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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	ybbO
Gene Synonym(s)	ECK0487, b0493, JW0482^[1], JW0482
Product Desc.	predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain^[1], B0493^[2]^[1], YbbO^[2]^[1] , ECK0487, JW0482, b0493
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybbO^[2]
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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Standard name	ybbO
Mnemonic	Systematic nomenclature
Synonyms	ECK0487, b0493, JW0482^[1], JW0482
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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	11.16 minutes	MG1655: 518373..517564 <gbrowseImage> name=NC_000913:517564..518373 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 491317..490508 <gbrowseImage> name=NC_012967:490508..491317 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 420323..421132 <gbrowseImage> name=NC_012759:420323..421132 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 518373..517564 <gbrowseImage> name=NC_007779:517564..518373 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 457704..456895 <gbrowseImage> name=NC_010473:456895..457704 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)	Reference	Availability
ΔybbO (Keio:JW0482)	deletion	deletion	PMID:16738554	Shigen CGSC8631^[5]
ΔybbO776::kan			PMID:16738554	CGSC:103666
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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
JW0482	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACTCATAAAGCAACGGAGAT Primer 2:CCCCCCTGCAATATTTTGTCCAT
7C12	Kohara Phage	Genobase	PMID:3038334
8E4	Kohara Phage	Genobase	PMID:3038334
gsk-3055::Tn10	Linked marker	CAG12154 = CGSC7341^[5]	est. P1 cotransduction: 56% ^[6] Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: 25% ^[6] Synonyms:purE79::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:G6269	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13262	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002877	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945337	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3050	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001709	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	YbbO
Synonyms	predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain^[1], B0493^[2]^[1], YbbO^[2]^[1] , ECK0487, JW0482, b0493
Product description	predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain^[2]^[3] Function unknown^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002198	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002198	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020904	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	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	rhsC	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	glpD	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	ybfO	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	groL	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	allB	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	rpoC	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	dadA	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	ytfN	PMID:16606699^[7]	Experiment(s):EBI-1136892
Protein	phnI	PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	ihfA	PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	hns	PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	rpoA	PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	hupA	PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	hupB	PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	rob	PMID:19402753^[8]	LCMS(ID Probability):99.6
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Notes

Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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Notes

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 MTHKATEILT GKVMQKSVLI TGCSSGIGLE SALELKRQGF HVLAGCRKPD DVERMNSMGF TGVLIDLDSP ESVDRAADEV IALTDNCLYG IFNNAGFGMY GPLSTISRAQ MEQQFSANFF GAHQLTMRLL PAMLPHGEGR IVMTSSVMGL ISTPGRGAYA ASKYALEAWS DALRMELRHS GIKVSLIEPG PIRTRFTDNV NQTQSDKPVE NPGIAARFTL GPEAVVDKVR HAFISEKPKM RYPVTLVTWA VMVLKRLLPG RVMDKILQG
Length	269
Mol. Wt	29.41 kDa
pI	9.1 (calculated)
Extinction coefficient	18,450 - 18,825 (calc based on 5 Y, 2 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
Domain	16..178	PF00106 short chain dehydrogenase		PMID:19920124^[9]
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<motif_map/>

Structure
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Structures

<beststructure> gene=ybbO 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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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:16128477	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945337	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001709	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFP4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6269	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13262	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945337	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002877	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3050	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	28.971+/-0.296	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.027812114	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	450	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	136	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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Transcription unit(s)
ybbO
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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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<gbrowseImage> name=NC_000913:518353..518393 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

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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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:b0493 (EcoliWiki Page)	NCBI GEO profiles for ybbO
microarray	GenExpDB:b0493 (EcoliWiki Page)	Summary of data for ybbO 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 ybbO Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6269	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3050	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0493
EcoGene	EcoGene:EG13262	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002877	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001709	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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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000014198 (score: 1.000; bootstrap: 53%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000005169 (score: 1.000; bootstrap: 81%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000013443 (score: 1.000; bootstrap: 55%) ENSBTAP00000023258 (score: 0.093)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00041685 (score: 1.000; bootstrap: 74%) WBGene00030887 (score: 1.000; bootstrap: 70%) WBGene00036041 (score: 1.000; bootstrap: 74%) WBGene00041240 (score: 0.179) WBGene00033287 (score: 0.164)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00000966 (score: 1.000; bootstrap: 61%) WBGene00000979 (score: 0.225) WBGene00000983 (score: 0.211) WBGene00018885 (score: 0.202)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000000083 (score: 1.000; bootstrap: 72%) ENSCAFP00000000221 (score: 0.439) ENSCAFP00000000212 (score: 0.353) ENSCAFP00000017708 (score: 0.305) ENSCAFP00000019689 (score: 0.092) ENSCAFP00000029598 (score: 0.052)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000012679 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-021115-3 (score: 1.000; bootstrap: 62%) ZDB-CDNA-040425-740 (score: 1.000; bootstrap: 61%) ZDB-CDNA-040425-2699 (score: 0.688) ZDB-GENE-040426-1759 (score: 0.688) ZDB-CDNA-050522-139 (score: 0.410) ZDB-GENE-050522-139 (score: 0.410) ZDB-GENE-040901-5 (score: 0.191)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0027583 (score: 1.000; bootstrap: 64%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000011241 (score: 1.000; bootstrap: 64%) ENSGALP00000011287 (score: 0.411) ENSGALP00000017653 (score: 0.121) ENSGALP00000008767 (score: 0.070)	From Inparanoid:20070104
Homo sapiens	ENSP00000257895 (score: 1.000; bootstrap: 57%) ENSP00000266988 (score: 0.400) ENSP00000318631 (score: 0.363) ENSP00000293502 (score: 0.334) ENSP00000316670 (score: 0.286) ENSP00000350914 (score: 0.085) ENSP00000316786 (score: 0.056)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000017380 (score: 1.000; bootstrap: 85%) ENSMMUP00000000730 (score: 0.299) ENSMMUP00000018186 (score: 0.289) ENSMMUP00000005015 (score: 0.216) ENSMMUP00000017600 (score: 0.204) ENSMMUP00000010103 (score: 0.171)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000006173 (score: 1.000; bootstrap: 52%) ENSMODP00000016114 (score: 0.492) ENSMODP00000002613 (score: 0.406) ENSMODP00000018644 (score: 0.118)	From Inparanoid:20070104
Mus musculus	MGI:2685028 (score: 1.000; bootstrap: 51%) MGI:105077 (score: 0.133)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000008612 (score: 1.000; bootstrap: 60%) ENSPTRP00000008693 (score: 0.400) ENSPTRP00000008692 (score: 0.329) ENSPTRP00000039297 (score: 0.282) ENSPTRP00000027176 (score: 0.087) ENSPTRP00000014053 (score: 0.056)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000033991 (score: 1.000; bootstrap: 59%) ENSRNOP00000026878 (score: 0.129)	From Inparanoid:20070104
Saccharomyces cerevisiae	YIL124W (score: 1.000; bootstrap: 70%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC23D31 (score: 1.000; bootstrap: 60%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000134374 (score: 1.000; bootstrap: 50%) NEWSINFRUP00000152809 (score: 0.668) NEWSINFRUP00000136645 (score: 0.459) NEWSINFRUP00000128887 (score: 0.220)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00015734001 (score: 1.000; bootstrap: 56%) GSTENP00013747001 (score: 0.370) GSTENP00022037001 (score: 0.202)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000037994 (score: 1.000; bootstrap: 60%) ENSXETP00000035399 (score: 0.433) ENSXETP00000035392 (score: 0.319) ENSXETP00000009623 (score: 0.286) ENSXETP00000009614 (score: 0.268) ENSXETP00000009610 (score: 0.256) ENSXETP00000009604 (score: 0.215) ENSXETP00000007492 (score: 0.106) ENSXETP00000007727 (score: 0.063) ENSXETP00000007485 (score: 0.063) ENSXETP00000032288 (score: 0.053)	From Inparanoid:20070104
Shigella flexneri	YBBO	From SHIGELLACYC
E. coli O157	YBBO	From ECOO157CYC
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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
Pfam (EcoliWiki Page)	PF00106 short chain dehydrogenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Panther (EcoliWiki Page)	PTHR24322:SF43
EcoCyc	EcoCyc:G6269	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13262	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002877	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3050	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001709	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 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).
↑ ^7.0 ^7.1 ^7.2 ^7.3 ^7.4 ^7.5 ^7.6 ^7.7 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 ^8.5 ^8.6 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

ybbO: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 ybbO Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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