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Gene |

Product(s) |

Expression|

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Standard Name	rcsD
Gene Synonym(s)	ECK2209, b2216, JW2204, yojN, yojP, yojQ^[1], yojQ
Product Desc.	putative 2-component sensor protein^[2]^[3] Intermediate facilitates phosphotransfer from rcsC to rcsB; histidine protein kinase^[4]
Product Synonyms(s)	phosphotransfer intermediate protein in two-component regulatory system with RcsBC^[1], B2216^[2]^[1], YojQ^[2]^[1], YojP^[2]^[1], RcsD^[2]^[1], YojN^[2]^[1] , ECK2209, JW2204, yojN, yojP, yojQ, b2216
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
Regulation/Activity
Quick Links
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Notes

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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	rcsD
Mnemonic	Regulator of capsule synthesis
Synonyms	ECK2209, b2216, JW2204, yojN, yojP, yojQ^[1], yojQ
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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	49.82 minutes, 49.82 minutes	MG1655: 2311510..2314182 <gbrowseImage> name=NC_000913:2311510..2314182 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2197315..2199987 <gbrowseImage> name=NC_012759:2197315..2199987 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2316822..2319494 <gbrowseImage> name=NC_007779:2316822..2319494 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2402498..2405170 <gbrowseImage> name=NC_010473:2402498..2405170 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)	Phenotype: Description	Reference	Availability	Comments
ΔrcsD (Keio:JW2204)	deletion	deletion		PMID:16738554	Shigen CGSC9782^[5]
yojN::Tn5KAN-I-SceI (FB20712)	Insertion at nt 1739 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20712	contains pKD46
yojNH842R		H842R	Unable to complement deletion of yojN			seeded from UniProt:P39838
ΔrcsD1332					CGSC:77147
ΔrcsD769::kan				PMID:16738554	CGSC:102614
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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
JW2204	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTCAGAAAGAGACAACGGC Primer 2:CCaAGCAAGCTCTTGACATAACT
22A6	Kohara Phage	Genobase	PMID:3038334
5A1	Kohara Phage	Genobase	PMID:3038334
napA722::Tn10	Linked marker	CAG12098 = CGSC7400^[5]	est. P1 cotransduction: 70% ^[6] Synonyms:zeg-722, zei-722::Tn10
atoS298::Tn10	Linked marker	CAG12177 gyrA+ = CGSC7525^[5]	est. P1 cotransduction: 75% ^[6] Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).
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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:EG12385	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12385	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002250	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946717	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2286	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007330	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	RcsD
Synonyms	phosphotransfer intermediate protein in two-component regulatory system with RcsBC^[1], B2216^[2]^[1], YojQ^[2]^[1], YojP^[2]^[1], RcsD^[2]^[1], YojN^[2]^[1] , ECK2209, JW2204, yojN, yojP, yojQ, b2216
Product description	putative 2-component sensor protein^[2]^[3] Intermediate facilitates phosphotransfer from rcsC to rcsB; histidine protein kinase^[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:0000155	two-component sensor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005467	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008207	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0902	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004673	protein histidine kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005467	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004673	protein histidine kinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.13.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004871	signal transducer activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008207	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003594	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0007165	signal transduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005467	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016301	kinase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0418	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0018106	peptidyl-histidine phosphorylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005467	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
Protein	yebS		PMID:16606699	Experiment(s):EBI-1142203
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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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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 MRQKETTATT RFSLLPGSIT RFFLLLIIVL LVTMGVMVQS AVNAWLKDKS YQIVDITHAI QKRVDNWRYV TWQIYDNIAA TTSPSSGEGL QETRLKQDVY YLEKPRRKTE ALIFGSHDNS TLEMTQRMST YLDTLWGAEN VPWSMYYLNG QDNSLVLIST LPLKDLTSGF KESTVSDIVD SRRAEMLQQA NALDERESFS NMRRLAWQNG HYFTLRTTFN QPGHLATVVA FDLPINDLIP PGMPLDSFRL EPDATATGNN DNEKEGTDSV SIHFNSTKIE ISSALNSTDM RLVWQVPYGT LLLDTLQNIL LPLLLNIGLL ALALFGYTTF RHFSSRSTEN VPSTAVNNEL RILRAINEEI VSLLPLGLLV HDQESNRTVI SNKIADHLLP HLNLQNITTM AEQHQGIIQA TINNELYEIR MFRSQVAPRT QIFIIRDQDR EVLVNKKLKQ AQRLYEKNQQ GRMIFMKNIG DALKEPAQSL AESAAKLNAP ESKQLANQAD VLVRLVDEIQ LANMLADDSW KSETVLFSVQ DLIDEVVPSV LPAIKRKGLQ LLINNHLKAH DMRRGDRDAL RRILLLLMQY AVTSTQLGKI TLEVDQDESS EDRLTFRILD TGEGVSIHEM DNLHFPFINQ TQNDRYGKAD PLAFWLSDQL ARKLGGHLNI KTRDGLGTRY SVHIKMLAAD PEVEEEEERL LDDVCVMVDV TSAEIRNIVT RQLENWGATC ITPDERLISQ DYDIFLTDNP SNLTASGLLL SDDESGVREI GPGQLCVNFN MSNAMQEAVL QLIEVQLAQE EVTESPLGGD ENAQLHASGY YALFVDTVPD DVKRLYTEAA TSDFAALAQT AHRLKGVFAM LNLVPGKQLC ETLEHLIREK DVPGIEKYIS DIDSYVKSLL
Length	890
Mol. Wt	100.374 kDa
pI	5.0 (calculated)
Extinction coefficient	87,780 - 88,280 (calc based on 22 Y, 10 W, and 4 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	565..677	PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	PMID:19920124
Domain	809..890	PF01627 Hpt 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=rcsD taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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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:16130153	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946717	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007330	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39838	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12385	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12385	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946717	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002250	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2286	Escherichia coli str. K-12 substr. MG1655
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Notes

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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	13.419+/-0.085	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
Protein	E. coli K-12 MG1655	287	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	179	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	187	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)
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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_000913:2311490..2311530 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:b2216 (EcoliWiki Page)	NCBI GEO profiles for rcsD
microarray	GenExpDB:b2216 (EcoliWiki Page)	Summary of data for rcsD 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 rcsD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12385	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2286	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2216
EcoGene	EcoGene:EG12385	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002250	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007330	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	YOJN	From SHIGELLACYC
E. coli O157	YOJN	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)	PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
Pfam (EcoliWiki Page)	PF01627 Hpt domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:47226
Superfamily (EcoliWiki Page)	SUPERFAMILY:55874
EcoCyc	EcoCyc:EG12385	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12385	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002250	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2286	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007330	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 ^1.12 ^1.13 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 ^2.11 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).

rcsD: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 rcsD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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