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Standard Name	rdgB
Gene Synonym(s)	yggV, ECK2949, b2954, JW2921^[1]^[2], JW2921
Product Desc.	G7530^[2]^[3] dITP/XTP pyrophosphatase, synthetic lethal with recA; mutant is hyper-recombinogenic^[4]
Product Synonyms(s)	dITP/XTP pyrophosphatase^[1], B2954^[2]^[1], YggV^[2]^[1], RdgB^[2]^[1] , ECK2949, JW2921, yggV, b2954
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yggS^[2]
Regulation/Activity
Quick Links
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Notes

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2'-deoxy-N-6-hydroxylaminopurine triphosphate (dHAPTP) is a preferred substrate (Burgis, 2006). Mutations in nfi suppress the synthetic lethality.^[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	rdgB
Mnemonic	Recombination-dependent growth
Synonyms	yggV, ECK2949, b2954, JW2921^[1]^[2], JW2921
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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	66.7 minutes	MG1655: 3094703..3095296 <gbrowseImage> name=NC_000913:3094703..3095296 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2982432..2983025 <gbrowseImage> name=NC_012967:2982432..2983025 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2981851..2982444 <gbrowseImage> name=NC_012759:2981851..2982444 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3095337..3095930 <gbrowseImage> name=NC_007779:3095337..3095930 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
ΔrdgB728::kan					PMID:16738554	CGSC:106308
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
23G4S	Kohara Phage	Genobase	PMID:3038334
12C6	Kohara Phage	Genobase	PMID:3038334
3A9	Kohara Phage	Genobase	PMID:3038334
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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:G7530	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12982	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004091	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947429	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2807	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009692	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	YggV
Synonyms	dITP/XTP pyrophosphatase^[1], B2954^[2]^[1], YggV^[2]^[1], RdgB^[2]^[1] , ECK2949, JW2921, yggV, b2954
Product description	G7530^[2]^[3] dITP/XTP pyrophosphatase, synthetic lethal with recA; mutant is hyper-recombinogenic^[4]
EC number (for enzymes)	3.6.1.-^[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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	PMID:12297000	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0009143	nucleoside triphosphate catabolic process	PMID:12297000	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0009143	nucleoside triphosphate catabolic process	PMID:19943897	IGI: Inferred from Genetic Interaction		P	Seeded from EcoCyc (v14.0)	Missing: with/from
	GO:0016151	nickel ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0533	F	Seeded from EcoCyc (v14.0)	complete
	GO:0017111	nucleoside-triphosphatase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01405	F	Seeded from EcoCyc (v14.0)	complete
	GO:0017111	nucleoside-triphosphatase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020922	F	Seeded from EcoCyc (v14.0)	complete
	GO:0017111	nucleoside-triphosphatase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.6.1.15	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc (v14.0)	complete
	GO:0047429	nucleoside-triphosphate diphosphatase activity	PMID:12297000	IDA: Inferred from Direct Assay		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	visC	PMID:16606699	Experiment(s):EBI-1144430
Protein	nusG	PMID:16606699	Experiment(s):EBI-1144430
Protein	pepB	PMID:16606699	Experiment(s):EBI-1144430
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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 MQKVVLATGN VGKVRELASL LSDFGLDIVA QTDLGVDSAE ETGLTFIENA ILKARHAAKV TALPAIADDS GLAVDVLGGA PGIYSARYSG EDATDQKNLQ KLLETMKDVP DDQRQARFHC VLVYLRHAED PTPLVCHGSW PGVITREPAG TGGFGYDPIF FVPSEGKTAA ELTREEKSAI SHRGQALKLL LDALRNG
Length	197
Mol. Wt	21.038 kDa
pI	5.2 (calculated)
Extinction coefficient	11,460 - 11,710 (calc based on 4 Y, 1 W, and 2 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	4..194	PF01725 Ham1 family		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=rdgB 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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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:16130855	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947429	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009692	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P52061	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7530	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12982	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947429	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004091	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2807	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	41.471+/-0.235	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.037099494	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	1397	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	448	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	930	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)
yggS
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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_000913:3094683..3094723 source=MG1655 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:b2954 (EcoliWiki Page)	NCBI GEO profiles for rdgB
microarray	GenExpDB:b2954 (EcoliWiki Page)	Summary of data for rdgB 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 rdgB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7530	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2807	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2954
EcoGene	EcoGene:EG12982	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004091	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009692	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	ENSANGP00000019707 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000027155 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G13720 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000018301 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00040023 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00001823 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000009580 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0215619 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0031663 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21395-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000005130 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000262928 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000006769 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:96622 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000022599 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000028838 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YJR069C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC8300 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000178010 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00003704001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGGV	From SHIGELLACYC
E. coli O157	YGGV	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)	PF01725 Ham1 family
Panther (EcoliWiki Page)	PTHR11067:SF1
Superfamily (EcoliWiki Page)	SUPERFAMILY:52972
EcoCyc	EcoCyc:G7530	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12982	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004091	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2807	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009692	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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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.

rdgB: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 rdgB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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