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On One Page

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Expression|

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Standard Name	cobS
Gene Synonym(s)	ECK1987, b1992, JW1970^[1], JW1970
Product Desc.	COBS^[2]^[3] Partial cobalamin biosynthesis pathway present in E. coli^[4]
Product Synonyms(s)	cobalamin 5'-phosphate synthase^[1], B1992^[2]^[1], CobS^[2]^[1] , ECK1987, JW1970, b1992
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	cobS
Mnemonic	Cobalamin, coenzyme B12
Synonyms	ECK1987, b1992, JW1970^[1], JW1970
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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	44.45 minutes	MG1655: 2063246..2062503 <gbrowseImage> name=NC_000913:2062503..2063246 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2003222..2002479 <gbrowseImage> name=NC_012967:2002479..2003222 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1954986..1955729 <gbrowseImage> name=NC_012759:1954986..1955729 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2067359..2066616 <gbrowseImage> name=NC_007779:2066616..2067359 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2154254..2153511 <gbrowseImage> name=NC_010473:2153511..2154254 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
ΔcobS (Keio:JW1970)	deletion	deletion			PMID:16738554	Shigen CGSC9634^[5]
cobS::Tn5KAN-2 (FB20562)	Insertion at nt 288 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20562	contains pKD46
cobS::Tn5KAN-2 (FB20563)	Insertion at nt 288 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20563	does not contain pKD46
ΔcobS763::kan					PMID:16738554	CGSC:100362
cobS6::Tn10dTc	Tn10dTc insertion 551 bp downstream of cobS translation start.		Auxotrophies	Mutant cannot synthesize vitamin B12 because it cannot produce Ado-Cobalamin.	PMID:7592411		See Table 2 and Figure 1.
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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
JW1970	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTAAATTATTTTGGGCGAT Primer 2:CCTAGCAGTGCCAGCAGGAAGAC
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: 38% ^[6]
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 47% ^[6] 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:EG12150	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12150	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002049	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946520	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2070	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006613	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	CobS
Synonyms	cobalamin 5'-phosphate synthase^[1], B1992^[2]^[1], CobS^[2]^[1] , ECK1987, JW1970, b1992
Product description	COBS^[2]^[3] Partial cobalamin biosynthesis pathway present in E. coli^[4]
EC number (for enzymes)	2.-.-.-^[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:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00719	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008818	cobalamin 5'-phosphate synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003805	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009236	cobalamin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003805	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_00719	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	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	References	Evidence
Protein	ybhK	PMID:16606699	Experiment(s):EBI-1141591
Protein	rmlA1	PMID:16606699	Experiment(s):EBI-1141591
Protein	yfbN	PMID:16606699	Experiment(s):EBI-1141591
Protein	hchA	PMID:16606699	Experiment(s):EBI-1141591
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Notes

Localization

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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 MSKLFWAMLS FITRLPVPRR WSQGLDFEHY SRGIITFPLI GLLLGAISGL VFMVLQAWCG APLAALFSVL VLVLMTGGFH LDGLADTCDG VFSARSRDRM LEIMRDSRLG THGGLALIFV VLAKILVLSE LALRGESILA SLAAACAVSR GTAALLMYRH RYAREEGLGN VFIGKIDGRQ TCVTLGLAAI FAAVLLPGMH GVAAMVVTMV AIFILGQLLK RTLGGQTGDT LGAAIELGEL VFLLALL
Length	247
Mol. Wt	26.386 kDa
pI	9.0 (calculated)
Extinction coefficient	20,970 - 21,470 (calc based on 3 Y, 3 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	5..246	PF02654 Cobalamin-5-phosphate synthase		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
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Structures

<beststructure> gene=cobS 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:16129933	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946520	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006613	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36561	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12150	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12150	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946520	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002049	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2070	Escherichia coli str. K-12 substr. MG1655
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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	382	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	149	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	357	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_000913:2063226..2063266 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:b1992 (EcoliWiki Page)	NCBI GEO profiles for cobS
microarray	GenExpDB:b1992 (EcoliWiki Page)	Summary of data for cobS 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 cobS Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12150	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2070	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1992
EcoGene	EcoGene:EG12150	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002049	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006613	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
Shigella flexneri	COBS	From SHIGELLACYC
E. coli O157	COBS	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)	PF02654 Cobalamin-5-phosphate synthase
EcoCyc	EcoCyc:EG12150	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12150	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002049	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2070	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006613	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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↑ ^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 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 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).

cobS: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 cobS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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