frmA: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

frmA

Gene Synonym(s)

ECK0353, b0356, JW0347, adhC[1], adhC

Product Desc.

FrmA[2][3];

Component of formaldehyde dehydrogenase, glutathione-dependent[2][3]

Product Synonyms(s)

alcohol dehydrogenase class III/glutathione-dependent formaldehyde dehydrogenase[1], B0356[2][1], AdhC[2][1] , adhC, ECK0353, JW0347, b0356

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): frmB[2]

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

frmA

Mnemonic

Formaldehyde

Synonyms

ECK0353, b0356, JW0347, adhC[1], adhC

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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

8.14 minutes 

MG1655: 378795..377686
<gbrowseImage> name=NC_000913:377686..378795 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 351928..350819
<gbrowseImage> name=NC_012967:350819..351928 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 280445..281554
<gbrowseImage> name=NC_012759:280445..281554 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 378795..377686
<gbrowseImage> name=NC_007779:377686..378795 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 318126..317017
<gbrowseImage> name=NC_010473:317017..318126 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

Coding Start (SO:0000323)

MG1655

377686

Edman degradation

PMID:1731906


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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

frmA(del) (Keio:JW0347)

deletion

deletion

PMID:16738554

Shigen

CGSC8536[4]

frmA726(del)::kan

PMID:16738554

CGSC:101010


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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

JW0347

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAATCACGTGCTGCCGTTGC

Primer 2:CCGTAACGAATTACGGTTCGAAT

8F10

Kohara Phage

Genobase

PMID:3038334

mhpC281::Tn10

Linked marker

CAG12080 = CGSC7333[4]

est. P1 cotransduction: 80% [5]
Synonyms:zah-281::Tn10

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[4]

est. P1 cotransduction: 55% [5]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

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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:EG50010

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG50010

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002569

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944988

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4303

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001221

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

FrmA

Synonyms

alcohol dehydrogenase class III/glutathione-dependent formaldehyde dehydrogenase[1], B0356[2][1], AdhC[2][1] , adhC, ECK0353, JW0347, b0356

Product description

FrmA[2][3];

Component of formaldehyde dehydrogenase, glutathione-dependent[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:0005737

cytoplasm

PMID:1731906

IDA: Inferred from Direct Assay

C

complete

GO:0004024

alcohol dehydrogenase activity, zinc-dependent

PMID:1731906

IDA: Inferred from Direct Assay

F

complete

GO:0008270

zinc ion binding

PMID:1731906

IDA: Inferred from Direct Assay

F

complete

GO:0051903

S-(hydroxymethyl)glutathione dehydrogenase activity

PMID:1731906

IDA: Inferred from Direct Assay

F

complete

GO:0042803

protein homodimerization activity

PMID:1731906

IDA: Inferred from Direct Assay

F

complete

GO:0046294

formaldehyde catabolic process

PMID:1731906

IMP: Inferred from Mutant Phenotype

P

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006069

ethanol oxidation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014183

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014183

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0051903

S-(hydroxymethyl)glutathione dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014183

F

Seeded from EcoCyc (v14.0)

complete

GO:0051903

S-(hydroxymethyl)glutathione dehydrogenase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.284

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014183

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

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

Subunits of formaldehyde dehydrogenase, glutathione-dependent

could be indirect

Protein

rhlE

PMID:16606699

Experiment(s):EBI-1136364

Protein

yjiR

PMID:16606699

Experiment(s):EBI-1136364

Protein

glpD

PMID:16606699

Experiment(s):EBI-1136364
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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

cytoplasm

From EcoCyc[3]


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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 

MKSRAAVAFA PGKPLEIVEI DVAPPKKGEV LIKVTHTGVC HTDAFTLSGD DPEGVFPVVL
GHEGAGVVVE VGEGVTSVKP GDHVIPLYTA ECGECEFCRS GKTNLCVAVR ETQGKGLMPD
GTTRFSYNGQ PLYHYMGCST FSEYTVVAEV SLAKINPEAN HEHVCLLGCG VTTGIGAVHN
TAKVQPGDSV AVFGLGAIGL AVVQGARQAK AGRIIAIDTN PKKFDLARRF GATDCINPND
YDKPIKDVLL DINKWGIDHT FECIGNVNVM RAALESAHRG WGQSVIIGVA VAGQEISTRP
FQLVTGRVWK GSAFGGVKGR SQLPGMVEDA MKGDIDLEPF VTHTMSLDEI NDAFDLMHEG
KSIRTVIRY
Length

369

Mol. Wt

39.357 kDa

pI

6.2 (calculated)

Extinction coefficient

26,930 - 28,180 (calc based on 7 Y, 3 W, and 10 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

197..332

PF00107 Zinc-binding dehydrogenase

PMID:19920124

Domain

27..155

PF08240 Alcohol dehydrogenase GroES-like domain

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=frmA taxon=12017 </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:16128341

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944988

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001221

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P25437

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG50010

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG50010

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944988

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002569

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4303

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

28.569+/-0.397

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

Protein

E. coli K-12 MG1655

4204

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

736

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

1558

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)

frmB

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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_000913:378775..378815 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:b0356 (EcoliWiki Page)

NCBI GEO profiles for frmA

microarray

GenExpDB:b0356 (EcoliWiki Page)

Summary of data for frmA 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 frmA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG50010

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4303

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0356

EcoGene

EcoGene:EG50010

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002569

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001221

Escherichia coli str. K-12 substr. MG1655

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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

  • ENSANGP00000020590 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000008775 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G43940 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000021304 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00037404 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00019240 (score: 1.000; bootstrap: 100%)
  • WBGene00021747 (score: 0.662)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000003403 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000015354 (score: 0.884)
  • ENSCAFP00000019163 (score: 0.528)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000017484 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-011003-1 (score: 1.000; bootstrap: 99%)
  • ZDB-CDNA-040425-11 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0204255 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0011768 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA19711-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000031489 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000019981 (score: 0.096)
  • ENSGALP00000019980 (score: 0.058)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000296412 (score: 1.000; bootstrap: 99%)
  • ENSP00000311351 (score: 0.848)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000004729 (score: 1.000; bootstrap: 99%)
  • ENSMMUP00000008134 (score: 0.407)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000025910 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000025908 (score: 0.425)
  • ENSMODP00000025912 (score: 0.316)
  • ENSMODP00000025905 (score: 0.301)

From Inparanoid:20070104

Mus musculus

  • MGI:87929 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Oryza gramene

  • P93629 (score: 1.000; bootstrap: 99%)
  • P93436 (score: 1.000; bootstrap: 99%)
  • Q6K6C1 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000028003 (score: 1.000; bootstrap: 99%)
  • ENSPTRP00000031308 (score: 0.831)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000031961 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDL168W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC13B114c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000162068 (score: 1.000; bootstrap: 99%)
  • NEWSINFRUP00000155510 (score: 0.558)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00010274001 (score: 1.000; bootstrap: 100%)
  • GSTENP00024391001 (score: 0.077)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000016720 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

ADHC

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)

PF00107 Zinc-binding dehydrogenase

Superfamily (EcoliWiki Page)

SUPERFAMILY:50129

Superfamily (EcoliWiki Page)

SUPERFAMILY:51735

Panther (EcoliWiki Page)

PTHR11695:SF4

Pfam (EcoliWiki Page)

PF08240 Alcohol dehydrogenase GroES-like domain

EcoCyc

EcoCyc:EG50010

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG50010

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002569

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4303

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001221

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 1.8 1.9 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 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 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).

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