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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	deoA
Gene Synonym(s)	ECK4374, b4382, JW4345, tpp-75, TP, tpp, ttg^[1], ttg
Product Desc.	DeoA^[2]^[3]; Component of DEOA-CPLX^[2] Thymidine phosphorylase; homodimeric^[4]
Product Synonyms(s)	thymidine phosphorylase ^[1], B4382 ^[2]^[1], Ttg ^[2]^[1], Tpp ^[2]^[1], DeoA ^[2]^[1] , ECK4374, JW4345, TP, tpp, ttg, b4382
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): deoCABD^[2], OP00024, deo
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	deoA
Mnemonic	Deoxyribose
Synonyms	ECK4374, b4382, JW4345, tpp-75, TP, tpp, ttg^[1], ttg
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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	99.5 minutes	MG1655: 4616252..4617574 <gbrowseImage> name=NC_000913:4616252..4617574 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4607463..4608785 <gbrowseImage> name=NC_012967:4607463..4608785 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4554736..4556058 <gbrowseImage> name=NC_012759:4554736..4556058 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4622909..4624231 <gbrowseImage> name=NC_007779:4622909..4624231 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4662714..4664036 <gbrowseImage> name=NC_010473:4662714..4664036 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)	Phenotype: Type	Phenotype: Description	Reference	Availability
deoA(del) (Keio:JW4345)	deletion	deletion			PMID:16738554	Shigen CGSC11100^[5]
deoA22						CGSC:5954
deoA0						CGSC:8278
deoA21						CGSC:8282
deoA75						CGSC:8638
deoA91						CGSC:23044
deoA778(del)::kan					PMID:16738554	CGSC:100574
tpp in strain PA0014			Resistant to	Resistance to Alafosfalin	PMID:6389761	Strain: PA0114
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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
JW4345	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTTCTCGCACAAGAAATTAT Primer 2:CCTTCGCTGATACGGCGATAGAC
15C9	Kohara Phage	Genobase	PMID:3038334
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: 43% ^[6] Synonyms:zjj-202::Tn10, zji-202::Tn10
thrA34::Tn10	Linked marker	CAG18442 = CGSC7320^[5]	est. P1 cotransduction: 42% ^[6] Synonyms:thr-34::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:EG10219	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10219	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000213	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948901	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0215	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014374	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	DeoA
Synonyms	thymidine phosphorylase ^[1], B4382 ^[2]^[1], Ttg ^[2]^[1], Tpp ^[2]^[1], DeoA ^[2]^[1] , ECK4374, JW4345, TP, tpp, ttg, b4382
Product description	DeoA^[2]^[3]; Component of DEOA-CPLX^[2] Thymidine phosphorylase; homodimeric^[4]
EC number (for enzymes)	2.4.2.4^[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:0006206	pyrimidine base metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000053	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006206	pyrimidine base metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017872	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006213	pyrimidine nucleoside metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013102	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000312	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009032	thymidine phosphorylase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01628	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009032	thymidine phosphorylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013465	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009032	thymidine phosphorylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.4.2.4	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		C	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:0016757	transferase activity, transferring glycosyl groups	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000312	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016757	transferase activity, transferring glycosyl groups	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0328	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016763	transferase activity, transferring pentosyl groups	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013102	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046104	thymidine metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01628	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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 DEOA-CPLX	could be indirect
Protein	ygjK		PMID:16606699	Experiment(s):EBI-1147949
Protein	dapB		PMID:19402753	LCMS(ID Probability):99.6
Protein	fur		PMID:19402753	LCMS(ID Probability):99.6
Protein	gcvP		PMID:19402753	LCMS(ID Probability):99.6
Protein	gabD		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 MFLAQEIIRK KRDGHALSDE EIRFFINGIR DNTISEGQIA ALAMTIFFHD MTMPERVSLT MAMRDSGTVL DWKSLHLNGP IVDKHSTGGV GDVTSLMLGP MVAACGGYIP MISGRGLGHT GGTLDKLESI PGFDIFPDDN RFREIIKDVG VAIIGQTSSL APADKRFYAT RDITATVDSI PLITASILAK KLAEGLDALV MDVKVGSGAF MPTYELSEAL AEAIVGVANG AGVRTTALLT DMNQVLASSA GNAVEVREAV QFLTGEYRNP RLFDVTMALC VEMLISGKLA KDDAEARAKL QAVLDNGKAA EVFGRMVAAQ KGPTDFVENY AKYLPTAMLT KAVYADTEGF VSEMDTRALG MAVVAMGGGR RQASDTIDYS VGFTDMARLG DQVDGQRPLA VIHAKDENNW QEAAKAVKAA IKLADKAPES TPTVYRRISE
Length	440
Mol. Wt	47.207 kDa
pI	5.1 (calculated)
Extinction coefficient	24,410 - 24,660 (calc based on 9 Y, 2 W, and 2 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	3..68	PF02885 Glycosyl transferase family, helical bundle domain	PMID:19920124
Domain	78..333	PF00591 Glycosyl transferase family, a/b domain	PMID:19920124
Domain	350..424	PF07831 Pyrimidine nucleoside phosphorylase 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=deoA taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16132199	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948901	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014374	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P07650	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10219	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10219	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948901	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000213	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0215	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	Reference(s)
Protein	E. coli K-12 MC4100	1.00E+04	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	E. coli K-12 MG1655	349	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	237	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	252	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)
deoCABD
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Figure courtesy of RegulonDB

</protect>

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_000913:4616232..4616272 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:b4382 (EcoliWiki Page)	NCBI GEO profiles for deoA
microarray	GenExpDB:b4382 (EcoliWiki Page)	Summary of data for deoA 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 (4615581..4615874) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:B3^[7]
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Notes

Accessions Related to deoA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10219	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0215	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4382
EcoGene	EcoGene:EG10219	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000213	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014374	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
Homo sapiens	ENSP00000252029 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000002352 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000007330 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1920212 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000040056 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000039935 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000182976 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00004058001 (score: 1.000; bootstrap: 100%) GSTENP00003167001 (score: 0.202)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000034300 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	DEOA	From SHIGELLACYC
E. coli O157	DEOA	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)	PF00591 Glycosyl transferase family, a/b domain
Pfam (EcoliWiki Page)	PF02885 Glycosyl transferase family, helical bundle domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:47648
Superfamily (EcoliWiki Page)	SUPERFAMILY:52418
Panther (EcoliWiki Page)	PTHR10515:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:54680
Pfam (EcoliWiki Page)	PF07831 Pyrimidine nucleoside phosphorylase C-terminal domain
EcoCyc	EcoCyc:EG10219	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10219	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000213	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0215	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014374	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 ^2.11 ^2.12 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 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

deoA: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 deoA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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