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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	codA
Gene Synonym(s)	ECK0334, b0337, JW0328^[1], JW0328
Product Desc.	Cytosine deaminase^[2]
Product Synonyms(s)	cytosine deaminase^[1], B0337^[3]^[1], CodA^[3]^[1] , ECK0334, JW0328, b0337
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): codBA^[3], OP00277
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	codA
Mnemonic	CytOsine Deaminase
Synonyms	ECK0334, b0337, JW0328^[1], JW0328
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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	7.66 minutes	MG1655: 355395..356678 <gbrowseImage> name=NC_000913:355395..356678 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 328727..330010 <gbrowseImage> name=NC_012967:328727..330010 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 355395..356678 <gbrowseImage> name=NC_007779:355395..356678 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
Coding Start (SO:0000323)	MG1655	355398	Edman degradation	PMID:1640834
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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: Description	Reference	Availability	Comments
codAR13W		R13W	(in strain: SO5076)			Strain variation; seeded from UniProt:P25524
codA(del) (Keio:JW0328)	deletion	deletion		PMID:16738554	Shigen CGSC8524^[4]
codA1					CGSC:5678
codA2					CGSC:10141
codA778(del)::kan				PMID:16738554	CGSC:100368
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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
JW0328	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCGAATAACGCTTTACAAAC Primer 2:CCACGTTTGTAATCGATGGCTTC
9F1	Kohara Phage	Genobase	PMID:3038334
10A6	Kohara Phage	Genobase	PMID:3038334
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[4]	est. P1 cotransduction: % ^[5]
lacI3042::Tn10	Linked marker	CAG18439 = CGSC7334^[4]	est. P1 cotransduction: 68% ^[5] Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).
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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:EG11326	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11326	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001297	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944996	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1302	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001161	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	CodA
Synonyms	cytosine deaminase^[1], B0337^[3]^[1], CodA^[3]^[1] , ECK0334, JW0328, b0337
Product description	Cytosine deaminase^[2]
EC number (for enzymes)	3.5.4.1^[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:0004131	cytosine deaminase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.4.1	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	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:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011059	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019858	cytosine metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0205	P	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	References	Evidence
Protein	carA	PMID:16606699	Experiment(s):EBI-1136290
Protein	nadE	PMID:16606699	Experiment(s):EBI-1136290
Protein	yfaQ	PMID:16606699	Experiment(s):EBI-1136290
Protein	napC	PMID:16606699	Experiment(s):EBI-1136290
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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 MSNNALQTII NARLPGEEGL WQIHLQDGKI SAIDAQSGVM PITENSLDAE QGLVIPPFVE PHIHLDTTQT AGQPNWNQSG TLFEGIERWA ERKALLTHDD VKQRAWQTLK WQIANGIQHV RTHVDVSDAT LTALKAMLEV KQEVAPWIDL QIVAFPQEGI LSYPNGEALL EEALRLGADV VGAIPHFEFT REYGVESLHK TFALAQKYDR LIDVHCDEID DEQSRFVETV AALAHHEGMG ARVTASHTTA MHSYNGAYTS RLFRLLKMSG INFVANPLVN IHLQGRFDTY PKRRGITRVK EMLESGINVC FGHDDVFDPW YPLGTANMLQ VLHMGLHVCQ LMGYGQINDG LNLITHHSAR TLNLQDYGIA AGNSANLIIL PAENGFDALR RQVPVRYSVR GGKVIASTQP AQTTVYLEQP EAIDYKR
Length	427
Mol. Wt	47.59 kDa
pI	6.1 (calculated)
Extinction coefficient	56,380 - 56,755 (calc based on 12 Y, 7 W, and 3 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
Initiator Methionine	1	Removed	UniProt:P25524
Domain	53..379	PF07969 Amidohydrolase family		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=codA 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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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:16128322	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944996	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001161	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P25524	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11326	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11326	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944996	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001297	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1302	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 MG1655	1426	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	2303	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	611	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)
codBA
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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_000913:355375..355415 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

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:b0337 (EcoliWiki Page)	NCBI GEO profiles for codA
microarray	GenExpDB:b0337 (EcoliWiki Page)	Summary of data for codA 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 codA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11326	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1302	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0337
EcoGene	EcoGene:EG11326	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001297	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001161	Escherichia coli str. K-12 substr. MG1655
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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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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
Superfamily (EcoliWiki Page)	SUPERFAMILY:51338
Superfamily (EcoliWiki Page)	SUPERFAMILY:51556
Panther (EcoliWiki Page)	PTHR11271:SF27
Pfam (EcoliWiki Page)	PF07969 Amidohydrolase family
EcoCyc	EcoCyc:EG11326	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11326	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001297	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1302	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001161	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 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).

codA: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 codA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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