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Standard Name	cobT
Gene Synonym(s)	ECK1986, b1991, JW1969^[1], JW1969
Product Desc.	CobT^[2]^[3]; Component of dimethylbenzimidazole phosphoribosyltransferase^[2]; nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase^[3] Partial cobalamin biosynthesis pathway present in E. coli^[4]
Product Synonyms(s)	nicotinate-nucleotide dimethylbenzimidazole-P phophoribosyl transferase^[1], B1991^[2]^[1], CobT^[2]^[1] , ECK1986, JW1969, b1991
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cobUST^[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	cobT
Mnemonic	Cobalamin, coenzyme B12
Synonyms	ECK1986, b1991, JW1969^[1], JW1969
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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	44.43 minutes	MG1655: 2062491..2061412 <gbrowseImage> name=NC_000913:2061412..2062491 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2002467..2001388 <gbrowseImage> name=NC_012967:2001388..2002467 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1953895..1954974 <gbrowseImage> name=NC_012759:1953895..1954974 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2066604..2065525 <gbrowseImage> name=NC_007779:2065525..2066604 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2153499..2152420 <gbrowseImage> name=NC_010473:2152420..2153499 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	Comments
ΔcobT (Keio:JW1969)	deletion	deletion			PMID:16738554	Shigen CGSC9633^[5]
cobT::Tn5KAN-2 (FB20560)	Insertion at nt 606 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20560	does not contain pKD46
cobT::Tn5KAN-2 (FB20561)	Insertion at nt 606 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20561	contains pKD46
ΔcobT762::kan	Deletion and replacement with FRT-KAN-FRT		Auxotrophies		PMID:16738554	CGSC:100364
cobT14::Tn10dTc	Tn10dTc insertion 647 bp downstream of cobT translation start.		Auxotrophies	Prevents synthesis of vitamin B12 because the mutant cannot produce dimethylbenzimidazole-ribose (DMB-ribose).	PMID:7592411		See Table 2. The Tn10dTc insertion is oriented to allow transcription of downstream genes from the transposon.^[6]
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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
JW1969	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAATACTTGCCGATTTACT Primer 2:CCACTGTTCAAATCAGAAGTCGT
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: 40% ^[7]
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 45% ^[7] Synonyms:zee-3129::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:EG12151	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002050	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946517	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2071	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006611	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	CobT
Synonyms	nicotinate-nucleotide dimethylbenzimidazole-P phophoribosyl transferase^[1], B1991^[2]^[1], CobT^[2]^[1] , ECK1986, JW1969, b1991
Product description	CobT^[2]^[3]; Component of dimethylbenzimidazole phosphoribosyltransferase^[2]; nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase^[3] Partial cobalamin biosynthesis pathway present in E. coli^[4]
EC number (for enzymes)	2.4.2.21^[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:0008939	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00230	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008939	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003200	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008939	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017846	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008939	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.4.2.21	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009163	nucleoside biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017846	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009236	cobalamin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003200	P	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:0015420	cobalamin-transporting ATPase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00230	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009236	cobalamin biosynthetic process	PMID:7592411	IMP: Inferred from Mutant Phenotype		P	Table 2	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 dimethylbenzimidazole phosphoribosyltransferase	could be indirect
Protein	glpD		PMID:16606699	Experiment(s):EBI-1141584
Protein	gshB		PMID:16606699	Experiment(s):EBI-1141584
Protein	zwf		PMID:16606699	Experiment(s):EBI-1141584
Protein	groL		PMID:16606699	Experiment(s):EBI-1141584
Protein	amn		PMID:16606699	Experiment(s):EBI-1141584
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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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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 MQILADLLNT IPAIDSTAMS RAQRHIDGLL KPVGSLGKLE VLAIQLAGMP GLNGIPHVGK KAVLVMCADH GVWEEGVAIS PKEVTAIQAE NMTRGTTGVC VLAEQAGANV HVIDVGIDTA EPIPGLINMR VARGSGNIAS APAMSRRQAE KLLLDVICYT QELAKNGVTL FGVGELGMAN TTPAAAIVST ITGRDPEEVV GIGANLPTDK LANKIDVVRR AITLNQPNPQ DGVDVLAKVG GFDLVGIAGV MLGAASCGLP VLLDGFLSYA AALAACQMSP AIKPYLIPSH LSAEKGARIA LSHLGLEPYL NMEMRLGEGS GAALAMPIIE AACAIYNNMG ELAASNIVLP GNTTSDLNS
Length	359
Mol. Wt	36.987 kDa
pI	5.1 (calculated)
Extinction coefficient	12,950 - 13,700 (calc based on 5 Y, 1 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	7..347	PF02277 Phosphoribosyltransferase		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=cobT 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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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:16129932	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946517	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006611	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36562	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12151	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12151	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946517	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002050	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2071	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	Ecoli K-12	6.713+/-0.072	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.024559778	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	186	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	109	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	203	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)
cobUST
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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_000913:2062471..2062511 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:b1991 (EcoliWiki Page)	NCBI GEO profiles for cobT
microarray	GenExpDB:b1991 (EcoliWiki Page)	Summary of data for cobT 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 cobT Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12151	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2071	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1991
EcoGene	EcoGene:EG12151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002050	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006611	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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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Shigella flexneri	COBT	From SHIGELLACYC
E. coli O157	COBT	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)	PF02277 Phosphoribosyltransferase
Superfamily (EcoliWiki Page)	SUPERFAMILY:52733
Panther (EcoliWiki Page)	PTHR21712:SF4
EcoCyc	EcoCyc:EG12151	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002050	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2071	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006611	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 ^1.9 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 ^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 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
↑ Lawrence, JG & Roth, JR (1995) The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli. J. Bacteriol. 177 6371-80 PubMed
↑ ^7.0 ^7.1 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).

cobT: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 cobT Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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