{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	argF
Gene Synonym(s)	ECK0274, b0273, JW0266, Arg5^[1], Arg5, argD
Product Desc.	ArgF^[2]^[3]; Component of ornithine carbamoyltransferase^[2]^[3] Ornithine carbamoyltransferase; ornithine transcarbamylase; OTCase; CP4-6 putative prophage remnant^[4]
Product Synonyms(s)	CP4-6 prophage; ornithine carbamoyltransferase 2, chain F^[1], B0273^[2]^[1], ArgF^[2]^[1] , Arg5, argD, ECK0274, JW0266, b0273
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): argF^[2], OP00007
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

argI and argF have same enzyme activity. ArgF and ArgI form both homotrimers and heterotrimers (Legrain, 1972).^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	argF
Mnemonic	Arginine
Synonyms	ECK0274, b0273, JW0266, Arg5^[1], Arg5, argD
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	6.22 minutes	MG1655: 289529..288525 <gbrowseImage> name=NC_000913:288525..289529 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 289529..288525 <gbrowseImage> name=NC_007779:288525..289529 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 265079..264075 <gbrowseImage> name=NC_010473:264075..265079 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	288528	Edman degradation	PMID:3968036
edit table

Notes

Alleles and Phenotypes

[back to top]

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Reference	Availability
ΔargF (Keio:JW0266)	deletion	deletion	Auxotrophies	PMID:16738554	Shigen CGSC8482^[5]
argF45			Auxotrophies		CGSC:5160
argF58			Auxotrophies	PMID:4873401	CGSC:5173
argF80			Auxotrophies		CGSC:5196
ΔargF788::kan	deletion	deletion	Auxotrophies	PMID:16738554	CGSC:100046
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW0266	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCCGATTTATACAAAAAACA Primer 2:CCCTCCCCAAGCGTTGCCATCAT
3C7	Kohara Phage	Genobase	PMID:3038334
21C10	Kohara Phage	Genobase	PMID:3038334
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[5]	est. P1 cotransduction: 33% ^[6]
lacI3042::Tn10	Linked marker	CAG18439 = CGSC7334^[5]	est. P1 cotransduction: % ^[6] Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10067	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10067	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944844	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000063	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0065	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000939	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	ArgF
Synonyms	CP4-6 prophage; ornithine carbamoyltransferase 2, chain F^[1], B0273^[2]^[1], ArgF^[2]^[1] , Arg5, argD, ECK0274, JW0266, b0273
Product description	ArgF^[2]^[3]; Component of ornithine carbamoyltransferase^[2]^[3] Ornithine carbamoyltransferase; ornithine transcarbamylase; OTCase; CP4-6 putative prophage remnant^[4]
EC number (for enzymes)	2.1.3.3^[1]
edit table

Notes

Function

[back to top]

<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:0004585	ornithine carbamoyltransferase activity	PMID:4873401	IGI: Inferred from Genetic Interaction		F	Table 4 shows specific activity of ornithine transcarbamylase in argF.	Missing: with/from
	GO:0004585	ornithine carbamoyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01109	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004585	ornithine carbamoyltransferase activity	PMID:4558857	IGI: Inferred from Genetic Interaction		F	Activity of enzyme presented in Fig. 3. Table 1 displays quantification of enzyme protocol.	Missing: with/from
	GO:0004585	ornithine carbamoyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002292	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004585	ornithine carbamoyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.1.3.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01109	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:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002292	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006130	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006131	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006132	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006526	arginine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0055	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008652	cellular amino acid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0028	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009348	ornithine carbamoyltransferase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002292	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016597	amino acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006130	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016597	amino acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006131	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
edit table

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 ornithine carbamoyltransferase	argF is able to produce a functional ornithine carbamoyltransferase	PMID:4558857
Protein	yegQ		PMID:16606699	Experiment(s):EBI-1136063
Protein	purR		PMID:16606699	Experiment(s):EBI-1136063
Protein	ahpF		PMID:16606699	Experiment(s):EBI-1136063
Protein	yhhI		PMID:16606699	Experiment(s):EBI-1136063
Protein	rplQ		PMID:16606699	Experiment(s):EBI-1136063
Protein	yfcU		PMID:16606699	Experiment(s):EBI-1136063
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MSDLYKKHFL KLLDFTPAQF TSLLTLAAQL KADKKNGKEV QKLTGKNIAL IFEKDSTRTR CSFEVAAFDQ GARVTYLGPS GSQIGHKESI KDTARVLGRM YDGIQYRGHG QEVVETLAQY AGVPVWNGLT NEFHPTQLLA DLMTMQEHLP GKAFNEMTLV YAGDARNNMG NSMLEAAALT GLDLRLLAPK ACWPEESLVA ECSALAEKHG GKITLTEDVA AGVKGADFIY TDVWVSMGEA KEKWAERIAL LRGYQVNAQM MALTDNPNVK FLHCLPAFHD DQTTLGKQMA KEFDLHGGME VTDEVFESAA SIVFDQAENR MHTIKAVMMA TLGE
Length	334
Mol. Wt	36.827 kDa
pI	5.9 (calculated)
Extinction coefficient	33,920 - 34,420 (calc based on 8 Y, 4 W, and 4 C residues)
edit table

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
Initiator Methionine	1	Removed	UniProt:P06960
Domain	155..331	PF00185 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain		PMID:19920124
Domain	7..148	PF02729 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain		PMID:19920124
edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=argF taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16128258	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944844	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000939	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P06960	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10067	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10067	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944844	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000063	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0065	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	209	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	2536	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	147	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
argF
edit table

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

[back to top]

<protect><gbrowseImage> name=NC_000913:289509..289549 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

</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

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0273 (EcoliWiki Page)	NCBI GEO profiles for argF
microarray	GenExpDB:b0273 (EcoliWiki Page)	Summary of data for argF from multiple microarray studies
edit table

Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to argF Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10067	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0065	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0273
EcoGene	EcoGene:EG10067	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000063	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000939	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Apis mellifera	ENSAPMP00000022451 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G75330 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000001947 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000020690 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000029680 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000039007 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000017738 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000026385 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:97448 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6YVI0 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000037399 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000004686 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YJL088W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC4G90 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000176157 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000172677 (score: 0.621)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00025982001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000018777 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00185 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
Pfam (EcoliWiki Page)	PF02729 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:53671
PFAM (EcoliWiki Page)	PFAM:PF02729
EcoCyc	EcoCyc:EG10067	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10067	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000063	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0065	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000939	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 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 ^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).

argF:On One Page

Quickview

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 argF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search