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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	ycbX
Gene Synonym(s)	ECK0938, b0947, JW5126^[1], JW5126
Product Desc.	predicted 2Fe-2S cluster-containing protein^[2]^[3] 6-N-hydroxylaminopurine resistance, Molybdenum cofactor binding protein^[4]^[5]^[6]
Product Synonyms(s)	predicted 2Fe-2S cluster-containing protein^[1], YcbX^[2]^[1], B0947^[2]^[1] , ECK0938, JW5126, b0947
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycbX^[2]
Regulation/Activity
Quick Links
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Notes

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Molybdenum cofactor (MoCo), YcbX and YiiM are involved in the detoxification of 6-N-hydroxylaminopurine (HAP), which proceeds by a reduction to adenine (Kozmin, 2008).^[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	ycbX
Mnemonic	Systematic nomenclature
Synonyms	ECK0938, b0947, JW5126^[1], JW5126
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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	21.68 minutes	MG1655: 1006823..1005714 <gbrowseImage> name=NC_000913:1005714..1006823 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1024691..1023582 <gbrowseImage> name=NC_012967:1023582..1024691 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 908682..909791 <gbrowseImage> name=NC_012759:908682..909791 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1008022..1006913 <gbrowseImage> name=NC_007779:1006913..1008022 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1060751..1059642 <gbrowseImage> name=NC_010473:1059642..1060751 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
ΔycbX (Keio:JW5126)	deletion	deletion	PMID:16738554	Shigen CGSC11193^[7]
ΔycbX763::kan			PMID:16738554	CGSC:103940
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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
JW5126	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCGACATTAATCCGGCTTTT Primer 2:CCACGCGCCAACTTAAGTGCAGT
9E9	Kohara Phage	Genobase	PMID:3038334
E2E5	Kohara Phage	Genobase	PMID:3038334
zcb-3059::Tn10	Linked marker	CAG12094 = CGSC7358^[7]	est. P1 cotransduction: 89% ^[8]
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[7]	est. P1 cotransduction: 6% ^[8]
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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:G6487	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13716	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003087	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945563	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3480	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003206	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	YcbX
Synonyms	predicted 2Fe-2S cluster-containing protein^[1], YcbX^[2]^[1], B0947^[2]^[1] , ECK0938, JW5126, b0947
Product description	predicted 2Fe-2S cluster-containing protein^[2]^[3] 6-N-hydroxylaminopurine resistance, Molybdenum cofactor binding protein^[4]^[5]^[6]
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:IPR005302	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001041	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006058	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030151	molybdenum ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005302	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005302	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001041	F	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	cysI	PMID:15690043	Experiment(s):EBI-881190
Protein	cysJ	PMID:15690043	Experiment(s):EBI-881190, EBI-888332
Protein	cysJ	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):35.746306
Protein	cysJ	^[6]	Indirect genetic 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 MATLIRLFIH PVKSMRGIGL THALADVSGL AFDRIFMITE PDGTFITARQ FPQMVRFTPS PVHDGLHLTA PDGSSAYVRF ADFATQDAPT EVWGTHFTAR IAPDAINKWL SGFFSREVQL RWVGPQMTRR VKRHNTVPLS FADGYPYLLA NEASLRDLQQ RCPASVKMEQ FRPNLVVSGA SAWEEDRWKV IRIGDVVFDV VKPCSRCIFT TVSPEKGQKH PAGEPLKTLQ SFRTAQDNGD VDFGQNLIAR NSGVIRVGDE VEILATAPAK IYGAAAADDT ANITQQPDAN VDIDWQGQAF RGNNQQVLLE QLENQGIRIP YSCRAGICGS CRVQLLEGEV TPLKKSAMGD DGTILCCSCV PKTALKLAR
Length	369
Mol. Wt	40.644 kDa
pI	7.7 (calculated)
Extinction coefficient	40,450 - 41,575 (calc based on 5 Y, 6 W, and 9 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	291..362	PF00111 2Fe-2S iron-sulfur cluster binding domain	PMID:19920124
Domain	1..117	PF03476 MOSC N-terminal beta barrel domain	PMID:19920124
Domain	128..263	PF03473 MOSC domain	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=ycbX taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

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:16128914	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945563	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003206	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75863	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6487	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13716	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945563	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003087	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3480	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	Reference(s)
Protein	E. coli K-12 MG1655	649	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	305	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	641	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)
ycbX
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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_000913:1006803..1006843 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:b0947 (EcoliWiki Page)	NCBI GEO profiles for ycbX
microarray	GenExpDB:b0947 (EcoliWiki Page)	Summary of data for ycbX 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 ycbX Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6487	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3480	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0947
EcoGene	EcoGene:EG13716	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003087	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003206	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
Anopheles gambiae	ENSANGP00000011887 (score: 1.000; bootstrap: 99%) ENSANGP00000011906 (score: 0.315)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000005547 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G30910 (score: 1.000; bootstrap: 100%) AT5G44720 (score: 0.524)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000008440 (score: 1.000; bootstrap: 93%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00024825 (score: 1.000; bootstrap: 88%) WBGene00028864 (score: 0.397)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00018925 (score: 1.000; bootstrap: 86%) WBGene00009049 (score: 0.397) WBGene00018758 (score: 0.389)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000016681 (score: 1.000; bootstrap: 65%) ENSCAFP00000016677 (score: 0.335) ENSCAFP00000003691 (score: 0.088)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000008801 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050327-95 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050327-95 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0187811 (score: 1.000; bootstrap: 56%) DDB0169540 (score: 0.395) DDB0201869 (score: 0.143) DDB0204360 (score: 0.135)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0033451 (score: 1.000; bootstrap: 76%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA14085-PA (score: 1.000; bootstrap: 85%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000015369 (score: 1.000; bootstrap: 90%)	From Inparanoid:20070104
Homo sapiens	ENSP00000236452 (score: 1.000; bootstrap: 95%) ENSP00000263907 (score: 0.583)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000020312 (score: 1.000; bootstrap: 95%) ENSMMUP00000020310 (score: 0.326)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000005720 (score: 1.000; bootstrap: 92%) ENSMODP00000005735 (score: 0.542)	From Inparanoid:20070104
Mus musculus	MGI:1913362 (score: 1.000; bootstrap: 94%) MGI:1914497 (score: 0.376)	From Inparanoid:20070104
Oryza gramene	Q653D6 (score: 1.000; bootstrap: 100%) Q653D7 (score: 0.760)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000003357 (score: 1.000; bootstrap: 95%) ENSPTRP00000003356 (score: 0.586)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000035967 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000158258 (score: 1.000; bootstrap: 82%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00019937001 (score: 1.000; bootstrap: 89%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000005941 (score: 1.000; bootstrap: 100%) ENSXETP00000030894 (score: 0.208)	From Inparanoid:20070104
Shigella flexneri	S1013	From SHIGELLACYC
E. coli O157	Z1297	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)	PF03476 MOSC N-terminal beta barrel domain
Pfam (EcoliWiki Page)	PF03473 MOSC domain
Pfam (EcoliWiki Page)	PF00111 2Fe-2S iron-sulfur cluster binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:50800
Panther (EcoliWiki Page)	PTHR14237:SF3
Superfamily (EcoliWiki Page)	SUPERFAMILY:54292
Superfamily (EcoliWiki Page)	SUPERFAMILY:141673
EcoCyc	EcoCyc:G6487	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13716	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003087	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3480	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003206	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 ^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 Kozmin, SG et al. (2008) YcbX and yiiM, two novel determinants for resistance of Escherichia coli to N-hydroxylated base analogues. Mol. Microbiol. 68 51-65 PubMed
↑ ^6.0 ^6.1 ^6.2 Kozmin, SG et al. (2010) Role for CysJ flavin reductase in molybdenum cofactor-dependent resistance of Escherichia coli to 6-N-hydroxylaminopurine. J. Bacteriol. 192 2026-33 PubMed
↑ ^7.0 ^7.1 ^7.2 CGSC: The Coli Genetics Stock Center
↑ ^8.0 ^8.1 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).

ycbX: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 ycbX Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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