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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	rdgC
Gene Synonym(s)	ECK0388, b0393, JW0384, yaiD^[1], yaiD
Product Desc.	nonspecific DNA binding protein; nucleoid component^[2]^[3] Competitive inhibitor of RecA function; nucleoid-associated ssDNA and dsDNA binding protein; synthetic lethal with priA^[4]
Product Synonyms(s)	DNA-binding protein, non-specific^[1], B0393^[2]^[1], YaiD^[2]^[1], RdgC^[2]^[1] , ECK0388, JW0384, yaiD, b0393
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rdgC^[2]
Regulation/Activity
Quick Links
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Notes

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Growth in recBC sbcBC rdgC strains is dependent on recombination proteins.^[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	rdgC
Mnemonic	Recombination-dependent growth
Synonyms	ECK0388, b0393, JW0384, yaiD^[1], yaiD
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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	8.8 minutes	MG1655: 409243..408332 <gbrowseImage> name=NC_000913:408332..409243 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 378442..377531 <gbrowseImage> name=NC_012967:377531..378442 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 311091..312002 <gbrowseImage> name=NC_012759:311091..312002 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 409243..408332 <gbrowseImage> name=NC_007779:408332..409243 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 348574..347663 <gbrowseImage> name=NC_010473:347663..348574 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
Coding Start (SO:0000323)	MG1655	408332	Edman degradation	PMID:10368163
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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
ΔrdgC (Keio:JW0384)	deletion	deletion			PMID:16738554	Shigen CGSC8560^[5]
yaiD::Tn5KAN-I-SceI (FB20168)	Insertion at nt 339 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20168	does not contain pKD46
yaiD::Tn5KAN-I-SceI (FB20169)	Insertion at nt 339 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20169	contains pKD46
ΔyaiD::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔrdgC758::kan					PMID:16738554	CGSC:102618
rdgC	deletion		Sensitivity to	increases sensitivity to bicyclomycin	PMID:21357484		mutation didn't affect sensitivity to any of 22 other antibiotics tested. fig 2
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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
JW0384	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTGTGGTTCAAAAATTTAAT Primer 2:CCACGTTGTGCTTCGCCACCTAA
6A12	Kohara Phage	Genobase	PMID:3038334
9G9	Kohara Phage	Genobase	PMID:3038334
zai-3053::Tn10	Linked marker	CAG18091 = CGSC7336^[5]	est. P1 cotransduction: 61% ^[6] Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).
tsx-247::Tn10	Linked marker	CAG12148 = CGSC7337^[5]	est. P1 cotransduction: 42% ^[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:EG12158	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12158	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002055	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948585	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2078	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001366	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	RdgC
Synonyms	DNA-binding protein, non-specific^[1], B0393^[2]^[1], YaiD^[2]^[1], RdgC^[2]^[1] , ECK0388, JW0384, yaiD, b0393
Product description	nonspecific DNA binding protein; nucleoid component^[2]^[3] Competitive inhibitor of RecA function; nucleoid-associated ssDNA and dsDNA binding protein; synthetic lethal with priA^[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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00194	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006310	DNA recombination	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00194	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006310	DNA recombination	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007476	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006310	DNA recombination	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0233	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009295	nucleoid	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0187	C	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
Protein	prs		PMID:16606699	Experiment(s):EBI-1136445
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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
cytoplasm			From EcoCyc^[3]
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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 MLWFKNLMVY RLSREISLRA EEMEKQLASM AFTPCGSQDM AKMGWVPPMG SHSDALTHVA NGQIVICARK EEKILPSPVI KQALEAKIAK LEAEQARKLK KTEKDSLKDE VLHSLLPRAF SRFSQTMMWI DTVNGLIMVD CASAKKAEDT LALLRKSLGS LPVVPLSMEN PIELTLTEWV RSGSAAQGFQ LLDEAELKSL LEDGGVIRAK KQDLTSEEIT NHIEAGKVVT KLALDWQQRI QFVMCDDGSL KRLKFCDELR DQNEDIDRED FAQRFDADFI LMTGELAALI QNLIEGLGGE AQR
Length	303
Mol. Wt	33.994 kDa
pI	5.2 (calculated)
Extinction coefficient	28,990 - 29,615 (calc based on 1 Y, 5 W, and 5 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	2..302	PF04381 Putative exonuclease, RdgC		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=rdgC 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:16128378	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948585	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001366	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36767	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12158	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12158	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948585	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002055	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2078	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 MC4100	3.82E+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	E. coli K-12 MG1655	2964	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	681	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	1686	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)
rdgC
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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_000913:409223..409263 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:b0393 (EcoliWiki Page)	NCBI GEO profiles for rdgC
microarray	GenExpDB:b0393 (EcoliWiki Page)	Summary of data for rdgC 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 rdgC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12158	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2078	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0393
EcoGene	EcoGene:EG12158	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002055	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001366	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
Xenopus tropicalis	ENSXETP00000040126 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YAID	From SHIGELLACYC
E. coli O157	YAID	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)	PF04381 Putative exonuclease, RdgC
EcoCyc	EcoCyc:EG12158	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12158	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002055	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2078	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001366	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 ^1.8 ^1.9 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 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 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).

rdgC:On One Page

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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 rdgC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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