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Standard Name	xapA
Gene Synonym(s)	ECK2401, b2407, JW2398, pndA^[1], pndA
Product Desc.	XapA^[2]^[3]; Component of xanthosine phosphorylase^[2]^[3]
Product Synonyms(s)	purine nucleoside phosphorylase II^[1], B2407^[2]^[1], PndA^[2]^[1], XapA^[2]^[1] , ECK2401, JW2398, pndA, b2407
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): xapAB^[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	xapA
Mnemonic	XAnthosine Phosphorylase
Synonyms	ECK2401, b2407, JW2398, pndA^[1], pndA
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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	54.36 minutes	MG1655: 2522900..2522067 <gbrowseImage> name=NC_000913:2522067..2522900 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2407872..2408705 <gbrowseImage> name=NC_012759:2407872..2408705 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2530324..2529491 <gbrowseImage> name=NC_007779:2529491..2530324 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2614665..2613832 <gbrowseImage> name=NC_010473:2613832..2614665 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
ΔxapA (Keio:JW2398)	deletion	deletion	PMID:16738554	Shigen CGSC9914^[4]
xapA::Tn5KAN-2 (FB20785)	Insertion at nt 192 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20785	contains pKD46
ΔxapA737::kan			PMID:16738554	CGSC:103400
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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
JW2398	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCTCAGGTTCAATTTTCTCA Primer 2:CCGGCAATTTTGCGCAGAAAGCC
4G10	Kohara Phage	Genobase	PMID:3038334
3E7	Kohara Phage	Genobase	PMID:3038334
nupC510::Tn10	Linked marker	CAG18468 = CGSC7410^[4]	est. P1 cotransduction: 66% ^[5]
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[4]	est. P1 cotransduction: 1% ^[5]
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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:G85	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG20250	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004462	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946878	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4152	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007927	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	XapA
Synonyms	purine nucleoside phosphorylase II^[1], B2407^[2]^[1], PndA^[2]^[1], XapA^[2]^[1] , ECK2401, JW2398, pndA, b2407
Product description	XapA^[2]^[3]; Component of xanthosine phosphorylase^[2]^[3]
EC number (for enzymes)	2.4.2.1^[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:0005737	cytoplasm	PMID:15808857	IDA: Inferred from Direct Assay		C		complete
	GO:0015949	nucleobase, nucleoside and nucleotide interconversion	PMID:7559336	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	PMID:7559336	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0004731	purine-nucleoside phosphorylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011268	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004731	purine-nucleoside phosphorylase activity	PMID:15808857	IDA: Inferred from Direct Assay		F		complete
	GO:0009116	nucleoside metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000845	P	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 xanthosine phosphorylase	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1142735
Protein	nadE		PMID:16606699	Experiment(s):EBI-1142735
Protein	prs		PMID:16606699	Experiment(s):EBI-1142735
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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 MSQVQFSHNP LFCIDIIKTY KPDFTPRVAF ILGSGLGALA DQIENAVAIS YEKLPGFPVS TVHGHAGELV LGHLQGVPVV CMKGRGHFYE GRGMTIMTDA IRTFKLLGCE LLFCTNAAGS LRPEVGAGSL VALKDHINTM PGTPMVGLND DRFGERFFSL ANAYDAEYRA LLQKVAKEEG FPLTEGVFVS YPGPNFETAA EIRMMQIIGG DVVGMSVVPE VISARHCDLK VVAVSAITNM AEGLSDVKLS HAQTLAAAEL SKQNFINLIC GFLRKIA
Length	277
Mol. Wt	29.834 kDa
pI	6.5 (calculated)
Extinction coefficient	8,940 - 9,690 (calc based on 6 Y, 0 W, and 6 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	27..274	PF01048 Phosphorylase superfamily		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=xapA 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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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:16130333	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946878	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007927	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P45563	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G85	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG20250	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946878	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004462	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4152	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	2^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	4^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)
xapAB
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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_000913:2522880..2522920 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:b2407 (EcoliWiki Page)	NCBI GEO profiles for xapA
microarray	GenExpDB:b2407 (EcoliWiki Page)	Summary of data for xapA 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 (2522819..2523227) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:H10^[6]
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Notes

Accessions Related to xapA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G85	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4152	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2407
EcoGene	EcoGene:EG20250	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004462	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007927	Escherichia coli str. K-12 substr. MG1655
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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
Anopheles gambiae	ENSANGP00000025345 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000007359 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000010279 (score: 1.000; bootstrap: 99%) ENSBTAP00000036122 (score: 0.864) ENSBTAP00000036197 (score: 0.657)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00034258 (score: 1.000; bootstrap: 99%) WBGene00036760 (score: 0.186)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00019298 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000008083 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000016539 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1800 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-2740 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-3500 (score: 0.496) ZDB-GENE-040426-2553 (score: 0.496) ZDB-CDNA-040912-56 (score: 0.438) ZDB-GENE-040912-54 (score: 0.438) ZDB-CDNA-040425-2827 (score: 0.427) ZDB-GENE-040426-1887 (score: 0.427) ZDB-CDNA-040625-125 (score: 0.366) ZDB-GENE-040625-83 (score: 0.366)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0035348 (score: 1.000; bootstrap: 100%) FBgn0034898 (score: 0.079)	From Inparanoid:20070104
Drosophila pseudoobscura	GA14131-PA (score: 1.000; bootstrap: 100%) GA14805-PA (score: 0.124)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000003703 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000354532 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000025146 (score: 1.000; bootstrap: 100%) ENSMMUP00000022513 (score: 0.987)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000008744 (score: 1.000; bootstrap: 99%) ENSMODP00000024108 (score: 0.864) ENSMODP00000001651 (score: 0.838) ENSMODP00000015545 (score: 0.690) ENSMODP00000025446 (score: 0.609) ENSMODP00000009564 (score: 0.301) ENSMODP00000022025 (score: 0.260) ENSMODP00000011116 (score: 0.246)	From Inparanoid:20070104
Mus musculus	MGI:97365 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000010346 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000013582 (score: 1.000; bootstrap: 100%) ENSRNOP00000030744 (score: 0.431)	From Inparanoid:20070104
Saccharomyces cerevisiae	YLR209C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC18056c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000157233 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000159668 (score: 0.697) NEWSINFRUP00000181254 (score: 0.359)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00014282001 (score: 1.000; bootstrap: 100%) GSTENP00011807001 (score: 0.690) GSTENP00038767001 (score: 0.179)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000036902 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
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Notes

Families

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

Database	Accession	Notes
Panther (EcoliWiki Page)	PTHR11904:SF9
Superfamily (EcoliWiki Page)	SUPERFAMILY:53167
Pfam (EcoliWiki Page)	PF01048 Phosphorylase superfamily
EcoCyc	EcoCyc:G85	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG20250	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004462	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4152	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007927	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 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 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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

xapA:On One Page

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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 xapA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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