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Expression|

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Standard Name	ycgF
Gene Synonym(s)	ECK1150, b1163, JW1150^[1], JW1150
Product Desc.	predicted FAD-binding phosphodiesterase^[2]^[3] Putative cyclic-di-GMP phosphodiesterase, function unknown; cold shock gene, binds FAD^[4]
Product Synonyms(s)	predicted FAD-binding phosphodiesterase^[1], B1163^[2]^[1], YcgF^[2]^[1], Blrp^[2]^[1] , ECK1150, JW1150, b1163
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycgF^[2]
Regulation/Activity
Quick Links
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Notes

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The cold-inducibility of ycgF is dependent on the presence of the pnp gene. YcgF has an N-terminal blue light-responsive FAD-binding BLUF domain, and a C-terminal cyclic-di-GMP phosphodiesterase EAL domain.^[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	ycgF
Mnemonic	Systematic nomenclature
Synonyms	ECK1150, b1163, JW1150^[1], JW1150
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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	26.15 minutes	MG1655: 1214698..1213487 <gbrowseImage> name=NC_000913:1213487..1214698 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1215636..1214425 <gbrowseImage> name=NC_012967:1214425..1215636 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1102208..1103419 <gbrowseImage> name=NC_012759:1102208..1103419 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1217052..1215841 <gbrowseImage> name=NC_007779:1215841..1217052 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1254939..1253728 <gbrowseImage> name=NC_010473:1253728..1254939 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
ΔycgF (Keio:JW1150)	deletion	deletion	PMID:16738554	Shigen CGSC9069^[5]
ΔycgF752::kan			PMID:16738554	CGSC:104016
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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
JW1150	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTTACCACCCTTATTTATCG Primer 2:CCTTTTTTCTCTGGCCACGCTAT
3E11	Kohara Phage	Genobase	PMID:3038334
4D1	Kohara Phage	Genobase	PMID:3038334
zcf-117::Tn10	Linked marker	CAG18463 = CGSC7363^[5]	est. P1 cotransduction: 92% ^[6]
fadR13::Tn10	Linked marker	CAG18497 = CGSC7365^[5]	est. P1 cotransduction: 47% ^[6]
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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 (EcoliWiki Page)	GeneID:947592	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	YcgF
Synonyms	predicted FAD-binding phosphodiesterase^[1], B1163^[2]^[1], YcgF^[2]^[1], Blrp^[2]^[1] , ECK1150, JW1150, b1163
Product description	predicted FAD-binding phosphodiesterase^[2]^[3] Putative cyclic-di-GMP phosphodiesterase, function unknown; cold shock gene, binds FAD^[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
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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	aceE	PMID:15690043	Experiment(s):EBI-881743, EBI-889250
Protein	lpdA	PMID:15690043	Experiment(s):EBI-881743, EBI-889250
Protein	dnaB	PMID:16606699	Experiment(s):EBI-1139025
Protein	lon	PMID:16606699	Experiment(s):EBI-1139025
Protein	dnaE	PMID:16606699	Experiment(s):EBI-1139025
Protein	rtcB	PMID:16606699	Experiment(s):EBI-1139025
Protein	sucB	PMID:16606699	Experiment(s):EBI-1139025
Protein	rsuA	PMID:16606699	Experiment(s):EBI-1139025
Protein	aceF	PMID:15690043	Experiment(s):EBI-889250
Protein	groL	PMID:15690043	Experiment(s):EBI-889250
Protein	rplL	PMID:15690043	Experiment(s):EBI-889250
Protein	grcA	PMID:15690043	Experiment(s):EBI-889250
Protein	groS	PMID:19402753	LCMS(ID Probability):99.5
Protein	yfiD	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

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 MLTTLIYRSH IRDDEPVKKI EEMVSIANRR NMQSDVTGIL LFNGSHFFQL LEGPEEQVKM IYRAICQDPR HYNIVELLCD YAPARRFGKA GMELFDLRLH ERDDVLQAVF DKGTSKFQLT YDDRALQFFR TFVLATEQST YFEIPAEDSW LFIADGSDKE LDSCALSPTI NDHFAFHPIV DPLSRRIIAF EAIVQKNEDS PSAIAVGQRK DGEIYTADLK SKALAFTMAH ALELGDKMIS INLLPMTLVN EPDAVSFLLN EIKANALVPE QIIVEFTESE VISRFDEFAE AIKSLKAAGI SVAIDHFGAG FAGLLLLSRF QPDRIKISQE LITNVHKSGP RQAIIQAIIK CCTSLEIQVS AMGVATPEEW MWLESAGIEM FQGDLFAKAK LNGIPSIAWP EKK
Length	403
Mol. Wt	45.296 kDa
pI	4.9 (calculated)
Extinction coefficient	32,430 - 33,055 (calc based on 7 Y, 4 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	2..94	PF04940 Sensors of blue-light using FAD	PMID:19920124
Domain	164..389	PF00563 EAL 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=ycgF 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:16129126	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947592	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75990	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947592	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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 MG1655	11^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	41	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	13^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
ycgF
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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_000913:1214678..1214718 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:b1163 (EcoliWiki Page)	NCBI GEO profiles for ycgF
microarray	GenExpDB:b1163 (EcoliWiki Page)	Summary of data for ycgF 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 (1214598..1215043) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:F6^[7]
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Notes

Accessions Related to ycgF Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1163
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF00563 EAL domain
Pfam (EcoliWiki Page)	PF04940 Sensors of blue-light using FAD
Superfamily (EcoliWiki Page)	SUPERFAMILY:54975
Superfamily (EcoliWiki Page)	SUPERFAMILY:141868
PFAM (EcoliWiki Page)	PFAM:PF04940
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 ^1.8 ^1.9 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 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

ycgF: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 ycgF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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