tfaP: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

tfaP

Gene Synonym(s)

ECK1141, b1155, JW5171, ymfS[1], JW5171, ymfS

Product Desc.

hypothetical protein[2][3]

Function unknown, e14 prophage[4]

Product Synonyms(s)

e14 prophage; predicted protein[1], B1155[2][1], TfaP[2][1] , ECK1141, JW5171, ymfS, b1155

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ymfT[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

tfaP

Mnemonic
Synonyms

ECK1141, b1155, JW5171, ymfS[1], JW5171, ymfS

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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

26.02 minutes 

MG1655: 1207355..1207768
<gbrowseImage> name=NC_000913:1207355..1207768 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1209709..1210122
<gbrowseImage> name=NC_007779:1209709..1210122 source=W3110 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

ΔymfS (Keio:JW5171)

deletion

deletion

PMID:16738554

Shigen


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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

JW5171

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAATATACTGTTGCTTAAA

Primer 2:CCTCTGGCCTGAACTGCCGGAGG

2E7

Kohara Phage

Genobase

PMID:3038334

3E11

Kohara Phage

Genobase

PMID:3038334

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[5]

est. P1 cotransduction: 8% [6]

zcf-117::Tn10

Linked marker

CAG18463 = CGSC7363[5]

est. P1 cotransduction: 89% [6]

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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:G6598

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4083

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1155

EcoGene

EcoGene:EG14337

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003878

Escherichia coli str. K-12 substr. MG1655

EcoCyc (EcoliWiki Page)

ECOCYC:G6598

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945724

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003193

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

TfaP

Synonyms

e14 prophage; predicted protein[1], B1155[2][1], TfaP[2][1] , ECK1141, JW5171, ymfS, b1155

Product description

hypothetical protein[2][3]

Function unknown, e14 prophage[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

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

yfdK

PMID:19402753

LCMS(ID Probability):99.6

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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

MKIYCCLNTV GFFMDGCGVI PPDSKEITAE HWQSLLKSQA EGGVIDFSVF PPSIKEVIRT
HDDEVADANF QKQMLISDAT DFINSRQWQG KAALGRLKED ELKQYNLWLD YLEALELVDT
SSAPDIEWPT PPAVQAR
Length

137

Mol. Wt

15.434 kDa

pI

4.4 (calculated)

Extinction coefficient

26,470 - 26,845 (calc based on 3 Y, 4 W, and 3 C residues)


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

13..133

PF02413 Caudovirales tail fibre assembly protein

PMID:19920124

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ymfS 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:16129118

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945724

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003878

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P09154

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6598

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14337

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945724

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003193

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4083

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

13a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

18

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

9a

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

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)

ymfT

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_000913:1207335..1207375 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

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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


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b1155 (EcoliWiki Page)

NCBI GEO profiles for ymfS

microarray

GenExpDB:b1155 (EcoliWiki Page)

Summary of data for ymfS from multiple microarray studies


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 tfaP Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6598

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4083

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1155

EcoGene

EcoGene:EG14337

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003193

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003878

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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

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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)

PF02413 Caudovirales tail fibre assembly protein

PFAM (EcoliWiki Page)

PFAM:PF02413

EcoCyc

EcoCyc:G6598

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14337

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003193

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4083

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003878

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. 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. 5.0 5.1 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).

Categories

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