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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	rsmD
Gene Synonym(s)	yhhF, ECK3449, b3465, JW3430^[1]^[2], JW3430
Product Desc.	predicted methyltransferase^[3]; 16S rRNA m²G966 methyltransferase^[2] 16S rRNA m(2)G966 methyltransferase, SAM-dependent^[4]
Product Synonyms(s)	predicted methyltransferase^[1], B3465^[3]^[1], YhhF^[3]^[1], RsmD^[2]^[1] , ECK3449, JW3430, yhhF, b3465
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yhhF^[3]
Regulation/Activity
Quick Links
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Notes

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A yhhF mutation confers a slight growth disadvantage. Modifies intact 30S subunits.^[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	rsmD
Mnemonic	Ribosomal Small subunit Methyltransferase
Synonyms	yhhF, ECK3449, b3465, JW3430^[1]^[2], JW3430
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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	77.64 minutes	MG1655: 3602416..3603012 <gbrowseImage> name=NC_000913:3602416..3603012 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3535081..3535677 <gbrowseImage> name=NC_012967:3535081..3535677 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3490910..3491506 <gbrowseImage> name=NC_012759:3490910..3491506 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4036022..4035426 <gbrowseImage> name=NC_007779:4035426..4036022 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
ΔrsmD720::kan					PMID:16738554	CGSC:106326
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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:
7H7	Kohara Phage	Genobase	PMID:3038334
1B6	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:EG10343	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10343	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000337	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947977	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0339	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011321	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	YhhF
Synonyms	predicted methyltransferase^[1], B3465^[3]^[1], YhhF^[3]^[1], RsmD^[2]^[1] , ECK3449, JW3430, yhhF, b3465
Product description	predicted methyltransferase^[3]; 16S rRNA m²G966 methyltransferase^[2] 16S rRNA m(2)G966 methyltransferase, SAM-dependent^[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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002052	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008990	rRNA (guanine-N2-)-methyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.1.1.52	F	Seeded from EcoCyc (v14.0)	complete
	GO:0070475	rRNA base methylation	PMID:17189261	IMP: Inferred from Mutant Phenotype		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	References	Evidence
Protein	ompW	PMID:16606699	Experiment(s):EBI-1145973
Protein	lldR	PMID:16606699	Experiment(s):EBI-1145973
Protein	rplB	PMID:16606699	Experiment(s):EBI-1145973
Protein	tufA	PMID:15690043	Experiment(s):EBI-883806
Protein	dnaK	PMID:15690043	Experiment(s):EBI-890983
Protein	tufB	PMID:19402753	MALDI(Z-score):24.184033
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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 MKKPNHSGSG QIRIIGGQWR GRKLPVPDSP GLRPTTDRVR ETLFNWLAPV IVDAQCLDCF AGSGALGLEA LSRYAAGATL IEMDRAVSQQ LIKNLATLKA GNARVVNSNA MSFLAQKGTP HNIVFVDPPF RRGLLEETIN LLEDNGWLAD EALIYVESEV ENGLPTVPAN WSLHREKVAG QVAYRLYQRE AQGESDAD
Length	198
Mol. Wt	21.677 kDa
pI	6.3 (calculated)
Extinction coefficient	27,960 - 28,210 (calc based on 4 Y, 4 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	12..188	PF03602 Conserved hypothetical protein 95		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=rsmD 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:16131337	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947977	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011321	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ADX9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10343	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10343	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947977	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000337	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0339	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	14.486+/-0.155	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.026845638	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	745	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	178	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	311	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)
yhhF
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File:.jpg

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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_000913:3602396..3602436 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:b3465 (EcoliWiki Page)	NCBI GEO profiles for rsmD
microarray	GenExpDB:b3465 (EcoliWiki Page)	Summary of data for rsmD 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
	GFP Fusion	Intergenic region (3601802..3602086) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:H10^[5]
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Notes

Accessions Related to rsmD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10343	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0339	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3465
EcoGene	EcoGene:EG10343	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000337	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011321	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	ENSANGP00000001003 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YHHF	From SHIGELLACYC
E. coli O157	YHHF	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)	PF03602 Conserved hypothetical protein 95
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
EcoCyc	EcoCyc:EG10343	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10343	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000337	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0339	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011321	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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 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.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rsmD: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 rsmD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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