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Gene |

Product(s) |

Expression|

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Standard Name	galF
Gene Synonym(s)	ECK2036, b2042, JW2027, wcaN, yefG^[1]^[2]
Product Desc.	predicted subunit with GalU^[2]^[3]; Component of UTP-glucose-1-phosphate uridylyltransferase^[2]^[3] Putative regulatory subunit for GalU^[4]
Product Synonyms(s)	predicted subunit with GalU^[1], B2042^[2]^[1], YefG^[2]^[1], WcaN^[2]^[1], GalF^[2]^[1] , ECK2036, JW2027, wcaN, b2042
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
Regulation/Activity
Quick Links
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Notes

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Not required for colanic acid synthesis. Does not have UDP-glucose pyrophosphorylase actvitiy. Homologous to GalU.^[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	galF
Mnemonic	Galactose
Synonyms	ECK2036, b2042, JW2027, wcaN, yefG^[1]^[2]
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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	45.51 minutes, 45.51 minutes	MG1655: 2112351..2111458 <gbrowseImage> name=NC_000913:2111458..2112351 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2047558..2046665 <gbrowseImage> name=NC_012967:2046665..2047558 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2003941..2004834 <gbrowseImage> name=NC_012759:2003941..2004834 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2116464..2115571 <gbrowseImage> name=NC_007779:2115571..2116464 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2203359..2202466 <gbrowseImage> name=NC_010473:2202466..2203359 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	Comments
ΔgalF (Keio:JW2027)	deletion	deletion	PMID:16738554	Shigen CGSC9664^[5]
galF::Tn5KAN-2 (FB20593)	Insertion at nt 520 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20593	does not contain pKD46
galF::Tn5KAN-2 (FB20594)	Insertion at nt 520 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20594	contains pKD46
ΔgalF731::kan			PMID:16738554	CGSC:101076
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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
JW2027	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACGAATTTAAAAGCAGTTAT Primer 2:CCTTCGCTTAACAGCTTCTCAAT
21H10	Kohara Phage	Genobase	PMID:3038334
1G1	Kohara Phage	Genobase	PMID:3038334
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 34% ^[6] Synonyms:zee-3129::Tn10
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: 3% ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::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:G7093	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13578	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003679	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946560	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3348	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006771	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	GalF
Synonyms	predicted subunit with GalU^[1], B2042^[2]^[1], YefG^[2]^[1], WcaN^[2]^[1], GalF^[2]^[1] , ECK2036, JW2027, wcaN, b2042
Product description	predicted subunit with GalU^[2]^[3]; Component of UTP-glucose-1-phosphate uridylyltransferase^[2]^[3] Putative regulatory subunit for GalU^[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:0003983	UTP:glucose-1-phosphate uridylyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006011	UDP-glucose metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005774	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009058	biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005835	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0448	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005835	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0548	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030234	enzyme regulator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005774	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	Notes	References	Evidence
Protein	Subunits of UTP-glucose-1-phosphate uridylyltransferase	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1141725
Protein	groL		PMID:16606699	Experiment(s):EBI-1141725
Protein	ddpC		PMID:16606699	Experiment(s):EBI-1141725
Protein	arpB		PMID:16606699	Experiment(s):EBI-1141725
Protein	galU		PMID:16606699	Experiment(s):EBI-1141725
Protein	dps		PMID:16606699	Experiment(s):EBI-1141725
Protein	cdh		PMID:16606699	Experiment(s):EBI-1141725
Protein	atpD		PMID:16606699	Experiment(s):EBI-1141725
Protein	galU		PMID:19402753	MALDI(Z-score):33.076286
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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 MTNLKAVIPV AGLGMHMLPA TKAIPKEMLP IVDKPMIQYI VDEIVAAGIK EILLVTHASK NAVENHFDTS YELESLLEQR VKRQLLAEVQ SICPPGVTIM NVRQGEPLGL GHSILCARPA IGDNPFVVVL PDVVIDDASA DPLRYNLAAM IARFNETGRS QVLAKRMPGD LSEYSVIQTK EPLDREGKVS RIVEFIEKPD QPQTLDSDIM AVGRYVLSAD IWPELERTQP GAWGRIQLTD AIAELAKKQS VDAMLMTGDS YDCGKKMGYM QAFVKYGLRN LKEGAKFRKG IEKLLSE
Length	297
Mol. Wt	32.829 kDa
pI	5.9 (calculated)
Extinction coefficient	22,920 - 23,295 (calc based on 8 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	Notes	References
Domain	5..278	PF00483 Nucleotidyl transferase		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=galF 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:16129982	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946560	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006771	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AAB6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7093	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13578	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946560	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003679	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3348	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	5.61E+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	231.012+/-3.809	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.17934+/-0.02415	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.357782755	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	5078	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	2808	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	3761	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)
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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_000913:2112331..2112371 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:b2042 (EcoliWiki Page)	NCBI GEO profiles for galF
microarray	GenExpDB:b2042 (EcoliWiki Page)	Summary of data for galF 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 galF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7093	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3348	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2042
EcoGene	EcoGene:EG13578	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003679	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006771	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
Apis mellifera	ENSAPMP00000034883 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G55590 (score: 1.000; bootstrap: 100%) AT2G39770 (score: 1.000; bootstrap: 100%) AT4G30570 (score: 0.662) AT2G04650 (score: 0.194) AT1G74910 (score: 0.194)	From Inparanoid:20070104
Homo sapiens	ENSP00000309092 (score: 1.000; bootstrap: 100%) ENSP00000315925 (score: 0.182)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000019150 (score: 1.000; bootstrap: 100%) ENSMMUP00000023579 (score: 0.131)	From Inparanoid:20070104
Mus musculus	MGI:2660880 (score: 1.000; bootstrap: 100%) MGI:1916330 (score: 0.200)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000025774 (score: 1.000; bootstrap: 100%) ENSPTRP00000022137 (score: 0.147)	From Inparanoid:20070104
Shigella flexneri	GALF	From SHIGELLACYC
E. coli O157	GALF	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)	PF00483 Nucleotidyl transferase
Superfamily (EcoliWiki Page)	SUPERFAMILY:53448
EcoCyc	EcoCyc:G7093	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13578	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003679	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3348	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006771	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 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 ^2.13 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).

galF: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 galF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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