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Standard Name	ykfC
Gene Synonym(s)	ECK0260, b0258, JW5813^[1], JW5813
Product Desc.	hypothetical protein^[2]; CP4-6 prophage; conserved protein^[3]
Product Synonyms(s)	CP4-6 prophage; conserved protein^[1], B0258^[2]^[1], YkfC^[2]^[1] , ECK0260, JW5813, b0258
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ykfC^[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	ykfC
Mnemonic
Synonyms	ECK0260, b0258, JW5813^[1], JW5813
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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	5.86 minutes	MG1655: 272071..273216 <gbrowseImage> name=NC_000913:272071..273216 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 272071..273216 <gbrowseImage> name=NC_007779:272071..273216 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 246175..247282 <gbrowseImage> name=NC_010473:246175..247282 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
ykfC(del) (Keio:JW5813)	deletion	deletion			PMID:16738554	Shigen
ykfC::Tn5KAN-I-SceI (FB20104)	Insertion at nt 517 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20104	contains pKD46
ykfC::Tn5KAN-I-SceI (FB20105)	Insertion at nt 517 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20105	does not contain pKD46
ykfC(del)::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
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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
JW5813	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATAATCAGCGAAATGCAACG Primer 2:CCGCCGAGAAGAATTTCCCCGCT
8G4	Kohara Phage	Genobase	PMID:3038334
5A5	Kohara Phage	Genobase	PMID:3038334
3C7	Kohara Phage	Genobase	PMID:3038334
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[4]	est. P1 cotransduction: 65% ^[5]
lacI3042::Tn10	Linked marker	CAG18439 = CGSC7334^[4]	est. P1 cotransduction: % ^[5] Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).
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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:G6133	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13341	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002753	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944940	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3125	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000885	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	YkfC
Synonyms	CP4-6 prophage; conserved protein^[1], B0258^[2]^[1], YkfC^[2]^[1] , ECK0260, JW5813, b0258
Product description	hypothetical protein^[2]; CP4-6 prophage; conserved protein^[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:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000477	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003964	RNA-directed DNA polymerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000477	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006278	RNA-dependent DNA replication	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000477	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003674	molecular function	N/A	ND: No biological Data available		F		Missing: reference
	GO:0005575	cellular component	N/A	ND: No biological Data available		C		Missing: reference
	GO:0008150	biological process	N/A	ND: No biological Data available		P		Missing: reference
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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
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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 MQRKLATWAA TDPSLRIQRL LRLITQPEWL AEAARITLSS KGAHTPGVDG VNKTMLQARL AVELQILRDE LLSGHYQPLP ARRVYIPKSN GKLRPLGIPA LRDRIVQRAM LMAMEPIWES DFHTLSYGFR PERSVHHAIR TVKLQLTDCG ETRGRWVIEG DLSSYFDTVH HRLLMKAVRR RISDARFMTL LWKTIKAGHI DVGLFRAASE GVPQGGVISP LLSNIMLNEF DQYLHERYLS GKARKDRWYW NNSIQRGRST AVRENWQWKP AVAYCRYADD FVLIVKGTKA QVEAIREECR GVLEGSLKLR LNMDKTKIPH VNDGFIFLGH RLIRKRSRYG EMRVVSTIPQ EKARNFAASL TALLWKVRIS GEILLG
Length	376
Mol. Wt	43.166 kDa
pI	10.7 (calculated)
Extinction coefficient	69,900 - 70,275 (calc based on 10 Y, 10 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	86..332	PF00078 Reverse transcriptase (RNA-dependent DNA polymerase)		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=ykfC 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
ASAP	ASAP:ABE-0000885	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944940	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q47688	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6133	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13341	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944940	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002753	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3125	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)
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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)
ykfC
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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_000913:272051..272091 source=MG1655 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:b0258 (EcoliWiki Page)	NCBI GEO profiles for ykfC
microarray	GenExpDB:b0258 (EcoliWiki Page)	Summary of data for ykfC 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 ykfC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6133	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3125	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0258
EcoGene	EcoGene:EG13341	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002753	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000885	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	AT1G30010 (score: 1.000; bootstrap: 89%) AT5G46920 (score: 0.452)	From Inparanoid:20070104
Oryza gramene	Q8S7E2 (score: 1.000; bootstrap: 83%) Q7XC02 (score: 1.000; bootstrap: 81%)	From Inparanoid:20070104
Saccharomyces cerevisiae	Q0055 (score: 1.000; bootstrap: 100%) Q0050 (score: 0.347)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPMIT6 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	S3181	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
Pfam (EcoliWiki Page)	PF00078 Reverse transcriptase (RNA-dependent DNA polymerase)
Panther (EcoliWiki Page)	PTHR19446:SF105
EcoCyc	EcoCyc:G6133	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13341	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002753	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3125	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000885	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 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 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 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

ykfC: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 ykfC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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