paaF: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 |
paaF |
|---|---|
| Gene Synonym(s) |
ECK1390, b1393, JW1388, ydbS, ydbR[1], ydbR |
| Product Desc. |
putative enoyl-CoA hydratase/isomerase of phenylacetate degradation[2][3] Phenylacetic acid degradation; mutants are unable to use phenylacetate as a carbon source[4] |
| Product Synonyms(s) |
enoyl-CoA hydratase-isomerase[1], B1393[2][1], YdbR[2][1], YdbS[2][1], PaaF[2][1] , ECK1390, JW1388, ydbR, b1393 |
| Function from GO |
<GO_nr /> |
| Knock-Out Phenotype | |
| Regulation/Expression |
transcription unit(s): paaABCDEFGHIJK[2] |
| Regulation/Activity | |
| Quick Links |
|
| edit table |
</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>
Notes
paaF mutants accumulate delta3-dehydroadipate.[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
paaF |
|---|---|
| Mnemonic |
Phenylacetic acid |
| Synonyms |
ECK1390, b1393, JW1388, ydbS, ydbR[1], ydbR |
| edit table |
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Notes
Location(s) and DNA Sequence
<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 |
31.37 minutes |
MG1655: 1455521..1456288 |
||
|
NC_012759: 1347580..1348347 |
||||
|
W3110 |
|
W3110: 1459211..1459978 |
||
|
DH10B: 1546116..1546883 |
||||
| 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 |
|---|---|---|---|---|---|
| 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 |
|---|---|---|---|---|---|---|---|
|
ΔpaaF (Keio:JW1388) |
deletion |
deletion |
PMID:16738554 |
||||
|
paaFR11Q |
R11Q |
(in strain: W) |
Strain variation; seeded from UniProt:P76082 | ||||
|
paaFM32T |
M32T |
(in strain: W) |
Strain variation; seeded from UniProt:P76082 | ||||
|
paaFT45S |
T45S |
(in strain: W) |
Strain variation; seeded from UniProt:P76082 | ||||
|
ΔpaaF757::kan |
PMID:16738554 |
| |||||
| 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 |
|---|---|---|---|
|
JW1388 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCAGCGAACTGATCGTCAGCCG Primer 2:CCGCGTCCTTTAAAGTCGGGCGT | |
|
Kohara Phage |
PMID:3038334 | ||
|
Kohara Phage |
PMID:3038334 | ||
|
Linked marker |
est. P1 cotransduction: 45% [6] | ||
|
Linked marker |
est. P1 cotransduction: 20% [6] | ||
| 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:G6714 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG13740 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120003308 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EchoBASE:EB3503 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0004659 |
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 |
PaaF |
|---|---|
| Synonyms |
enoyl-CoA hydratase-isomerase[1], B1393[2][1], YdbR[2][1], YdbS[2][1], PaaF[2][1] , ECK1390, JW1388, ydbR, b1393 |
| Product description |
putative enoyl-CoA hydratase/isomerase of phenylacetate degradation[2][3] Phenylacetic acid degradation; mutants are unable to use phenylacetate as a carbon source[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:0003824 |
catalytic activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001753 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0003824 |
catalytic activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR018376 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0004300 |
enoyl-CoA hydratase activity |
GOA:spec |
IEA: Inferred from Electronic Annotation |
EC:4.2.1.17 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006629 |
lipid metabolic process |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0443 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006631 |
fatty acid metabolic process |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0276 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0008152 |
metabolic process |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001753 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0008152 |
metabolic process |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR018376 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0016829 |
lyase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0456 |
F |
Seeded from EcoCyc (v14.0) |
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 |
|---|---|---|---|---|
| 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 |
MSELIVSRQQ RVLLLTLNRP AARNALNNAL LMQLVNELEA AATDTSISVC VITGNARFFA AGADLNEMAE KDLAATLNDT RPQLWARLQA FNKPLIAAVN GYALGAGCEL ALLCDVVVAG ENARFGLPEI TLGIMPGAGG TQRLIRSVGK SLASKMVLSG ESITAQQAQQ AGLVSDVFPS DLTLEYALQL ASKMARHSPL ALQAAKQALR QSQEVALQAG LAQERQLFTL LAATEDRHEG ISAFLQKRTP DFKGR |
| Length |
255 |
| Mol. Wt |
27.237 kDa |
| pI |
7.9 (calculated) |
| Extinction coefficient |
8,480 - 8,855 (calc based on 2 Y, 1 W, and 3 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-0004659 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EcoCyc:G6714 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG13740 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120003308 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB3503 |
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 |
Ecoli K-12 |
0.699+/-0.028 |
Molecules/cell |
|
Single Molecule Fluorescence |
PMID:20671182 | |
|
mRNA |
Ecoli K-12 |
0.00065189 |
Molecules/cell |
|
by RNA_Seq |
PMID:20671182 | |
|
Protein |
E. coli K-12 MG1655 |
2a |
molecules/cell/generation |
|
Ribosome Profiling |
Low confidence in the sequencing data set. |
PMID: 24766808 |
|
Protein |
E. coli K-12 MG1655 |
3a |
molecules/cell/generation |
|
Ribosome Profiling |
Low confidence in the sequencing data set. |
PMID: 24766808 |
|
Protein |
E. coli K-12 MG1655 |
0a |
molecules/cell/generation |
|
Ribosome Profiling |
Low confidence in the sequencing data set. |
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_000913:1455501..1455541
source=MG1655
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
This picture shows the sequence around the N-terminus.
</protect>
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 paaF | |
|
microarray |
Summary of data for paaF 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 |
|---|---|---|---|---|
| edit table |
<protect></protect>
Notes
Accessions Related to paaF Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:G6714 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB3503 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG13740 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120003308 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0004659 |
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 |
|
Caenorhabditis briggsae |
|
From Inparanoid:20070104 |
|
Caenorhabditis elegans |
|
From Inparanoid:20070104 |
|
Canis familiaris |
|
From Inparanoid:20070104 |
|
Ciona intestinalis |
|
From Inparanoid:20070104 |
|
Danio rerio |
|
From Inparanoid:20070104 |
|
Dictyostelium discoideum |
|
From Inparanoid:20070104 |
|
Drosophila melanogaster |
|
From Inparanoid:20070104 |
|
Drosophila pseudoobscura |
|
From Inparanoid:20070104 |
|
Gallus gallus |
|
From Inparanoid:20070104 |
|
Homo sapiens |
|
From Inparanoid:20070104 |
|
Macaca mulatta |
|
From Inparanoid:20070104 |
|
Monodelphis domestica |
|
From Inparanoid:20070104 |
|
Mus musculus |
|
From Inparanoid:20070104 |
|
Oryza gramene |
|
From Inparanoid:20070104 |
|
Pan troglodytes |
|
From Inparanoid:20070104 |
|
Rattus norvegicus |
|
From Inparanoid:20070104 |
|
Saccharomyces cerevisiae |
|
From Inparanoid:20070104 |
|
Schizosaccharomyces pombe |
|
From Inparanoid:20070104 |
|
Takifugu rubripes |
|
From Inparanoid:20070104 |
|
Tetraodon nigroviridis |
|
From Inparanoid:20070104 |
|
Xenopus tropicalis |
|
From Inparanoid:20070104 |
| 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:G6714 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG13740 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120003308 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB3503 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0004659 |
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 1.12 1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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 5.2 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).
Categories
- 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 Caenorhabditis briggsae
- Genes with homologs in Caenorhabditis elegans
- Genes with homologs in Canis familiaris
- Genes with homologs in Ciona intestinalis
- 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 Gallus gallus
- Genes with homologs in Homo sapiens
- Genes with homologs in Macaca mulatta
- Genes with homologs in Monodelphis domestica
- Genes with homologs in Mus musculus
- Genes with homologs in Oryza gramene
- Genes with homologs in Pan troglodytes
- Genes with homologs in Rattus norvegicus
- Genes with homologs in Saccharomyces cerevisiae
- Genes with homologs in Schizosaccharomyces pombe
- Genes with homologs in Takifugu rubripes
- Genes with homologs in Tetraodon nigroviridis
- Genes with homologs in Xenopus tropicalis
