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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	prfA
Gene Synonym(s)	ECK1199, b1211, JW1202, sueB, uar, ups
Product Desc.	peptide chain release factor RF1^[1]^[2] Peptide chain release factor 1, RF-1; translation termination factor recognizes UAG and UAA.^[3]
Product Synonyms(s)	peptide chain release factor RF-1^[4], B1211^[1]^[4], Uar^[1]^[4], SueB^[1]^[4], PrfA^[1]^[4] , ECK1199, JW1202, sueB, uar, b1211, ups?
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hemA^[1]
Regulation/Activity
Quick Links
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Notes

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Overexpression causes filamentous biofilm formation.^[3]

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	prfA
Mnemonic	Protein release factor
Synonyms	ECK1199, b1211, JW1202, sueB, uar, ups
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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	27.25 minutes	MG1655: 1264235..1265317 <gbrowseImage> name=NC_000913:1264235..1265317 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1265162..1266244 <gbrowseImage> name=NC_012967:1265162..1266244 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1152956..1154038 <gbrowseImage> name=NC_012759:1152956..1154038 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1266589..1267671 <gbrowseImage> name=NC_007779:1266589..1267671 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1304476..1305558 <gbrowseImage> name=NC_010473:1304476..1305558 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: Type	Phenotype: Description	Reference	Availability	Comments
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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
JW1202	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGCCTTCTATCGTTGCCAA Primer 2:CCTTCCTGCTCGGACAACGCCGC
4D10	Kohara Phage	Genobase	PMID:3038334
13H6	Kohara Phage	Genobase	PMID:3038334
fadR13::Tn10	Linked marker	CAG18497 = CGSC7365^[5]	est. P1 cotransduction: 31% ^[6]
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[5]	est. P1 cotransduction: 19% ^[6] Synonyms:zch-506::Tn10, zci-506::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:EG10761	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10761	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000752	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949002	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0754	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004066	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	PrfA
Synonyms	peptide chain release factor RF-1^[4], B1211^[1]^[4], Uar^[1]^[4], SueB^[1]^[4], PrfA^[1]^[4] , ECK1199, JW1202, sueB, uar, b1211, ups?
Product description	peptide chain release factor RF1^[1]^[2] Peptide chain release factor 1, RF-1; translation termination factor recognizes UAG and UAA.^[3]
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:0003747	translation release factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000352	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00093	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004373	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005139	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0648	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006415	translational termination	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00093	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006415	translational termination	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000352	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006415	translational termination	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004373	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006415	translational termination	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005139	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016149	translation release factor activity, codon specific	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00093	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016149	translation release factor activity, codon specific	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004373	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016149	translation release factor activity, codon specific	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005139	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	References	Evidence
Protein	nadE	PMID:16606699	Experiment(s):EBI-1139187
Protein	groL	PMID:16606699	Experiment(s):EBI-1139187
Protein	gabT	PMID:16606699	Experiment(s):EBI-1139187
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1139187
Protein	rplD	PMID:16606699	Experiment(s):EBI-1139187
Protein	waaU	PMID:15690043	Experiment(s):EBI-889124
Protein	yghE	PMID:15690043	Experiment(s):EBI-889124
Protein	yhgA	PMID:15690043	Experiment(s):EBI-889124
Protein	ycjY	PMID:15690043	Experiment(s):EBI-889124
Protein	basS	PMID:15690043	Experiment(s):EBI-889124
Protein	frdC	PMID:15690043	Experiment(s):EBI-889124
Protein	hyfR	PMID:15690043	Experiment(s):EBI-889124
Protein	pheA	PMID:15690043	Experiment(s):EBI-889124
Protein	leuS	PMID:19402753	MALDI(Z-score):27.752698
Protein	ycjY	PMID:19402753	LCMS(ID Probability):99.0
Protein	basS	PMID:19402753	LCMS(ID Probability):99.0
Protein	hyfR	PMID:19402753	LCMS(ID Probability):99.0
Protein	pheA	PMID:19402753	LCMS(ID Probability):99.0
Protein	yhgA	PMID:19402753	LCMS(ID Probability):99.0
Protein	frdC	PMID:19402753	LCMS(ID Probability):99.0
Protein	waaU	PMID:19402753	LCMS(ID Probability):99.0
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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 MKPSIVAKLE ALHERHEEVQ ALLGDAQTIA DQERFRALSR EYAQLSDVSR CFTDWQQVQE DIETAQMMLD DPEMREMAQD ELREAKEKSE QLEQQLQVLL LPKDPDDERN AFLEVRAGTG GDEAALFAGD LFRMYSRYAE ARRWRVEIMS ASEGEHGGYK EIIAKISGDG VYGRLKFESG GHRVQRVPAT ESQGRIHTSA CTVAVMPELP DAELPDINPA DLRIDTFRSS GAGGQHVNTT DSAIRITHLP TGIVVECQDE RSQHKNKAKA LSVLGARIHA AEMAKRQQAE ASTRRNLLGS GDRSDRNRTY NFPQGRVTDH RINLTLYRLD EVMEGKLDML IEPIIQEHQA DQLAALSEQE
Length	360
Mol. Wt	40.517 kDa
pI	5.1 (calculated)
Extinction coefficient	21,430 - 21,805 (calc based on 7 Y, 2 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	References
Domain	63..178	PF03462 PCRF domain	PMID:19920124
Domain	208..321	PF00472 RF-1 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=prfA taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16129174	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949002	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004066	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7I0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10761	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10761	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949002	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000752	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0754	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	E. coli K-12 MC4100	2.12E+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	Ecoli K-12	25.663+/-0.315	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.049907579	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	1059	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	210	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	440	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)
hemA
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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_000913:1264215..1264255 source=MG1655 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

</protect>

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:b1211 (EcoliWiki Page)	NCBI GEO profiles for prfA
microarray	GenExpDB:b1211 (EcoliWiki Page)	Summary of data for prfA 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 prfA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10761	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0754	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1211
EcoGene	EcoGene:EG10761	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000752	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004066	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	ENSANGP00000013776 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G47020 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000012219 (score: 1.000; bootstrap: 100%) ENSBTAP00000016261 (score: 0.089)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00039181 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00020993 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000000769 (score: 1.000; bootstrap: 100%) ENSCAFP00000007157 (score: 0.139)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050220-8 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050220-8 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0185395 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0032486 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA19071-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000022101 (score: 1.000; bootstrap: 100%) ENSGALP00000027347 (score: 0.091)	From Inparanoid:20070104
Homo sapiens	ENSP00000229760 (score: 1.000; bootstrap: 100%) ENSP00000318184 (score: 0.934) ENSP00000326351 (score: 0.113)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000025081 (score: 1.000; bootstrap: 100%) ENSMMUP00000018725 (score: 0.444) ENSMMUP00000026571 (score: 0.294) ENSMMUP00000023630 (score: 0.137)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000010552 (score: 1.000; bootstrap: 100%) ENSMODP00000018475 (score: 0.110)	From Inparanoid:20070104
Mus musculus	MGI:1918830 (score: 1.000; bootstrap: 100%) MGI:2384815 (score: 0.140)	From Inparanoid:20070104
Oryza gramene	Q6I547 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000031947 (score: 1.000; bootstrap: 100%) ENSPTRP00000009897 (score: 0.111)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000025398 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGL143C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC2F77 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000129372 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000148055 (score: 0.083)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00014302001 (score: 1.000; bootstrap: 100%) GSTENP00031834001 (score: 0.084)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000013952 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PRFA	From SHIGELLACYC
E. coli O157	PRFA	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)	PF03462 PCRF domain
Panther (EcoliWiki Page)	PTHR11075:SF9
Superfamily (EcoliWiki Page)	SUPERFAMILY:75620
Pfam (EcoliWiki Page)	PF00472 RF-1 domain
EcoCyc	EcoCyc:EG10761	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10761	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000752	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0754	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004066	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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^2.0 ^2.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^4.0 ^4.1 ^4.2 ^4.3 ^4.4 ^4.5 ^4.6 ^4.7 ^4.8 ^4.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^5.0 ^5.1 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).

prfA: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 prfA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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