trmI:On One Page

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

Quickview

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Standard Name

trmI

Gene Synonym(s)

yggH, ECK2955, b2960, JW2927, trmB[1][2][3], trmB?

Product Desc.

tRNA (m7G46) methyltransferase[3][2]

tRNA (m7G46) methyltransferase, SAM-dependent; monomeric[4]

Product Synonyms(s)

tRNA (m7G46) methyltransferase, SAM-dependent[1], B2960[3][1], YggH[3][1], TrmB[3][1], TrmI[2][1] , ECK2955, JW2927, trmB?, yggH, b2960

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yggL[3]

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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yggH is renamed trmI in Bjork and Hagervall's EcoSal Module 4.6.2. trmI is a non-essential gene. Although trmB was mapped to 6', trmI is at 66'; trmB may be regulator of the structural gene trmI, although it is also being used as a synonym of trmI(yggH). AFMB Structural Genomics target No. 128 (http://afmb.cnrs-mrs.fr/article171.html).[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

trmI

Mnemonic

tRNA methyltransferase

Synonyms

yggH, ECK2955, b2960, JW2927, trmB[1][2][3], trmB?

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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

66.82 minutes 

MG1655: 3100874..3100155
<gbrowseImage> name=NC_000913:3100155..3100874 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2987794..2988513
<gbrowseImage> name=NC_012967:2987794..2988513 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2987303..2988022
<gbrowseImage> name=NC_012759:2987303..2988022 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3101508..3100789
<gbrowseImage> name=NC_007779:3100789..3101508 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3195943..3195224
<gbrowseImage> name=NC_010473:3195224..3195943 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

trmBN152A

N152A

No effect

seeded from UniProt:P0A8I5

trmBE220A

E220A

Reduces catalytic activity 10-fold

seeded from UniProt:P0A8I5

trmBR150A

R150A

Reduces catalytic activity about 3- fold

seeded from UniProt:P0A8I5

trmBR155A

R155A

Loss of activity

seeded from UniProt:P0A8I5

trmBD180A

D180A

Reduces catalytic activity over 10- fold

seeded from UniProt:P0A8I5

trmBH151A

H151A

Reduces catalytic activity over 10- fold

seeded from UniProt:P0A8I5

trmBT217A

T217A

Reduces catalytic activity over 10- fold

seeded from UniProt:P0A8I5

trmBR26A

R26A

Reduces catalytic activity over 10- fold

seeded from UniProt:P0A8I5

trmBD144A

D144A

Loss of activity

seeded from UniProt:P0A8I5

trmBR154A

R154A

Loss of activity

seeded from UniProt:P0A8I5

ΔyggH735::kan

PMID:16738554

CGSC:104996

trmB1

CGSC:13081


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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:

12C6

Kohara Phage

Genobase

PMID:3038334

3A9

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:EG11779

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11779

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001713

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947448

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1727

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009714

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

YggH

Synonyms

tRNA (m7G46) methyltransferase, SAM-dependent[1], B2960[3][1], YggH[3][1], TrmB[3][1], TrmI[2][1] , ECK2955, JW2927, trmB?, yggH, b2960

Product description

tRNA (m7G46) methyltransferase[3][2]

tRNA (m7G46) methyltransferase, SAM-dependent; monomeric[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0006400

tRNA modification

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01057

P

Seeded from EcoCyc (v14.0)

complete

GO:0006400

tRNA modification

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003358

P

Seeded from EcoCyc (v14.0)

complete

GO:0008033

tRNA processing

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0819

P

Seeded from EcoCyc (v14.0)

complete

GO:0008168

methyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0489

F

Seeded from EcoCyc (v14.0)

complete

GO:0008176

tRNA (guanine-N7-)-methyltransferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01057

F

Seeded from EcoCyc (v14.0)

complete

GO:0008176

tRNA (guanine-N7-)-methyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003358

F

Seeded from EcoCyc (v14.0)

complete

GO:0008176

tRNA (guanine-N7-)-methyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.1.33

F

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

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

ybhS

PMID:16606699

Experiment(s):EBI-1144466

Protein

pheA

PMID:16606699

Experiment(s):EBI-1144466

Protein

groL

PMID:16606699

Experiment(s):EBI-1144466

Protein

aceE

PMID:15690043

Experiment(s):EBI-882273

Protein

yncD

PMID:15690043

Experiment(s):EBI-882273

Protein

deaD

PMID:15690043

Experiment(s):EBI-882273

Protein

dnaK

PMID:15690043

Experiment(s):EBI-882273

Protein

glnS

PMID:15690043

Experiment(s):EBI-882273

Protein

hrpA

PMID:15690043

Experiment(s):EBI-882273

Protein

lpdA

PMID:15690043

Experiment(s):EBI-882273

Protein

mglB

PMID:15690043

Experiment(s):EBI-882273

Protein

pssA

PMID:15690043

Experiment(s):EBI-882273

Protein

rplB

PMID:15690043

Experiment(s):EBI-882273

Protein

rplC

PMID:15690043

Experiment(s):EBI-882273

Protein

rplD

PMID:15690043

Experiment(s):EBI-882273

Protein

rplE

PMID:15690043

Experiment(s):EBI-882273

Protein

rplF

PMID:15690043

Experiment(s):EBI-882273

Protein

rplI

PMID:15690043

Experiment(s):EBI-882273

Protein

rplJ

PMID:15690043

Experiment(s):EBI-882273

Protein

rplM

PMID:15690043

Experiment(s):EBI-882273

Protein

rplS

PMID:15690043

Experiment(s):EBI-882273

Protein

rplV

PMID:15690043

Experiment(s):EBI-882273, EBI-889884

Protein

rplX

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsA

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsB

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsC

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsD

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsE

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsG

PMID:15690043

Experiment(s):EBI-882273, EBI-889884

Protein

rpsM

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsP

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsU

PMID:15690043

Experiment(s):EBI-882273

Protein

srmB

PMID:15690043

Experiment(s):EBI-882273

Protein

ybeZ

PMID:15690043

Experiment(s):EBI-882273

Protein

ycbY

PMID:15690043

Experiment(s):EBI-882273

Protein

yfiF

PMID:15690043

Experiment(s):EBI-882273

Protein

ygiF

PMID:15690043

Experiment(s):EBI-882273

Protein

ynbC

PMID:15690043

Experiment(s):EBI-882273

Protein

rpsF

PMID:15690043

Experiment(s):EBI-889884

Protein

rpsT

PMID:15690043

Experiment(s):EBI-889884

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

MALDI(Z-score):20.937463

Protein

rplM

PMID:19402753

MALDI(Z-score):29.894375

Protein

rplI

PMID:19402753

MALDI(Z-score):30.476627

Protein

rlmL

PMID:19402753

MALDI(Z-score):22.605475

Protein

rpsM

PMID:19402753

MALDI(Z-score):20.695589

Protein

ygiF

PMID:19402753

MALDI(Z-score):23.709548

Protein

srmB

PMID:19402753

MALDI(Z-score):22.178982

Protein

rpsC

PMID:19402753

MALDI(Z-score):34.335309

Protein

rpsD

PMID:19402753

MALDI(Z-score):36.279654

Protein

rplB

PMID:19402753

MALDI(Z-score):31.970126

Protein

glnS

PMID:19402753

MALDI(Z-score):17.053160

Protein

pssA

PMID:19402753

MALDI(Z-score):18.875040

Protein

rplD

PMID:19402753

MALDI(Z-score):24.245773

Protein

yfiF

PMID:19402753

MALDI(Z-score):36.673169

Protein

ybeZ

PMID:19402753

MALDI(Z-score):23.079093

Protein

deaD

PMID:19402753

MALDI(Z-score):25.207967

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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 

MKNDVISPEF DENGRPLRRI RSFVRRQGRL TKGQEHALEN YWPVMGVEFS EDMLDFPALF
GREAPVTLEI GFGMGASLVA MAKDRPEQDF LGIEVHSPGV GACLASAHEE GLSNLRVMCH
DAVEVLHKMI PDNSLRMVQL FFPDPWHKAR HNKRRIVQVP FAELVKSKLQ LGGVFHMATD
WEPYAEHMLE VMSSIDGYKN LSESNDYVPR PASRPVTKFE QRGHRLGHGV WDLMFERVK
Length

239

Mol. Wt

27.306 kDa

pI

6.9 (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

42..238

PF02390 Putative 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=trmI 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:16130861

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947448

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009714

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A8I5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11779

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11779

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947448

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001713

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1727

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

30.843+/-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

0.074408901

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

4353

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

627

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

1741

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)

yggL

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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_000913:3100854..3100894 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:b2960 (EcoliWiki Page)

NCBI GEO profiles for trmI

microarray

GenExpDB:b2960 (EcoliWiki Page)

Summary of data for trmI 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 (3100795..3101047) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ13; Well:B8[5]

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Notes

Accessions Related to trmI Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11779

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1727

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2960

EcoGene

EcoGene:EG11779

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001713

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009714

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

  • ENSANGP00000025559 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G17660 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q5JLD6 (score: 1.000; bootstrap: 100%)
  • Q7XE19 (score: 0.192)

From Inparanoid:20070104

Shigella flexneri

YGGH

From SHIGELLACYC

E. coli O157

YGGH

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)

PF02390 Putative methyltransferase

Panther (EcoliWiki Page)

PTHR23417:SF1

Superfamily (EcoliWiki Page)

SUPERFAMILY:53335

EcoCyc

EcoCyc:EG11779

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11779

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001713

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1727

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009714

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 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 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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.
  5. ↑ 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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