rlmN:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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<protect>

Standard Name

rlmN

Gene Synonym(s)

ECK2513, b2517, JW2501, yfgB[1], JW2501, yfgB

Product Desc.

predicted enzyme[2][3]

Product Synonyms(s)

predicted enzyme[1], B2517[2][1], YfgB[2][1] , ECK2513, JW2501, yfgB, b2517

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression
Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

rlmN

Mnemonic

rRNA large-subunit methylation

Synonyms

ECK2513, b2517, JW2501, yfgB[1], JW2501, yfgB

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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

56.93 minutes 

MG1655: 2642305..2641151
<gbrowseImage> name=NC_000913:2641151..2642305 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2526956..2528110
<gbrowseImage> name=NC_012759:2526956..2528110 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2642939..2641785
<gbrowseImage> name=NC_007779:2641785..2642939 source=W3110 preset=GeneLocation </gbrowseImage>

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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

ΔyfgB (Keio:JW2501)

deletion

deletion

PMID:16738554

Shigen
CGSC9992[4]

yfgB::Tn5KAN-I-SceI (FB20783)

Insertion at nt 617 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20838

contains pKD46

yfgB::Tn5KAN-I-SceI (FB20783)

Insertion at nt 617 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20839

does not contain pKD46

ΔyfgB763::kan

PMID:16738554

CGSC:104754


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Notes

Genetic Interactions

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<protect>

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

JW2501

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGAACAATTAGTCACACC

Primer 2:CCGACCGCTTTAATGTCGATGGC

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[4]

est. P1 cotransduction: 12% [5]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[4]

est. P1 cotransduction: 44% [5]
Synonyms:zff-208::Tn10

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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:EG12401

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12401

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002263

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946249

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2301

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008287

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

YfgB

Synonyms

predicted enzyme[1], B2517[2][1], YfgB[2][1] , ECK2513, JW2501, yfgB, b2517

Product description

predicted enzyme[2][3]

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. 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:0005506

iron ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01849

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004383

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:0046677

response to antibiotic

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

P

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007197

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0411

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0004

F

Seeded from EcoCyc (v14.0)

complete

GO:0070475

rRNA base methylation

PMID:18025251

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 Notes References Evidence

Protein

lysS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rfaD

PMID:19402753

MALDI(Z-score):25.932326

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

infB

PMID:19402753

MALDI(Z-score):26.605010

Protein

elaB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):30.986328

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

secA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):16.723487

Protein

clpB

PMID:19402753

MALDI(Z-score):22.784016

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):9.192511

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):23.490134

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):30.179799

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.2 MALDI(Z-score):35.892124

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

fusA

PMID:19402753

MALDI(Z-score):26.914739

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):34.015328

Protein

hinT

PMID:19402753

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753

MALDI(Z-score):22.219262

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):14.946552

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.399261

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.986539

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.836453

Protein

pstB

PMID:19402753

MALDI(Z-score):28.023991

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.942739

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

nuoC

PMID:19402753

MALDI(Z-score):38.228192

Protein

recA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):35.679941

Protein

mreB

PMID:19402753

MALDI(Z-score):37.383035

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):30.745275

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):8.450310

Protein

gyrB

PMID:19402753

MALDI(Z-score):18.463811

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):37.449591

Protein

rcsB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.6

Protein

dapF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rlmL

PMID:19402753

MALDI(Z-score):27.542715

Protein

rpmA

PMID:19402753

LCMS(ID Probability):99.6

Protein

clpA

PMID:19402753

MALDI(Z-score):27.167522

Protein

ompC

PMID:19402753

MALDI(Z-score):30.094344

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):25.533076

Protein

metK

PMID:19402753

MALDI(Z-score):38.312024

Protein

skp

PMID:19402753

LCMS(ID Probability):99.6

Protein

yfiF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.671956

Protein

yhbY

PMID:19402753

LCMS(ID Probability):99.6

Protein

yhiR

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.859002

Protein

srmB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):31.809558

Protein

rnr

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.990622

Protein

infC

PMID:19402753

LCMS(ID Probability):99.6

Protein

fruR

PMID:19402753

MALDI(Z-score):24.026284

Protein

deaD

PMID:19402753

MALDI(Z-score):26.413910

Protein

rluB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):37.990218

Protein

hrpA

PMID:19402753

MALDI(Z-score):18.791775

Protein

pnp

PMID:19402753

MALDI(Z-score):28.088568

Protein

yibL

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.299484

Protein

spoT

PMID:19402753

MALDI(Z-score):25.925192

Protein

ydcP

PMID:19402753

MALDI(Z-score):21.312156

Protein

selB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):24.293550

Protein

phoR

PMID:19402753

LCMS(ID Probability):99.6

Protein

tsr

PMID:19402753

LCMS(ID Probability):99.6

Protein

wcaD

PMID:19402753

LCMS(ID Probability):99.6

Protein

melB

PMID:19402753

LCMS(ID Probability):99.6

Protein

nupX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

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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 

MSEQLVTPEN VTTKDGKINL LDLNRQQMRE FFKDLGEKPF RADQVMKWMY HYCCDNFDEM
TDINKVLRGK LKEVAEIRAP EVVEEQRSSD GTIKWAIAVG DQRVETVYIP EDDRATLCVS
SQVGCALECK FCSTAQQGFN RNLRVSEIIG QVWRAAKIVG AAKVTGQRPI TNVVMMGMGE
PLLNLNNVVP AMEIMLDDFG FGLSKRRVTL STSGVVPALD KLGDMIDVAL AISLHAPNDE
IRDEIVPINK KYNIETFLAA VRRYLEKSNA NQGRVTIEYV MLDHVNDGTE HAHQLAELLK
DTPCKINLIP WNPFPGAPYG RSSNSRIDRF SKVLMSYGFT TIVRKTRGDD IDAACGQLAG
DVIDRTKRTL RKRMQGEAID IKAV
Length

384

Mol. Wt

43.085 kDa

pI

3.5 (calculated)

Extinction coefficient

33,920 - 34,920 (calc based on 8 Y, 4 W, and 8 C residues)

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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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

119..299

PF04055 Radical SAM superfamily

PMID:19920124

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See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rlmN taxon=562,83333 </beststructure>

Models

View models at:

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See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

</protect>

Structure figures

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</protect>

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:16130442

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946249

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008287

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P36979

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12401

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12401

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946249

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002263

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2301

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

27.658+/-0.195

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.089688042

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

3887

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

544

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

1377

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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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

yfgB

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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_000913:2642285..2642325 source=MG1655 flip=1 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:b2517 (EcoliWiki Page)

NCBI GEO profiles for yfgB

microarray

GenExpDB:b2517 (EcoliWiki Page)

Summary of data for yfgB 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 (2642213..2642518) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ10; Well:D7[6]

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Notes

Accessions Related to rlmN Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12401

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2301

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2517

EcoGene

EcoGene:EG12401

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002263

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008287

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Arabidopsis thaliana

  • AT1G60230 (score: 1.000; bootstrap: 83%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0187849 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000009563 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q5JM88 (score: 1.000; bootstrap: 82%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000026897 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YFGB

From SHIGELLACYC

E. coli O157

YFGB

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF04055 Radical SAM superfamily

Superfamily (EcoliWiki Page)

SUPERFAMILY:102114

EcoCyc

EcoCyc:EG12401

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12401

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002263

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2301

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008287

Escherichia coli str. K-12 substr. MG1655

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  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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