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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	deoC
Gene Synonym(s)	ECK4373, b4381, JW4344, dra, thyR, tlr^[1], tlr
Product Desc.	DEOXYRIBOSE-P-ALD- 2-deoxy-D-ribose 5-phosphate aldolase (DERA); deoxyriboaldolase; binds selenium^[2]
Product Synonyms(s)	2-deoxyribose-5-phosphate aldolase, NAD(P)-linked^[1], B4381^[3]^[1], Tlr^[3]^[1], Dra^[3]^[1], ThyR^[3]^[1], DeoC^[3]^[1] , dra, ECK4373, JW4344, thyR, tlr, b4381
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): deoCABD^[3], OP00024, deo
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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Half of the native protein still retains the initial Met.^[2]

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	deoC
Mnemonic	Deoxyribose
Synonyms	ECK4373, b4381, JW4344, dra, thyR, tlr^[1], tlr
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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	99.48 minutes, 99.48 minutes	MG1655: 4615346..4616125 <gbrowseImage> name=NC_000913:4615346..4616125 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4606557..4607336 <gbrowseImage> name=NC_012967:4606557..4607336 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4553830..4554609 <gbrowseImage> name=NC_012759:4553830..4554609 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4622003..4622782 <gbrowseImage> name=NC_007779:4622003..4622782 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4661808..4662587 <gbrowseImage> name=NC_010473:4661808..4662587 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
Coding Start (SO:0000323)	MG1655	4615349	Edman degradation	PMID:6749498 PMID:12084818
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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
ΔdeoC (Keio:JW4344)	deletion	deletion	PMID:16738554	Shigen CGSC11099^[4]
deoC2				CGSC:4794
deoC1				CGSC:5232
deoC3				CGSC:5251
deoC4				CGSC:6966
deoC34				CGSC:7786
deoC5				CGSC:8356
deoC76				CGSC:8825
deoC8				CGSC:12262
deoC999				CGSC:39228
ΔdeoC777::kan			PMID:16738554	CGSC:100578
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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
JW4344	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACTGATCTGAAAGCAAGCAG Primer 2:CCGTAGCTGCTGGCGCTCTTACC
15C9	Kohara Phage	Genobase	PMID:3038334
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[4]	est. P1 cotransduction: 44% ^[5] Synonyms:zjj-202::Tn10, zji-202::Tn10
thrA34::Tn10	Linked marker	CAG18442 = CGSC7320^[4]	est. P1 cotransduction: 40% ^[5] 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:EG10221	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10221	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000215	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948902	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0217	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014371	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	DeoC
Synonyms	2-deoxyribose-5-phosphate aldolase, NAD(P)-linked^[1], B4381^[3]^[1], Tlr^[3]^[1], Dra^[3]^[1], ThyR^[3]^[1], DeoC^[3]^[1] , dra, ECK4373, JW4344, thyR, tlr, b4381
Product description	DEOXYRIBOSE-P-ALD- 2-deoxy-D-ribose 5-phosphate aldolase (DERA); deoxyriboaldolase; binds selenium^[2]
EC number (for enzymes)	4.1.2.4^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004139	deoxyribose-phosphate aldolase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00592	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004139	deoxyribose-phosphate aldolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011343	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004139	deoxyribose-phosphate aldolase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.2.4	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0015949	nucleobase, nucleoside and nucleotide interconversion	PMID:5340684	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009264	deoxyribonucleotide catabolic process	PMID:5340684	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0009264	deoxyribonucleotide catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011343	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016052	carbohydrate catabolic process	PMID:6749498	IDA: Inferred from Direct Assay		P		complete
	GO:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	PMID:6749498	IDA: Inferred from Direct Assay		F		complete
	GO:0016052	carbohydrate catabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00592	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004139	deoxyribose-phosphate aldolase activity	PMID:6749498	IDA: Inferred from Direct Assay		F		complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
	GO:0005829	cytosol	PMID:16397293	ISS: Inferred from Sequence or Structural Similarity	PMID:16397293	C	Riley et al. used a variety of methods to determine cell location, including examination of the literature and predictions of transmembrane helices and signal peptides.	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	References	Evidence
Protein	gltX	PMID:16606699	Experiment(s):EBI-1147944
Protein	nadE	PMID:16606699	Experiment(s):EBI-1147944
Protein	pepD	PMID:16606699	Experiment(s):EBI-1147944
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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
cytoplasm			From EcoCyc^[6]
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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 MTDLKASSLR ALKLMDLTTL NDDDTDEKVI ALCHQAKTPV GNTAAICIYP RFIPIARKTL KEQGTPEIRI ATVTNFPHGN DDIDIALAET RAAIAYGADE VDVVFPYRAL MAGNEQVGFD LVKACKEACA AANVLLKVII ETGELKDEAL IRKASEISIK AGADFIKTST GKVAVNATPE SARIMMEVIR DMGVEKTVGF KPAGGVRTAE DAQKYLAIAD ELFGADWADA RHYRFGASSL LASLLKALGH GDGKSASSY
Length	259
Mol. Wt	27.734 kDa
pI	5.5 (calculated)
Extinction coefficient	14,440 - 14,940 (calc based on 6 Y, 1 W, and 4 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	10..246	PF01791 DeoC/LacD family aldolase		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=deoC 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:16132198	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948902	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014371	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A6L0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10221	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10221	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948902	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000215	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0217	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	6.71E+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	1596	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	636	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	725	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_000913:4615326..4615366 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

</protect>

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:b4381 (EcoliWiki Page)	NCBI GEO profiles for deoC
microarray	GenExpDB:b4381 (EcoliWiki Page)	Summary of data for deoC 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 (4614535..4614950) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:E6^[7]
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Notes

Accessions Related to deoC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10221	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0217	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4381
EcoGene	EcoGene:EG10221	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000215	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014371	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
Anopheles gambiae	ENSANGP00000016811 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000007367 (score: 1.000; bootstrap: 94%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00025441 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00017283 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000018626 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000017567 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-041010-200 (score: 1.000; bootstrap: 100%) ZDB-CDNA-041010-200 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0033735 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21137-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000021349 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000025429 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000017503 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000022318 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1913762 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000008082 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000009998 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000151357 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00013892001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000048765 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	DEOC	From SHIGELLACYC
E. coli O157	DEOC	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)	PF01791 DeoC/LacD family aldolase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51569
Panther (EcoliWiki Page)	PTHR10889:SF0
EcoCyc	EcoCyc:EG10221	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10221	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000215	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0217	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014371	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 EcoCyc (release 10.6; 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).
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

deoC: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 deoC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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