTTTGCGGAACTCGGTATT
16G1	Kohara Phage	Genobase	PMID:3038334
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[5]	est. P1 cotransduction: 62% ^[6] Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
fad-751::Tn10	Linked marker	CAG18496 = CGSC7465^[5]	est. P1 cotransduction: 85% ^[6] Synonyms:fadAB101::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:EG10839	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10839	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000830	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948327	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0832	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012553	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	RfaH
Synonyms	DNA-binding transcriptional antiterminator^[1], B3842^[2]^[1], SfrB^[2]^[1], HlyT^[2]^[1], RfaH^[2]^[1] , ECK3834, hlyT, JW3818, sfrB, b3842
Product description	DNA-binding transcriptional antiterminator^[2]; Transcriptional regulatory protein RfaH^[3] Transcription antitermination factor, LPS biosynthesis genes; negatively controls expression and surface presentation of Ag43 (Flu), reducing adhesion and biofilm; also regulates F-factor sex pilus and hemolysin genes^[4]
EC number (for enzymes)
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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:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003711	transcription elongation regulator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006645	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003711	transcription elongation regulator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010215	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010215	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:0032968	positive regulation of RNA elongation from RNA polymerase II promoter	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006645	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	References	Evidence
Protein	dnaJ	PMID:16606699	Experiment(s):EBI-1146766
Protein	phoB	PMID:16606699	Experiment(s):EBI-1146766
Protein	slyD	PMID:16606699	Experiment(s):EBI-1146766
Protein	mobA	PMID:16606699	Experiment(s):EBI-1146766
Protein	nadE	PMID:16606699	Experiment(s):EBI-1146766
Protein	fre	PMID:16606699	Experiment(s):EBI-1146766
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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 MQSWYLLYCK RGQLQRAQEH LERQAVNCLA PMITLEKIVR GKRTAVSEPL FPNYLFVEFD PEVIHTTTIN ATRGVSHFVR FGASPAIVPS AVIHQLSVYK PKDIVDPATP YPGDKVIITE GAFEGFQAIF TEPDGEARSM LLLNLINKEI KHSVKNTEFR KL
Length	162
Mol. Wt	18.34 kDa
pI	8.6 (calculated)
Extinction coefficient	12,950 - 13,200 (calc based on 5 Y, 1 W, and 2 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	2..91	PF02357 Transcription termination factor nusG		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=rfaH 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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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
NCBI (Protein) (EcoliWiki Page)	GI:16131688	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948327	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012553	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFW0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10839	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10839	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948327	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000830	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0832	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	596	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	193	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	205	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)
rfaH
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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_000913:4022824..4022864 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:b3842 (EcoliWiki Page)	NCBI GEO profiles for rfaH
microarray	GenExpDB:b3842 (EcoliWiki Page)	Summary of data for rfaH 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 (4022311..4022616) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:E7^[7]
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Notes

Accessions Related to rfaH Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10839	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0832	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3842
EcoGene	EcoGene:EG10839	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000830	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012553	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	RFAH	From SHIGELLACYC
E. coli O157	RFAH	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF02357 Transcription termination factor nusG
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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 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 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

rfaH: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 rfaH Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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