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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	ydbK
Gene Synonym(s)	ECK1374, b1378, JW1372, nifJ^[1]
Product Desc.	G6701^[2]^[3] Probable pyruvate-flavodoxin oxidoreductase^[4]
Product Synonyms(s)	fused predicted pyruvate-flavodoxin oxidoreductase: conserved protein^[1], conserved protein^[1], FeS binding protein^[1], B1378^[2]^[1], YdbK^[2]^[1] , ECK1374, JW1372, b1378
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydbK^[2]
Regulation/Activity
Quick Links
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Notes

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ydbK is SoxS-regulated in Salmonella. ydbK is a nifJ-like gene, with a probable iron-sulfur center. Salmonella ybdK mutant is paraquat sensitive.^[4]

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	ydbK
Mnemonic	Systematic nomenclature
Synonyms	ECK1374, b1378, JW1372, nifJ^[1]
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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	30.94 minutes	MG1655: 1438808..1435284 <gbrowseImage> name=NC_000913:1435284..1438808 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1432390..1428866 <gbrowseImage> name=NC_012967:1428866..1432390 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1327343..1330867 <gbrowseImage> name=NC_012759:1327343..1330867 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1442498..1438974 <gbrowseImage> name=NC_007779:1438974..1442498 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1529403..1525879 <gbrowseImage> name=NC_010473:1525879..1529403 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
ΔydbK (Keio:JW1372)	deletion	deletion	PMID:16738554	Shigen CGSC9214^[5]
ΔydbK741::kan			PMID:16738554	CGSC:104150
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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
JW1372	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTACTATTGACGGTAATGG Primer 2:CCATCGGTGTTGCTTTTTTCCGC
4E7	Kohara Phage	Genobase	PMID:3038334
1E7	Kohara Phage	Genobase	PMID:3038334
zhj-3076::Tn10	Linked marker	CAG18640 = CGSC7453^[5]	est. P1 cotransduction: 95% ^[6]
trg-2::Tn10	Linked marker	CAG12026 = CGSC7376^[5]	est. P1 cotransduction: 5% ^[6]
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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:G6701	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13183	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003296	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946587	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2975	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004613	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	YdbK
Synonyms	fused predicted pyruvate-flavodoxin oxidoreductase: conserved protein^[1], conserved protein^[1], FeS binding protein^[1], B1378^[2]^[1], YdbK^[2]^[1] , ECK1374, JW1372, b1378
Product description	G6701^[2]^[3] Probable pyruvate-flavodoxin oxidoreductase^[4]
EC number (for enzymes)
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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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009014	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011766	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011895	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:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009014	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002869	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002880	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:0016903	oxidoreductase activity, acting on the aldehyde or oxo group of donors	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011895	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016903	oxidoreductase activity, acting on the aldehyde or oxo group of donors	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016903	oxidoreductase activity, acting on the aldehyde or oxo group of donors	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019752	F	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030976	thiamin pyrophosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011766	F	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
	GO:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0411	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0004	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002869	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002880	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011895	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019456	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019752	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	Notes	References	Evidence
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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 MITIDGNGAV ASVAFRTSEV IAIYPITPSS TMAEQADAWA GNGLKNVWGD TPRVVEMQSE AGAIATVHGA LQTGALSTSF TSSQGLLLMI PTLYKLAGEL TPFVLHVAAR TVATHALSIF GDHSDVMAVR QTGCAMLCAA NVQEAQDFAL ISQIATLKSR VPFIHFFDGF RTSHEINKIV PLADDTILDL MPQVEIDAHR ARALNPEHPV IRGTSANPDT YFQSREATNP WYNAVYDHVE QAMNDFSAAT GRQYQPFEYY GHPQAERVII LMGSAIGTCE EVVDELLTRG EKVGVLKVRL YRPFSAKHLL QALPGSVRSV AVLDRTKEPG AQAEPLYLDV MTALAEAFNN GERETLPRVI GGRYGLSSKE FGPDCVLAVF AELNAAKPKA RFTVGIYDDV TNLSLPLPEN TLPNSAKLEA LFYGLGSDGS VSATKNNIKI IGNSTPWYAQ GYFVYDSKKA GGLTVSHLRV SEQPIRSAYL ISQADFVGCH QLQFIDKYQM AERLKPGGIF LLNTPYSADE VWSRLPQEVQ AVLNQKKARF YVINAAKIAR ECGLAARINT VMQMAFFHLT QILPGDSALA ELQGAIAKSY SSKGQDLVER NWQALALARE SVEEVPLQPV NPHSANRPPV VSDAAPDFVK TVTAAMLAGL GDALPVSALP PDGTWPMGTT RWEKRNIAEE IPIWKEELCT QCNHCVAACP HSAIRAKVVP PEAMENAPAS LHSLDVKSRD MRGQKYVLQV APEDCTGCNL CVEVCPAKDR QNPEIKAINM MSRLEHVEEE KINYDFFLNL PEIDRSKLER IDIRTSQLIT PLFEYSGACS GCGETPYIKL LTQLYGDRML IANATGCSSI YGGNLPSTPY TTDANGRGPA WANSLFEDNA EFGLGFRLTV DQHRVRVLRL LDQFADKIPA ELLTALKSDA TPEVRREQVA ALRQQLNDVA EAHELLRDAD ALVEKSIWLI GGDGWAYDIG FGGLDHVLSL TENVNILVLD TQCYSNTGGQ ASKATPLGAV TKFGEHGKRK ARKDLGVSMM MYGHVYVAQI SLGAQLNQTV KAIQEAEAYP GPSLIIAYSP CEEHGYDLAL SHDQMRQLTA TGFWPLYRFD PRRADEGKLP LALDSRPPSE APEETLLHEQ RFRRLNSQQP EVAEQLWKDA AADLQKRYDF LAQMAGKAEK SNTD
Length	1,174
Mol. Wt	128.825 kDa
pI	5.7 (calculated)
Extinction coefficient	132,130 - 134,505 (calc based on 37 Y, 14 W, and 19 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	References
Domain	426..610	PF01558 Pyruvate ferredoxin/flavodoxin oxidoreductase	PMID:19920124
Domain	12..244	PF01855 domain	PMID:19920124
Domain	940..1067	PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain	PMID:19920124
Domain	620..679	PF10371 Domain of unknown function	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=ydbK taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

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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:16129339	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946587	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004613	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P52647	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6701	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13183	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946587	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003296	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2975	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	E. coli K-12 MC4100	1.19E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	14.723+/-0.122	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.034477866	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	924	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	304	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	399	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)
ydbK
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Figure courtesy of RegulonDB

</protect>

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_000913:1438788..1438828 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b1378 (EcoliWiki Page)	NCBI GEO profiles for ydbK
microarray	GenExpDB:b1378 (EcoliWiki Page)	Summary of data for ydbK 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 ydbK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6701	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2975	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1378
EcoGene	EcoGene:EG13183	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003296	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004613	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	YDBK	From SHIGELLACYC
E. coli O157	YDBK	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)	PF01855 domain
Pfam (EcoliWiki Page)	PF01558 Pyruvate ferredoxin/flavodoxin oxidoreductase
Panther (EcoliWiki Page)	PTHR19384:SF15
Superfamily (EcoliWiki Page)	SUPERFAMILY:52518
Superfamily (EcoliWiki Page)	SUPERFAMILY:52518
Superfamily (EcoliWiki Page)	SUPERFAMILY:52922
Superfamily (EcoliWiki Page)	SUPERFAMILY:53323
Superfamily (EcoliWiki Page)	SUPERFAMILY:54862
Pfam (EcoliWiki Page)	PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
Pfam (EcoliWiki Page)	PF10371 Domain of unknown function
PFAM (EcoliWiki Page)	PFAM:PF01855
EcoCyc	EcoCyc:G6701	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13183	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003296	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2975	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004613	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 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 ^4.2 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).

ydbK:On One Page

Quickview

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 ydbK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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