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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	rlmL
Gene Synonym(s)	ycbY, ECK0939, b0948, JW0931^[1]^[2], JW0931
Product Desc.	23S rRNA m²G2445 methyltransferase^[2]^[3] 23S rRNA mG2445 methyltransferase, SAM-dependent^[4]
Product Synonyms(s)	predicted methyltransferase^[1], YcbY^[2]^[1], B0948^[2]^[1], RlmL^[2]^[1] , ECK0939, JW0931, ycbY, b0948
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rlmL-uup^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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rlmL is a non-essential gene co-transcribed with downstream uup gene. RlmL methyltransferase mutants have a disadvantage in competitve growth cultures with wild type (Lesnyk, 2006).^[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	rlmL
Mnemonic	rRNA large-subunit methylation
Synonyms	ycbY, ECK0939, b0948, JW0931^[1]^[2], JW0931
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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	21.71 minutes	MG1655: 1007067..1009175 <gbrowseImage> name=NC_000913:1007067..1009175 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1024935..1027043 <gbrowseImage> name=NC_012967:1024935..1027043 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 910035..912143 <gbrowseImage> name=NC_012759:910035..912143 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1008266..1010374 <gbrowseImage> name=NC_007779:1008266..1010374 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1060995..1063103 <gbrowseImage> name=NC_010473:1060995..1063103 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)	Phenotype: Type	Phenotype: Description	Reference	Availability
δycbY::kan	deletion	Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔycbY::kan	deletion	Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔrlmL764::kan				PMID:16738554	CGSC:106316
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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:
9E9	Kohara Phage	Genobase	PMID:3038334
E2E5	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:G6488	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13717	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003088	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945564	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3481	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003211	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	RlmL
Synonyms	predicted methyltransferase^[1], YcbY^[2]^[1], B0948^[2]^[1], RlmL^[2]^[1] , ECK0939, JW0931, ycbY, b0948
Product description	23S rRNA m²G2445 methyltransferase^[2]^[3] 23S rRNA mG2445 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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002296	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01858	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017244	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:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:17010378	IC: Inferred by Curator	GO:0008990	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008990	rRNA (guanine-N2-)-methyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01858	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008990	rRNA (guanine-N2-)-methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017244	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:0031167	rRNA methylation	PMID:17010378	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0070475	rRNA base methylation	PMID:17010378	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	ynbC	PMID:15690043	Experiment(s):EBI-886140
Protein	rplA	PMID:15690043	Experiment(s):EBI-886140
Protein	yfiF	PMID:15690043	Experiment(s):EBI-886140, EBI-879491
Protein	rplA	PMID:16606699	Experiment(s):EBI-1138445
Protein	rpsC	PMID:16606699	Experiment(s):EBI-1138445
Protein	ygfJ	PMID:16606699	Experiment(s):EBI-1138445
Protein	nadE	PMID:16606699	Experiment(s):EBI-1138445
Protein	napC	PMID:16606699	Experiment(s):EBI-1138445
Protein	rplB	PMID:16606699	Experiment(s):EBI-1138445
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1138445
Protein	fdnG	PMID:16606699	Experiment(s):EBI-1138445
Protein	rpsG	PMID:16606699	Experiment(s):EBI-1138445
Protein	rpsD	PMID:16606699	Experiment(s):EBI-1138445
Protein	appY	PMID:16606699	Experiment(s):EBI-1138445
Protein	rsuA	PMID:16606699	Experiment(s):EBI-1138445
Protein	rplC	PMID:16606699	Experiment(s):EBI-1138445
Protein	lsrK	PMID:16606699	Experiment(s):EBI-1138445
Protein	yfgI	PMID:16606699	Experiment(s):EBI-1138445
Protein	rplQ	PMID:16606699	Experiment(s):EBI-1138445
Protein	rplA	PMID:19402753	MALDI(Z-score):33.144073
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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 MNSLFASTAR GLEELLKTEL ENLGAVECQV VQGGVHFKGD TRLVYQSLMW SRLASRIMLP LGECKVYSDL DLYLGVQAIN WTEMFNPGAT FAVHFSGLND TIRNSQYGAM KVKDAIVDAF TRKNLPRPNV DRDAPDIRVN VWLHKETASI ALDLSGDGLH LRGYRDRAGI APIKETLAAA IVMRSGWQPG TPLLDPMCGS GTLLIEAAML ATDRAPGLHR GRWGFSGWAQ HDEAIWQEVK AEAQTRARKG LAEYSSHFYG SDSDARVIQR ARTNARLAGI GELITFEVKD VAQLTNPLPK GPYGTVLSNP PYGERLDSEP ALIALHSLLG RIMKNQFGGW NLSLFSASPD LLSCLQLRAD KQYKAKNGPL DCVQKNYHVA ESTPDSKPAM VAEDYTNRLR KNLKKFEKWA RQEGIECYRL YDADLPEYNV AVDRYADWVV VQEYAPPKTI DAHKARQRLF DIIAATISVL GIAPNKLVLK TRERQKGKNQ YQKLGEKGEF LEVTEYNAHL WVNLTDYLDT GLFLDHRIAR RMLGQMSKGK DFLNLFSYTG SATVHAGLGG ARSTTTVDMS RTYLEWAERN LRLNGLTGRA HRLIQADCLA WLREANEQFD LIFIDPPTFS NSKRMEDAFD VQRDHLALMK DLKRLLRAGG TIMFSNNKRG FRMDLDGLAK LGLKAQEITQ KTLSQDFARN RQIHNCWLIT AA
Length	702
Mol. Wt	78.856 kDa
pI	9.1 (calculated)
Extinction coefficient	109,780 - 110,780 (calc based on 22 Y, 14 W, and 8 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	56..154	PF02926 THUMP domain	PMID:19920124
Domain	162..376	PF01170 Putative RNA methylase family UPF0020	PMID:19920124
Domain	427..669	PF10672 S-adenosylmethionine-dependent methyltransferase	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=rlmL taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16128915	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945564	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003211	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75864	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6488	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13717	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945564	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003088	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3481	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	0.418+/-0.04	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.034155598	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	1759	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	312	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	1006	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)
rlmL-uup
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Figure courtesy of RegulonDB

</protect>

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_000913:1007047..1007087 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b0948 (EcoliWiki Page)	NCBI GEO profiles for rlmL
microarray	GenExpDB:b0948 (EcoliWiki Page)	Summary of data for rlmL 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 rlmL Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6488	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3481	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0948
EcoGene	EcoGene:EG13717	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003088	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003211	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
Takifugu rubripes	NEWSINFRUP00000176149 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000136807 (score: 0.094)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00018665001 (score: 1.000; bootstrap: 100%) GSTENP00027309001 (score: 0.062)	From Inparanoid:20070104
Shigella flexneri	YCBY	From SHIGELLACYC
E. coli O157	YCBY	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
Panther (EcoliWiki Page)	PTHR18895:SF28
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
Pfam (EcoliWiki Page)	PF02926 THUMP domain
Pfam (EcoliWiki Page)	PF01170 Putative RNA methylase family UPF0020
Pfam (EcoliWiki Page)	PF10672 S-adenosylmethionine-dependent methyltransferase
EcoCyc	EcoCyc:G6488	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13717	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003088	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3481	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003211	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)
↑ ^2.00 ^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.

rlmL: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 rlmL Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

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