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Expression|

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Standard Name	ulaF
Gene Synonym(s)	ECK4194, b4198, JW4156, sgaE, yjfX^[1], yjfX
Product Desc.	L-ribulose 5-phosphate 4-epimerase^[2]^[3] L-ribulose 5-phosphate 4-epimerase; involved in the utilization of L-ascorbate by anaerobic fermentation^[4]
Product Synonyms(s)	L-ribulose 5-phosphate 4-epimerase^[1], B4198^[2]^[1], YjfX^[2]^[1], SgaE^[2]^[1], UlaF^[2]^[1] , ECK4194, JW4156, sgaE, yjfX, b4198
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ulaABCDEF^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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The ula divergon is comprised of the two divergent ulaGR and ulaABCDEF operons.^[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	ulaF
Mnemonic	Utilization of L-ascorbate
Synonyms	ECK4194, b4198, JW4156, sgaE, yjfX^[1], yjfX
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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	95.3 minutes	MG1655: 4421723..4422409 <gbrowseImage> name=NC_000913:4421723..4422409 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4401855..4402541 <gbrowseImage> name=NC_012967:4401855..4402541 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4360458..4361144 <gbrowseImage> name=NC_012759:4360458..4361144 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4428380..4429066 <gbrowseImage> name=NC_007779:4428380..4429066 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4522085..4522771 <gbrowseImage> name=NC_010473:4522085..4522771 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
ΔulaF (Keio:JW4156)	deletion	deletion	PMID:16738554	Shigen CGSC10993^[5]
ΔulaF748::kan			PMID:16738554	CGSC:103316
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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
JW4156	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAAAGCTAAAACAGCAGGT Primer 2:CCtTTCTGCCCGTAATAAGCGTT
1G10	Kohara Phage	Genobase	PMID:3038334
7E9	Kohara Phage	Genobase	PMID:3038334
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 3% ^[6] Synonyms:zjd-2231::Tn10
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[5]	est. P1 cotransduction: 86% ^[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
EcoCyc	EcoCyc:G7860	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12498	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004355	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948711	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2391	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013734	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	UlaF
Synonyms	L-ribulose 5-phosphate 4-epimerase^[1], B4198^[2]^[1], YjfX^[2]^[1], SgaE^[2]^[1], UlaF^[2]^[1] , ECK4194, JW4156, sgaE, yjfX, b4198
Product description	L-ribulose 5-phosphate 4-epimerase^[2]^[3] L-ribulose 5-phosphate 4-epimerase; involved in the utilization of L-ascorbate by anaerobic fermentation^[4]
EC number (for enzymes)	5.1.3.4^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008742	L-ribulose-phosphate 4-epimerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.1.3.4	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019852	L-ascorbic acid metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01952	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001303	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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
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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 MQKLKQQVFE ANMELPRYGL VTFTWGNVSA IDRERGLVVI KPSGVAYETM KAADMVVVDM SGKVVEGEYR PSSDTATHLE LYRRYPSLGG IVHTHSTHAT AWAQAGLAIP ALGTTHADYF FGDIPCTRGL SEEEVQGEYE LNTGKVIIET LGNAEPLHTP GIVVYQHGPF AWGKDAHDAV HNAVVMEEVA KMAWIARGIN PQLNHIDSFL MNKHFMRKHG PNAYYGQK
Length	228
Mol. Wt	25.276 kDa
pI	6.7 (calculated)
Extinction coefficient	36,900 - 37,025 (calc based on 10 Y, 4 W, and 1 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	6..194	PF00596 Class II Aldolase and Adducin N-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=ulaF 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:16132020	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948711	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013734	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39306	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7860	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12498	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948711	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004355	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2391	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	22	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	8	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	3^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)
ulaABCDEF
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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_000913:4421703..4421743 source=MG1655 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

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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:b4198 (EcoliWiki Page)	NCBI GEO profiles for ulaF
microarray	GenExpDB:b4198 (EcoliWiki Page)	Summary of data for ulaF 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 ulaF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7860	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2391	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4198
EcoGene	EcoGene:EG12498	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004355	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013734	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	ENSAPMP00000012633 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000028152 (score: 1.000; bootstrap: 100%) ENSBTAP00000004231 (score: 0.419) ENSBTAP00000011966 (score: 0.390)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000021828 (score: 1.000; bootstrap: 100%) ENSCAFP00000015741 (score: 0.400) ENSCAFP00000005087 (score: 0.366)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000025213 (score: 1.000; bootstrap: 100%) ENSGALP00000013902 (score: 0.395)	From Inparanoid:20070104
Homo sapiens	ENSP00000264758 (score: 1.000; bootstrap: 100%) ENSP00000348381 (score: 0.418) ENSP00000264436 (score: 0.376)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000010988 (score: 1.000; bootstrap: 100%) ENSMMUP00000013882 (score: 0.333) ENSMMUP00000008196 (score: 0.240)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000004673 (score: 1.000; bootstrap: 100%) ENSMODP00000013307 (score: 0.461) ENSMODP00000014253 (score: 0.427)	From Inparanoid:20070104
Mus musculus	MGI:87918 (score: 1.000; bootstrap: 100%) MGI:1351615 (score: 0.445) MGI:87919 (score: 0.413)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000027304 (score: 1.000; bootstrap: 100%) ENSPTRP00000020655 (score: 0.376) ENSPTRP00000042709 (score: 0.339)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000018072 (score: 1.000; bootstrap: 100%) ENSRNOP00000043399 (score: 0.449) ENSRNOP00000021491 (score: 0.414)	From Inparanoid:20070104
Saccharomyces cerevisiae	YJR024C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000177921 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000167802 (score: 0.347) NEWSINFRUP00000158333 (score: 0.320) NEWSINFRUP00000160493 (score: 0.301) NEWSINFRUP00000154131 (score: 0.182)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00024942001 (score: 1.000; bootstrap: 100%) GSTENP00031118001 (score: 1.000; bootstrap: 100%) GSTENP00020027001 (score: 0.494) GSTENP00014406001 (score: 0.320)	From Inparanoid:20070104
Shigella flexneri	SGAE	From SHIGELLACYC
E. coli O157	SGAE	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)	PF00596 Class II Aldolase and Adducin N-terminal domain
Panther (EcoliWiki Page)	PTHR22789:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:53639
EcoCyc	EcoCyc:G7860	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12498	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004355	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2391	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013734	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 ^1.12 ^1.13 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 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).

ulaF: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 ulaF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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