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Standard Name	yfjK
Gene Synonym(s)	ECK2623, b2627, JW2608^[1], JW2608
Product Desc.	CP4-57 prophage; conserved protein^[2]^[3] Function unknown, CP4-57 putative defective prophage^[4]
Product Synonyms(s)	CP4-57 prophage; conserved protein^[1], B2627^[2]^[1], YfjK^[2]^[1] , ECK2623, JW2608, b2627
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfjK^[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	yfjK
Mnemonic	Systematic nomenclature
Synonyms	ECK2623, b2627, JW2608^[1], JW2608
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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	59.47 minutes	MG1655: 2761562..2759373 <gbrowseImage> name=NC_000913:2759373..2761562 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2645185..2647374 <gbrowseImage> name=NC_012759:2645185..2647374 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2762196..2760007 <gbrowseImage> name=NC_007779:2760007..2762196 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2853327..2851138 <gbrowseImage> name=NC_010473:2851138..2853327 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
ΔyfjK (Keio:JW2608)	deletion	deletion	PMID:16738554	Shigen CGSC10062^[5]
ΔyfjK782::kan			PMID:16738554	CGSC:104828
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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
JW2608	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACAGAGATCTATGAACAGGC Primer 2:CCATGTCGTCTAATACCGAGCGC
24G1	Kohara Phage	Genobase	PMID:3038334
4C9	Kohara Phage	Genobase	PMID:3038334
pheA18::Tn10	Linked marker	CAG12158 = CGSC7421^[5]	est. P1 cotransduction: 44% ^[6]
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::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:G7362	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13197	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003930	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947111	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2989	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008648	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	YfjK
Synonyms	CP4-57 prophage; conserved protein^[1], B2627^[2]^[1], YfjK^[2]^[1] , ECK2623, JW2608, b2627
Product description	CP4-57 prophage; conserved protein^[2]^[3] Function unknown, CP4-57 putative defective prophage^[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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001650	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011545	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004386	helicase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001650	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001650	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011545	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008026	ATP-dependent helicase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011545	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	dnaK	PMID:15690043	Experiment(s):EBI-893852
Protein	gapA	PMID:15690043	Experiment(s):EBI-893852
Protein	groL	PMID:15690043	Experiment(s):EBI-893852
Protein	rplC	PMID:15690043	Experiment(s):EBI-893852
Protein	rplL	PMID:15690043	Experiment(s):EBI-893852
Protein	rplW	PMID:15690043	Experiment(s):EBI-893852
Protein	tufA	PMID:15690043	Experiment(s):EBI-893852
Protein	ppk	PMID:16606699	Experiment(s):EBI-1143531
Protein	aceE	PMID:16606699	Experiment(s):EBI-1143531
Protein	prs	PMID:16606699	Experiment(s):EBI-1143531
Protein	narZ	PMID:16606699	Experiment(s):EBI-1143531
Protein	rrmA	PMID:16606699	Experiment(s):EBI-1143531
Protein	hchA	PMID:16606699	Experiment(s):EBI-1143531
Protein	dnaE	PMID:16606699	Experiment(s):EBI-1143531
Protein	alaS	PMID:16606699	Experiment(s):EBI-1143531
Protein	lacZ	PMID:16606699	Experiment(s):EBI-1143531
Protein	ydbH	PMID:16606699	Experiment(s):EBI-1143531
Protein	pheT	PMID:16606699	Experiment(s):EBI-1143531
Protein	ybhK	PMID:16606699	Experiment(s):EBI-1143531
Protein	mrcA	PMID:16606699	Experiment(s):EBI-1143531
Protein	rplW	PMID:19402753	LCMS(ID Probability):99.6
Protein	groS	PMID:19402753	LCMS(ID Probability):99.6
Protein	gapA	PMID:19402753	LCMS(ID Probability):99.6
Protein	groL	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplL	PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

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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 MTEIYEQAKH SLQGEDFSSF NYLFAVNKLL SNPVSYDLGR DLIVRALDSR ERFSEHTTIL KNMVRKSGLF PYLKKEFTSL TPDDLRVLEL YRTPFSDGYV FHSMQFHIFD LLKSGQNVVL SAPTSMGKSA IVDSLLGMGT LKRLVLVVPT VALADETRRR LQERFGDRYQ IIHHSSQVCH SDQAVYVLTQ ERVNERDDIV DIDLFVIDEF YKLAFRQLKS GDIDHQDERV IELNIALSKL LKVSRQFYLT GPFVNSIRGL EKLGYPHTFV STDFNTVALD VKTFGIKAND DKAKLKALGE IAHACVDATI IYCKSPTVAG LVARELIRLG HGTPTENPHV DWVSEEFDAD WDYTVALRNG IGLHFGALPR ALQQYTADQF NAGKLRFLLC TSTIIEGVNT IAKNVVIYDN RDGTRSIDKF THGNIKGRAG RMGVHFVGKI FCLEEIPEDN LNQEVDIPLG IQGIDTPINL LASVQPDHLS EFSQDRFDEV FINDRVSIDL VKKHSYFRVE QFEMLQSMFE MMDDNEFSSL VFHWTPATNF LKTFAKIIAR LVPHTFSRNG VPVKPTDVMI AKLAGYLSAE SYSEYLKNQI DYARQWISEG EKRTLSIALN NDLKLITNTF GYTLPKVLSL MEDVVKHHAV KRGIRSKVDY THVKLAFESF HLPPGVNALE EIGIPIQTLH RLVDLLEFSD EADVDELSQY LRDTQDIWSR SIGYVDQMFI RRALGIRRH
Length	729
Mol. Wt	83.063 kDa
pI	6.4 (calculated)
Extinction coefficient	63,260 - 63,885 (calc based on 24 Y, 5 W, and 5 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	102..234	PF00270 DEAD/DEAH box helicase	PMID:19920124
Domain	355..433	PF00271 Helicase conserved C-terminal 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=yfjK 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:16130545	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947111	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008648	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P52126	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7362	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13197	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947111	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003930	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2989	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	Ecoli K-12	0.616+/-0.024	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.010050251	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	40	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	64	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	30	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)
yfjK
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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_000913:2761542..2761582 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:b2627 (EcoliWiki Page)	NCBI GEO profiles for yfjK
microarray	GenExpDB:b2627 (EcoliWiki Page)	Summary of data for yfjK 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 yfjK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7362	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2989	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2627
EcoGene	EcoGene:EG13197	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003930	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008648	Escherichia coli str. K-12 substr. MG1655
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Notes

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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
Caenorhabditis briggsae	WBGene00035572 (score: 1.000; bootstrap: 100%) WBGene00030750 (score: 0.054)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00020964 (score: 1.000; bootstrap: 100%) WBGene00021905 (score: 0.056)	From Inparanoid:20070104
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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)	PF00271 Helicase conserved C-terminal domain
Pfam (EcoliWiki Page)	PF00270 DEAD/DEAH box helicase
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Panther (EcoliWiki Page)	PTHR11752:SF41
PFAM (EcoliWiki Page)	PFAM:PF00271
EcoCyc	EcoCyc:G7362	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13197	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003930	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2989	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008648	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 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).

yfjK: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 yfjK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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