def: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 |
def |
|---|---|
| Gene Synonym(s) |
ECK3273, b3287, JW3248, fms[1], fms |
| Product Desc. |
Peptide deformylase; N-formylmethionylaminoacyl-tRNA deformylase[4] |
| Product Synonyms(s) |
peptide deformylase[1], B3287[2][1], Fms[2][1], Def[2][1] , ECK3273, fms, JW3248, b3287 |
| Function from GO |
<GO_nr /> |
| Knock-Out Phenotype | |
| Regulation/Expression | |
| Regulation/Activity | |
| Quick Links |
|
| edit table |
</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>
Notes
The def gene is essential unless the fmt formylase gene is also inactivated. Fe (II) is the metal co-factor in vivo (Rajagopalan et al., J. Am. Chem. Soc.,119:12418, 1997). Def was originally thought to be a zinc enzyme.[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
def |
|---|---|
| Mnemonic |
Deformylase |
| Synonyms |
ECK3273, b3287, JW3248, fms[1], fms |
| edit table |
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Notes
Location(s) and DNA Sequence
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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 |
73.96 minutes |
MG1655: 3431712..3432221 |
||
|
NC_012967: 3361595..3362104 |
||||
|
NC_012759: 3318869..3319378 |
||||
|
W3110 |
|
W3110: 4206726..4206217 |
||
|
DH10B: 3529457..3529966 |
||||
| edit table |
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Notes
Sequence Features
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) |
3431715 |
Edman degradation |
PMID:8244948 |
| |
| edit table |
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Notes
Alleles and Phenotypes
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 |
|---|---|---|---|---|---|---|---|
| edit table |
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Notes
Genetic Interactions
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| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
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Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW3248 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCTCAGTTTTGCAAGTGTTACA Primer 2:CCAGCCCGGGCTTTCAGACGATC | |
|
Linked marker |
est. P1 cotransduction: 91% [6] | ||
|
Linked marker |
est. P1 cotransduction: 1% [6] | ||
|
JM101Tr/ pUCdef |
Plasmid Clone |
PMID:8244948 | |
| edit table |
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001404 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EchoBASE:EB1410 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010779 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Product(s)
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Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
| Standard name |
Def |
|---|---|
| Synonyms |
peptide deformylase[1], B3287[2][1], Fms[2][1], Def[2][1] , ECK3273, fms, JW3248, b3287 |
| Product description |
Peptide deformylase; N-formylmethionylaminoacyl-tRNA deformylase[4] |
| EC number (for enzymes) | |
| edit table |
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Notes
Function
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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:0006412 |
translation |
GOA:hamap |
IEA: Inferred from Electronic Annotation |
HAMAP:MF_00163 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006412 |
translation |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR000181 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006412 |
translation |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0648 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0042586 |
peptide deformylase activity |
GOA:hamap |
IEA: Inferred from Electronic Annotation |
HAMAP:MF_00163 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0042586 |
peptide deformylase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR000181 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0042586 |
peptide deformylase activity |
GOA:spec |
IEA: Inferred from Electronic Annotation |
EC:3.5.1.88 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0008270 |
zinc ion binding |
PMID:11985624 |
IDA: Inferred from Direct Assay |
F |
complete | |||
|
GO:0008270 |
zinc ion binding |
PMID:8244948 |
IDA: Inferred from Direct Assay |
F |
complete | |||
|
GO:0042586 |
peptide deformylase activity |
PMID:7896716 |
IDA: Inferred from Direct Assay |
F |
complete | |||
|
GO:0008270 |
zinc ion binding |
PMID:7896716 |
IDA: Inferred from Direct Assay |
F |
complete | |||
|
GO:0016787 |
hydrolase activity |
PMID:7896716 |
IDA: Inferred from Direct Assay |
F |
complete | |||
|
GO:0031365 |
N-terminal protein amino acid modification |
PMID:7896716 |
IDA: Inferred from Direct Assay |
P |
complete | |||
| edit table |
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 |
rplD |
PMID:15690043 |
Experiment(s):EBI-880244 | |
|
Protein |
usg |
PMID:15690043 |
Experiment(s):EBI-883708 | |
|
Protein |
yaeB |
PMID:16606699 |
Experiment(s):EBI-1145366 | |
|
Protein |
usg |
PMID:19402753 |
LCMS(ID Probability):99.0 | |
|
Small Molecule |
1,10 phenanthroline |
inhibitor |
PMID:7896716 |
kinetic assay |
| edit table |
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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 |
|---|---|---|---|---|
| edit table |
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Notes
Structure and Physical Properties
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Physical Properties
See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE LEADGLLAIC IQHEMDHLVG KLFMDYLSPL KQQRIRQKVE KLDRLKARA |
| Length |
169 |
| Mol. Wt |
19.328 kDa |
| pI |
5.2 (calculated) |
| Extinction coefficient |
2,980 - 3,230 (calc based on 2 Y, 0 W, and 2 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
| </protect>
Structure figures<protect> | ||||||
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
| Resource type | Source | Notes/Reference |
|---|---|---|
| edit table |
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
ASAP:ABE-0010779 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EcoCyc:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120001404 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1410 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
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
| Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
|---|---|---|---|---|---|---|---|
|
Protein |
E. coli K-12 MC4100 |
1.68E+03 |
molecules/cell |
|
emPAI |
PMID:18304323 | |
|
Protein |
Ecoli K-12 |
52.034+/-0.493 |
Molecules/cell |
|
Single Molecule Fluorescence |
PMID:20671182 | |
|
mRNA |
Ecoli K-12 |
0.235756385 |
Molecules/cell |
|
by RNA_Seq |
PMID:20671182 | |
|
Protein |
E. coli K-12 MG1655 |
3887 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
673 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
2246 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
| edit table |
Notes
Transcription and Transcriptional Regulation
<protect>
|
See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
|
 Figure courtesy of RegulonDB |
</protect>
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
<protect><gbrowseImage>
name=NC_000913:3431692..3431732
source=MG1655
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
</protect>
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
<protect>
Mutations Affecting Expression
See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.
| Allele Name | Mutation | Phenotype | Reference |
|---|---|---|---|
| edit table |
Expression Studies
See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.
| Type | Reference | Notes |
|---|---|---|
|
microarray |
NCBI GEO profiles for def | |
|
microarray |
Summary of data for def from multiple microarray studies | |
| edit table |
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 (3431115..3431347) fused to gfpmut2. |
GFP fusion described in Zaslaver, et al. | ||
| edit table |
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Notes
Accessions Related to def Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1410 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001404 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010779 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Evolution
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Homologs in Other Organisms
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.
| Organism | Homologs (Statistics) | Comments |
|---|---|---|
|
Anopheles gambiae |
|
From Inparanoid:20070104 |
|
Apis mellifera |
|
From Inparanoid:20070104 |
|
Arabidopsis thaliana |
|
From Inparanoid:20070104 |
|
Bos taurus |
|
From Inparanoid:20070104 |
|
Canis familiaris |
|
From Inparanoid:20070104 |
|
Danio rerio |
|
From Inparanoid:20070104 |
|
Dictyostelium discoideum |
|
From Inparanoid:20070104 |
|
Drosophila melanogaster |
|
From Inparanoid:20070104 |
|
Drosophila pseudoobscura |
|
From Inparanoid:20070104 |
|
Monodelphis domestica |
|
From Inparanoid:20070104 |
|
Oryza gramene |
|
From Inparanoid:20070104 |
|
Rattus norvegicus |
|
From Inparanoid:20070104 |
|
Takifugu rubripes |
|
From Inparanoid:20070104 |
|
Tetraodon nigroviridis |
|
From Inparanoid:20070104 |
|
Xenopus tropicalis |
|
From Inparanoid:20070104 |
|
Shigella flexneri |
DEF |
From SHIGELLACYC |
|
E. coli O157 |
DEF |
From ECOO157CYC |
| edit table |
Do-It-Yourself Web Tools
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Notes
Families
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11440 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001404 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1410 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010779 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
<protect></protect>
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 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
- ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 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.
- ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
- ↑ 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).
- ↑ Meinnel, T & Blanquet, S (1993) Evidence that peptide deformylase and methionyl-tRNA(fMet) formyltransferase are encoded within the same operon in Escherichia coli. J. Bacteriol. 175 7737-40 PubMed
- ↑ Meinnel, T & Blanquet, S (1995) Enzymatic properties of Escherichia coli peptide deformylase. J. Bacteriol. 177 1883-7 PubMed
- ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed
Categories
- Genes in OpenBioSystems with Promoter Fusions
- Genes with homologs in Anopheles gambiae
- Genes with homologs in Apis mellifera
- Genes with homologs in Arabidopsis thaliana
- Genes with homologs in Bos taurus
- Genes with homologs in Canis familiaris
- Genes with homologs in Danio rerio
- Genes with homologs in Dictyostelium discoideum
- Genes with homologs in Drosophila melanogaster
- Genes with homologs in Drosophila pseudoobscura
- Genes with homologs in Monodelphis domestica
- Genes with homologs in Oryza gramene
- Genes with homologs in Rattus norvegicus
- Genes with homologs in Takifugu rubripes
- Genes with homologs in Tetraodon nigroviridis
- Genes with homologs in Xenopus tropicalis
- Genes with homologs in Shigella flexneri
- Genes with homologs in E. coli O157
