rimO: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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Standard Name

rimO

Gene Synonym(s)

ECK0825, b0835, JW0819, yliG[1], JW0819, yliG

Product Desc.

predicted SAM-dependent methylase[2][3]

Product Synonyms(s)

predicted SAM-dependent methyltransferase[1], B0835[2][1], YliG[2][1] , ECK0825, JW0819, yliG, b0835

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rimO[2]

Regulation/Activity
Quick Links

porteco.png

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

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Notes

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Name change to rimO proposed in [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

rimO

Mnemonic

Ribosomal modification

Synonyms

ECK0825, b0835, JW0819, yliG[1], JW0819, yliG

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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

18.88 minutes 

MG1655: 877258..875933
<gbrowseImage> name=NC_000913:875933..877258 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 869262..870587
<gbrowseImage> name=NC_012967:869262..870587 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 778901..780226
<gbrowseImage> name=NC_012759:778901..780226 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 878457..877132
<gbrowseImage> name=NC_007779:877132..878457 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 931186..929861
<gbrowseImage> name=NC_010473:929861..931186 source=DH10B 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

ΔyliG (Keio:JW0819)

deletion

deletion

PMID:16738554

Shigen
CGSC8859[5]

ΔyliG::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔyliG735::kan

PMID:16738554

CGSC:105708


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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

JW0819

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCAAAGTAACTCCCCAGCC

Primer 2:CCAACCCGGCTACCCCACAAATC

1E2

Kohara Phage

Genobase

PMID:3038334

3H12

Kohara Phage

Genobase

PMID:3038334

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: 7% [6]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 1% [6]
Synonyms:zbj-1230::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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0835

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0920

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YLIG

EcoCyc (EcoliWiki Page)

ECOCYC:G6435

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945465

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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

RimO

Synonyms

predicted SAM-dependent methyltransferase[1], B0835[2][1], YliG[2][1] , ECK0825, JW0819, yliG, b0835

Product description

predicted SAM-dependent methylase[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.

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:0005575

cellular component

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020612

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01865

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005840

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:0009451

RNA modification

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005839

P

Seeded from EcoCyc (v14.0)

complete

GO:0009451

RNA modification

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013848

P

Seeded from EcoCyc (v14.0)

complete

GO:0018339

peptidyl-L-beta-methylthioaspartic acid biosynthetic process from peptidyl-aspartic acid

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01865

P

Seeded from EcoCyc (v14.0)

complete

GO:0018339

peptidyl-L-beta-methylthioaspartic acid biosynthetic process from peptidyl-aspartic acid

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005840

P

Seeded from EcoCyc (v14.0)

complete

GO:0018339

peptidyl-L-beta-methylthioaspartic acid biosynthetic process from peptidyl-aspartic acid

PMID:19736993

IDA: Inferred from Direct Assay

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:0050497

transferase activity, transferring alkylthio groups

PMID:18252828

IMP: Inferred from Mutant Phenotype

F

Seeded from EcoCyc (v14.0)

complete

GO:0050497

transferase activity, transferring alkylthio groups

PMID:19736993

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01865

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005839

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005840

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013848

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020612

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:0051539

4 iron, 4 sulfur cluster binding

PMID:19736993

IDA: Inferred from Direct Assay

F

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

rplQ

PMID:16606699

Experiment(s):EBI-1138150

Protein

rpsE

PMID:16606699

Experiment(s):EBI-1138150

Protein

nadE

PMID:16606699

Experiment(s):EBI-1138150

Protein

fur

PMID:16606699

Experiment(s):EBI-1138150

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1138150

Protein

slyB

PMID:16606699

Experiment(s):EBI-1138150

Protein

rhsA

PMID:16606699

Experiment(s):EBI-1138150

Protein

rhsC

PMID:16606699

Experiment(s):EBI-1138150

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1138150

Protein

dtd

PMID:16606699

Experiment(s):EBI-1138150

Protein

stpA

PMID:16606699

Experiment(s):EBI-1138150

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1138150

Protein

ybgA

PMID:16606699

Experiment(s):EBI-1138150

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1138150

Protein

cybC

PMID:16606699

Experiment(s):EBI-1138150

Protein

iscS

PMID:16606699

Experiment(s):EBI-1138150

Protein

uspG

PMID:16606699

Experiment(s):EBI-1138150

Protein

secA

PMID:19402753

LCMS(ID Probability):99.6

Protein

gadB

PMID:19402753

LCMS(ID Probability):99.6

Protein

clpB

PMID:19402753

LCMS(ID Probability):99.6

Protein

elaB

PMID:19402753

LCMS(ID Probability):99.6

Protein

gnd

PMID:19402753

LCMS(ID Probability):99.6

Protein

purL

PMID:19402753

LCMS(ID Probability):99.2

Protein

slyD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaN

PMID:19402753

LCMS(ID Probability):99.6

Protein

dps

PMID:19402753

LCMS(ID Probability):99.6

Protein

ybiA

PMID:19402753

LCMS(ID Probability):99.0

Protein

ydfZ

PMID:19402753

LCMS(ID Probability):99.3

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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 

MSKVTPQPKI GFVSLGCPKN LVDSERILTE LRTEGYDVVP SYDDADMVIV NTCGFIDSAV
QESLEAIGEA LNENGKVIVT GCLGAKEDQI REVHPKVLEI TGPHSYEQVL EHVHHYVPKP
KHNPFLSLVP EQGVKLTPRH YAYLKISEGC NHRCTFCIIP SMRGDLVSRP IGEVLSEAKR
LVDAGVKEIL VISQDTSAYG VDVKHRTGFH NGEPVKTSMV SLCEQLSKLG IWTRLHYVYP
YPHVDDVIPL MAEGKILPYL DIPLQHASPR ILKLMKRPGS VDRQLARIKQ WREICPELTL
RSTFIVGFPG ETEEDFQMLL DFLKEARLDR VGCFKYSPVE GADANALPDQ VPEEVKEERW
NRFMQLQQQI SAERLQEKVG REILVIIDEV DEEGAIGRSM ADAPEIDGAV YLNGETNVKP
GDILRVKVEH ADEYDLWGSR V
Length

441

Mol. Wt

49.581 kDa

pI

5.3 (calculated)

Extinction coefficient

42,860 - 43,985 (calc based on 14 Y, 4 W, and 9 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

144..323

PF04055 Radical SAM superfamily

PMID:19920124

Domain

9..102

PF00919 Uncharacterized protein family UPF0004

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=yliG 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:16128803

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945465

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AEI4

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945465

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

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

E. coli K-12 MG1655

4329

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

718

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

1060

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)

yliG

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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_000913:877238..877278 source=MG1655 flip=1 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:b0835 (EcoliWiki Page)

NCBI GEO profiles for yliG

microarray

GenExpDB:b0835 (EcoliWiki Page)

Summary of data for yliG 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 (877160..877494) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ15; Well:E8[7]

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Notes

Accessions Related to rimO Expression

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

Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0835

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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

Apis mellifera

  • ENSAPMP00000015305 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000023511 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YLIG

From SHIGELLACYC

E. coli O157

YLIG

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

Panther (EcoliWiki Page)

PTHR11918:SF41

Superfamily (EcoliWiki Page)

SUPERFAMILY:102114

Pfam (EcoliWiki Page)

PF00919 Uncharacterized protein family UPF0004

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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 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 2.6 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. ↑ Anton, BP et al. (2008) RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 105 1826-31 PubMed
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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