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Standard Name	cobU
Gene Synonym(s)	ECK1988, b1993, JW1971^[1], JW1971
Product Desc.	CobU^[2]^[3]; Component of cobinamide-P guanylyltransferase^[2] Partial cobalamin biosynthesis pathway present in E. coli^[4]
Product Synonyms(s)	bifunctional cobinamide kinase and cobinamide phosphate guanylyltransferase^[1], B1993^[2]^[1], CobU^[2]^[1] , ECK1988, JW1971, b1993
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cobUST^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	cobU
Mnemonic	Cobalamin, coenzyme B12
Synonyms	ECK1988, b1993, JW1971^[1], JW1971
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Notes

Location(s) and DNA Sequence

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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	44.47 minutes	MG1655: 2063788..2063243 <gbrowseImage> name=NC_000913:2063243..2063788 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2003764..2003219 <gbrowseImage> name=NC_012967:2003219..2003764 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1955726..1956271 <gbrowseImage> name=NC_012759:1955726..1956271 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2067901..2067356 <gbrowseImage> name=NC_007779:2067356..2067901 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2154796..2154251 <gbrowseImage> name=NC_010473:2154251..2154796 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔcobU (Keio:JW1971)	deletion	deletion	PMID:16738554	Shigen CGSC9635^[5]
ΔcobU764::kan			PMID:16738554	CGSC:100366
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Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW1971	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATGATTTTGGTGACGGGGGG Primer 2:CCTTTGATTTTTACTCCAATACC
7D4	Kohara Phage	Genobase	PMID:3038334
9B2	Kohara Phage	Genobase	PMID:3038334
3B12	Kohara Phage	Genobase	PMID:3038334
zed-3069::Tn10	Linked marker	CAG18451 = CGSC7395^[5]	est. P1 cotransduction: 37% ^[6]
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 48% ^[6] Synonyms:zee-3129::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc	EcoCyc:EG13238	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13238	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002434	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946519	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3027	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006616	Escherichia coli str. K-12 substr. MG1655
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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	CobU
Synonyms	bifunctional cobinamide kinase and cobinamide phosphate guanylyltransferase^[1], B1993^[2]^[1], CobU^[2]^[1] , ECK1988, JW1971, b1993
Product description	CobU^[2]^[3]; Component of cobinamide-P guanylyltransferase^[2] Partial cobalamin biosynthesis pathway present in E. coli^[4]
EC number (for enzymes)
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Notes

Function

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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:0000166	nucleotide binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003203	F	Seeded from EcoCyc (v14.0)	complete
	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:0003824	catalytic activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0511	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:0005525	GTP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0342	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009236	cobalamin biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0169	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016301	kinase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0418	F	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:0043752	adenosylcobinamide kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003203	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043752	adenosylcobinamide kinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.1.156	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043753	adenosylcobinamide-phosphate guanylyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003203	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043753	adenosylcobinamide-phosphate guanylyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.62	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071^[7]	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 cobinamide-P guanylyltransferase	could be indirect
Protein	flgJ		PMID:16606699^[8]	Experiment(s):EBI-1141597
Protein	phnL		PMID:16606699^[8]	Experiment(s):EBI-1141597
Protein	gpmB		PMID:16606699^[8]	Experiment(s):EBI-1141597
Protein	mprA		PMID:16606699^[8]	Experiment(s):EBI-1141597
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Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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Structure and Physical Properties

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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 MMILVTGGAR SGKSRHAEAL IGDSSQVLYI ATSQILDDEM AARIEHHRQG RPEHWRTVER WQHLDELIHA DINPNEVVLL ECVTTMVTNL LFDYGGDKDP DEWDYQAMEQ AINAEIQSLI AACQRCPAKV VLVTNEVGMG IVPESRLARH FRDIAGRVNQ QLAAAANEVW LVVSGIGVKI K
Length	181
Mol. Wt	20.163 kDa
pI	5.4 (calculated)
Extinction coefficient	26,470 - 26,845 (calc based on 3 Y, 4 W, and 3 C residues)
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Domains/Motifs/Modification Sites

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Type	Residues	Description	Notes	References
Domain	3..180	PF02283 Cobinamide kinase / cobinamide phosphate guanyltransferase		PMID:19920124^[9]
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<motif_map/>

Structure
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Structures

<beststructure> gene=cobU taxon=562,83333 </beststructure>

Models

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Structure figures

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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Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129934	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946519	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006616	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AE76	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG13238	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13238	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946519	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002434	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3027	Escherichia coli str. K-12 substr. MG1655
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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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Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	102	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	52	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	118	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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Transcription unit(s)
cobUST
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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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<gbrowseImage> name=NC_000913:2063768..2063808 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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

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Experimental

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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:b1993 (EcoliWiki Page)	NCBI GEO profiles for cobU
microarray	GenExpDB:b1993 (EcoliWiki Page)	Summary of data for cobU 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 (2063716..273407) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:B2^[10]
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Notes

Accessions Related to cobU Expression

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Database	Accession	Notes
EcoCyc	EcoCyc:EG13238	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3027	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1993
EcoGene	EcoGene:EG13238	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002434	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006616	Escherichia coli str. K-12 substr. MG1655
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Notes

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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Organism	Homologs (Statistics)	Comments
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
Pfam (EcoliWiki Page)	PF02283 Cobinamide kinase / cobinamide phosphate guanyltransferase
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
EcoCyc	EcoCyc:EG13238	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13238	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002434	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3027	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006616	Escherichia coli str. K-12 substr. MG1655
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Notes

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Name	URL	Comments
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References

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↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 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 ^2.6 ^2.7 ^2.8 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).
↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
↑ ^8.0 ^8.1 ^8.2 ^8.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

cobU: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

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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 cobU Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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