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Standard Name	lyxK
Gene Synonym(s)	lyxKK, ECK3569, b3580, JW3552, yiaP, sgbK, xylK, xyl, lyx^[1]^[2]^[3], lyx
Product Desc.	LyxK^[3]; L-xylulose kinase^[2]; Component of L-xylulose kinase^[3]^[2] L-xylulose kinase; novel pathway for utilization of lyxKose via xylulose through rhamnose and pentose pathways; 3-keto-L-gulonate kinase; possibly involved in the utilization of L-dehydroascorbate (2,3-diketo-L-gulonate)^[4]
Product Synonyms(s)	L-xylulose kinase^[1], B3580^[3]^[1], XylK^[3]^[1], Xyl^[3]^[1], Lyx^[3]^[1], YiaP^[3]^[1], SgbK^[3]^[1], LyxK^[3]^[1] , ECK3569, JW3552, lyx, xylK, yiaP, b3580
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yiaKLMNO-lyxKK-sgbHUE^[3], yiaKLMNOPQRS
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	lyxK
Mnemonic	Lyxose
Synonyms	lyxKK, ECK3569, b3580, JW3552, yiaP, sgbK, xylK, xyl, lyx^[1]^[2]^[3], lyx
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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	80.72 minutes, 80.72 minutes	MG1655: 3745107..3746603 <gbrowseImage> name=NC_000913:3745107..3746603 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3677540..3679036 <gbrowseImage> name=NC_012967:3677540..3679036 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3633433..3634929 <gbrowseImage> name=NC_012759:3633433..3634929 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3893331..3891835 <gbrowseImage> name=NC_007779:3891835..3893331 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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)	Reference	Availability	Comments
lyxK::Tn5KAN-I-SceI (FB21309)	Insertion at nt 1195 in Plus orientation	PMID:15262929	E. coli Genome Project:FB21308	does not contain pKD46
lyxK::Tn5KAN-I-SceI (FB21309)	Insertion at nt 1195 in Plus orientation	PMID:15262929	E. coli Genome Project:FB21309	contains pKD46
ΔlyxK763::kan		PMID:16738554	CGSC:101718
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
9B3	Kohara Phage	Genobase	PMID:3038334
7C3	Kohara Phage	Genobase	PMID:3038334
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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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3580
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C4403
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:Z4878
CGSC (EcoliWiki Page)	CGSC:36908
EcoCyc (EcoliWiki Page)	ECOCYC:EG12284	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948101	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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	LyxK
Synonyms	L-xylulose kinase^[1], B3580^[3]^[1], XylK^[3]^[1], Xyl^[3]^[1], Lyx^[3]^[1], YiaP^[3]^[1], SgbK^[3]^[1], LyxK^[3]^[1] , ECK3569, JW3552, lyx, xylK, yiaP, b3580
Product description	LyxK^[3]; L-xylulose kinase^[2]; Component of L-xylulose kinase^[3]^[2] L-xylulose kinase; novel pathway for utilization of lyxKose via xylulose through rhamnose and pentose pathways; 3-keto-L-gulonate kinase; possibly involved in the utilization of L-dehydroascorbate (2,3-diketo-L-gulonate)^[4]
EC number (for enzymes)	2.7.1.53^[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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008744	L-xylulokinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.1.53	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 L-xylulose kinase	could be indirect
Protein	ahpC		PMID:16606699	Experiment(s):EBI-1146164
Protein	fliI		PMID:16606699	Experiment(s):EBI-1146164
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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 MTQYWLGLDC GGSWLKAGLY DREGREAGVQ RLPLCALSPQ PGWAERDMAE LWQCCMAVIR ALLTHSGVSG EQIVGIGISA QGKGLFLLDK NDKPLGNAIL SSDRRAMEIV RRWQEDGIPE KLYPLTRQTL WTGHPVSLLR WLKEHEPERY AQIGCVMMTH DYLRWCLTGV KGCEESNISE SNLYNMSLGE YDPCLTDWLG IAEINHALPP VVGSAEICGE ITAQTAALTG LKAGTPVVGG LFDVVSTALC AGIEDEFTLN AVMGTWAVTS GITRGLRDGE AHPYVYGRYV NDGEFIVHEA SPTSSGNLEW FTAQWGEISF DEINQAVASL PKAGGDLFFL PFLYGSNAGL EMTSGFYGMQ AIHTRAHLLQ AIYEGVVFSH MTHLNRMRER FTDVHTLRVT GGPAHSDVWM QMLADVSGLR IELPQVEETG CFGAALAARV GTGVYHNFSE AQRDLRHPVR TLLPDMTAHQ LYQKKYQRYQ HLIAALQGFH ARIKEHTL
Length	498
Mol. Wt	55.154 kDa
pI	6.0 (calculated)
Extinction coefficient	96,830 - 98,205 (calc based on 17 Y, 13 W, and 11 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	4..250	PF00370 FGGY family of carbohydrate kinases, N-terminal domain	PMID:19920124
Domain	259..442	PF02782 FGGY family of carbohydrate kinases, 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=lyx taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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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:16131451	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948101	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37677	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948101	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	1^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	1^a	molecules/cell/generation	Medium: MOPS Minimal 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	0^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)
yiaKLMNO-lyxK-sgbHUE
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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_000913:3745087..3745127 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

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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:b3580 (EcoliWiki Page)	NCBI GEO profiles for lyx
microarray	GenExpDB:b3580 (EcoliWiki Page)	Summary of data for lyx 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 lyxK 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:b3580
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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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Apis mellifera	ENSAPMP00000007716 (score: 1.000; bootstrap: 82%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGR194C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCPJ7322c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00025315001 (score: 1.000; bootstrap: 100%) GSTENP00011242001 (score: 0.265)	From Inparanoid:20070104
E. coli O157	Z4878	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)	PF00370 FGGY family of carbohydrate kinases, N-terminal domain
Pfam (EcoliWiki Page)	PF02782 FGGY family of carbohydrate kinases, C-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:53067
Superfamily (EcoliWiki Page)	SUPERFAMILY:53067
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.

↑ ^1.00 ^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 ^1.14 ^1.15 ^1.16 ^1.17 ^1.18 ^1.19 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 ^3.12 ^3.13 ^3.14 ^3.15 ^3.16 ^3.17 ^3.18 ^3.19 ^3.20 EcoCyc (release 10.6; 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.

lyxK:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Alleles and Phenotypes

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Genetic Interactions

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Genetic Resources

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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 lyxK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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