yfaA: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

yfaA

Gene Synonym(s)

ECK2222, b2230, JW2224, pufY, yfaA'[1][2]

Product Desc.

predicted protein[2][3]

Function unknown[4]

Product Synonyms(s)

predicted protein[1], B2230[2][1], PufY[2][1], YfaA[2][1] , ECK2222, JW2224, pufY, b2230

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yfaP[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

yfaA

Mnemonic

Systematic nomenclature

Synonyms

ECK2222, b2230, JW2224, pufY, yfaA'[1][2]

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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

50.28 minutes 

MG1655: 2334666..2332978
<gbrowseImage> name=NC_000913:2332978..2334666 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2283344..2281656
<gbrowseImage> name=NC_012967:2281656..2283344 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2218783..2220471
<gbrowseImage> name=NC_012759:2218783..2220471 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2341314..2339626
<gbrowseImage> name=NC_007779:2339626..2341314 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2425654..2423966
<gbrowseImage> name=NC_010473:2423966..2425654 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

ΔyfaA (Keio:JW2224)

deletion

deletion

PMID:16738554

Shigen
CGSC9795[5]

ΔyfaA784::kan

PMID:16738554

CGSC:104608


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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

JW2224

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTGGTGAAAAAAAGGCGAA

Primer 2:CCTAGCGGCTGCCAGGTTATGGG

4F12

Kohara Phage

Genobase

PMID:3038334

E13A5

Kohara Phage

Genobase

PMID:3038334

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[5]

est. P1 cotransduction: 63% [6]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[5]

est. P1 cotransduction: 71% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (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:EG11142

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11142

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001126

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946618

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1132

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007368

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

YfaA

Synonyms

predicted protein[1], B2230[2][1], PufY[2][1], YfaA[2][1] , ECK2222, JW2224, pufY, b2230

Product description

predicted protein[2][3]

Function unknown[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

rplB

PMID:16606699

Experiment(s):EBI-1142246

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1142246

Protein

ybcK

PMID:16606699

Experiment(s):EBI-1142246

Protein

groL

PMID:16606699

Experiment(s):EBI-1142246

Protein

gltD

PMID:16606699

Experiment(s):EBI-1142246

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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

MAVPVKNGWL YTRNVAMSGE KKAKGWRFYG LVGFGAIALL SAGVWALQYA GSGPEKTLSP
LVVHNNLQID LNEPDLFLDS DSLSQLPKDL LTIPFLHDVL SEDFVFYYQN HADRLGIEGS
IRRIVYEHDL TLKDKLFSSL LDQPAQAALW HDKQGHLSHY MVLIQRSGLS KLLEPLLFAA
TSDSQLSKTE ISSIKINSET VPVYQLRYNG NNALMFATYQ DKMLVFSSTD MLFKDDQQDT
EATAIAGDLL SGKKRWQASF GLEERTAEKT PVRQRIVVSA RWLGFGYQRL MPSFAGVRFE
MGNDGWHSFV ALNDESASVD ASFDFTPVWN SMPAGASFCV AVPYSHGIAE EMLSHISQEN
DKLNGALDGA AGLCWYEDSK LQTPLFVGQF DGTAEQAQLP GKLFTQNIGA HESKAPEGVL
PVSQTQQGEA QIWRREVSSR YGQYPKAQAA QPDQLMSDYF FRVSLAMQNK TLLFSLDDTL
VNNALQTLNK TRPAMVDVIP TDGIVPLYIN PQGIAKLLRN ETLTSLPKNL EPVFYNAAQT
LLMPKLDALS QQPRYVMKLA QMEPGAAWQW LPITWQPL
Length

578

Mol. Wt

64.473 kDa

pI

5.6 (calculated)

Extinction coefficient

99,810 - 100,060 (calc based on 19 Y, 13 W, and 2 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

8..559

PF09909 Uncharacterized protein conserved in bacteria (DUF2138)

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=yfaA 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:90111405

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946618

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007368

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P17994

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11142

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11142

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946618

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001126

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1132

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 MC4100

1.17E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

3a

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

1a

molecules/cell/generation

  • Medium: MOPS Minimal
  • 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

0a

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

Transcription unit(s)

yfaP

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_000913:2334646..2334686 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


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

Type Reference Notes

microarray

GEO Profiles:b2230 (EcoliWiki Page)

NCBI GEO profiles for yfaA

microarray

GenExpDB:b2230 (EcoliWiki Page)

Summary of data for yfaA 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 yfaA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11142

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1132

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2230

EcoGene

EcoGene:EG11142

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001126

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007368

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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Do-It-Yourself Web Tools

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Notes

Families

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

Organism Homologs (Statistics) Comments

E. coli O157

YFAA

From ECOO157CYC

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF09909 Uncharacterized protein conserved in bacteria (DUF2138)


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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. 2.00 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. 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 5.2 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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