rlmN:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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[4]

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[5]

LCMS(ID Probability):99.6

Protein

rfaD

PMID:19402753[5]

MALDI(Z-score):25.932326

Protein

rpmC

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

infB

PMID:19402753[5]

MALDI(Z-score):26.605010

Protein

elaB

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753[5]

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

Protein

rpsJ

PMID:19402753[5]

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

Protein

rpsN

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

secA

PMID:19402753[5]

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

Protein

clpB

PMID:19402753[5]

MALDI(Z-score):22.784016

Protein

rplS

PMID:19402753[5]

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

Protein

rpsM

PMID:19402753[5]

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

Protein

rplI

PMID:19402753[5]

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

Protein

rpsD

PMID:19402753[5]

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

Protein

rpsF

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

fusA

PMID:19402753[5]

MALDI(Z-score):26.914739

Protein

rplB

PMID:19402753[5]

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

Protein

hinT

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753[5]

MALDI(Z-score):22.219262

Protein

rplX

PMID:19402753[5]

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

Protein

rplM

PMID:19402753[5]

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

Protein

rplO

PMID:19402753[5]

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

Protein

rplA

PMID:19402753[5]

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

Protein

pstB

PMID:19402753[5]

MALDI(Z-score):28.023991

Protein

rpsC

PMID:19402753[5]

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

Protein

rplT

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

nuoC

PMID:19402753[5]

MALDI(Z-score):38.228192

Protein

recA

PMID:19402753[5]

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

Protein

mreB

PMID:19402753[5]

MALDI(Z-score):37.383035

Protein

rplE

PMID:19402753[5]

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

Protein

rplR

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753[5]

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

Protein

gyrB

PMID:19402753[5]

MALDI(Z-score):18.463811

Protein

rplW

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753[5]

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

Protein

rcsB

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rplQ

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

dapF

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rlmL

PMID:19402753[5]

MALDI(Z-score):27.542715

Protein

rpmA

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

clpA

PMID:19402753[5]

MALDI(Z-score):27.167522

Protein

ompC

PMID:19402753[5]

MALDI(Z-score):30.094344

Protein

rplD

PMID:19402753[5]

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

Protein

metK

PMID:19402753[5]

MALDI(Z-score):38.312024

Protein

skp

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

yfiF

PMID:19402753[5]

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

Protein

yhbY

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

yhiR

PMID:19402753[5]

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

Protein

srmB

PMID:19402753[5]

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

Protein

rnr

PMID:19402753[5]

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

Protein

infC

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

fruR

PMID:19402753[5]

MALDI(Z-score):24.026284

Protein

deaD

PMID:19402753[5]

MALDI(Z-score):26.413910

Protein

rluB

PMID:19402753[5]

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

Protein

hrpA

PMID:19402753[5]

MALDI(Z-score):18.791775

Protein

pnp

PMID:19402753[5]

MALDI(Z-score):28.088568

Protein

yibL

PMID:19402753[5]

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

Protein

spoT

PMID:19402753[5]

MALDI(Z-score):25.925192

Protein

ydcP

PMID:19402753[5]

MALDI(Z-score):21.312156

Protein

selB

PMID:19402753[5]

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

Protein

phoR

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

tsr

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

wcaD

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

melB

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

nupX

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753[5]

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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Domains/Motifs/Modification Sites

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Type Residues Description Notes References

Domain

119..299

PF04055 Radical SAM superfamily

PMID:19920124[6]

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<motif_map/>

Structure
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Structures

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

Models

View models at:

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</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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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ Toh, SM et al. (2008) The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA 14 98-106 PubMed
  5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 5.13 5.14 5.15 5.16 5.17 5.18 5.19 5.20 5.21 5.22 5.23 5.24 5.25 5.26 5.27 5.28 5.29 5.30 5.31 5.32 5.33 5.34 5.35 5.36 5.37 5.38 5.39 5.40 5.41 5.42 5.43 5.44 5.45 5.46 5.47 5.48 5.49 5.50 5.51 5.52 5.53 5.54 5.55 5.56 5.57 5.58 5.59 5.60 5.61 5.62 5.63 5.64 5.65 5.66 5.67 5.68 5.69 5.70 5.71 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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