fau: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

fau

Gene Synonym(s)

ECK2907, b2912, JW2879[1], ygfA

Product Desc.

putative ligase[2][3]

Function unknown, expressed second gene in ssrS operon[4]

Product Synonyms(s)

predicted ligase[1], B2912[2][1], YgfA[2][1] , Fau

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ygfA[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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Induced during biofilm formation. Belongs to the 5-formyltetrahydrofolate cyclo-ligase family.[4]



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

fau

Mnemonic

Systematic nomenclature

Synonyms

ECK2907, b2912, JW2879[1], ygfA

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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

65.83 minutes 

MG1655: 3054263..3054811
<gbrowseImage> name=NC_000913:3054263..3054811 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2941992..2942540
<gbrowseImage> name=NC_012967:2941992..2942540 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2941411..2941959
<gbrowseImage> name=NC_012759:2941411..2941959 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3054897..3055445
<gbrowseImage> name=NC_007779:3054897..3055445 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3148133..3148681
<gbrowseImage> name=NC_010473:3148133..3148681 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

ygfA(del) (Keio:JW2879)

deletion

deletion

PMID:16738554

Shigen
CGSC10233[5]

ygfA763(del)::kan

PMID:16738554

CGSC:104964

ygfA763(del)::FRTKanFRT

deletion

Mutagenesis rate

Decrease in stress induced mutagenesis (SIM).

PMID:23224554

Parent Strain: SMR4562 Experimental strain: SMR12316

The mutation conferred a medium decrease in SIM with a decrease in mutant freqency by 68 to 89 percent. See table S3 for full experimental data.

ygfA763(del)::FRTKanFRT

deletion

SDS-EDTA sensitivity

PMID:23224554

Parent Strain: SMR4562 Experimental strain: SMR12316

The mutation conferred an increase in SDS-EDTA sensitivity. See table S7 and S1 for a summary of experimental data.

CAG45114 ygfA763(del)::FRTKanFRT

Deletion

SigmaE activity

Decrease in sigmaE activity

PMID:23224554

Parental Strain: CAG54114 Experimental Strain: SMR15326

See table S11 for experimental data.

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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

JW2879

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATTCGGCAACGTCGTCGTGC

Primer 2:CCCCACTCCCAGACTTTCGACGG

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[5]

est. P1 cotransduction: % [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[5]

est. P1 cotransduction: 29% [6]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

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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:EG11158

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11158

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001141

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1147

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009559

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

Fau

Synonyms

predicted ligase[1], B2912[2][1], YgfA[2][1] , Fau

Product description

putative ligase[2][3]

Function unknown, expressed second gene in ssrS operon[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

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002698

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0009396

folic acid and derivative biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002698

P

Seeded from EcoCyc (v14.0)

complete

GO:0030272

5-formyltetrahydrofolate cyclo-ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002698

F

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

groL

PMID:16606699

Experiment(s):EBI-1144285

Protein

iciA

PMID:16606699

Experiment(s):EBI-1144285

Protein

yeiT

PMID:15690043

Experiment(s):EBI-884764

Protein

galM

PMID:15690043

Experiment(s):EBI-884764

Protein

nifU

PMID:15690043

Experiment(s):EBI-884764

Protein

groL

PMID:15690043

Experiment(s):EBI-884764

Protein

pqiB

PMID:15690043

Experiment(s):EBI-884764

Protein

rpsB

PMID:15690043

Experiment(s):EBI-884764

Protein

rlmF

PMID:15690043

Experiment(s):EBI-884764

Protein

yeiT

PMID:19402753

LCMS(ID Probability):99.0

Protein

iscU

PMID:19402753

LCMS(ID Probability):99.0

Protein

groL

PMID:19402753

LCMS(ID Probability):99.6

Protein

rlmF

PMID:19402753

LCMS(ID Probability):99.0

Protein

pqiB

PMID:19402753

LCMS(ID Probability):99.0

Protein

ndk

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):39.321848

Protein

galM

PMID:19402753

LCMS(ID Probability):99.0

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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 

MIRQRRRALT PEQQQEMGQQ AATRMMTYPP VVMAHTVAVF LSFDGELDTQ PLIEQLWRAG
KRVYLPVLHP FSAGNLLFLN YHPQSELVMN RLKIHEPKLD VRDVLPLSRL DVLITPLVAF
DEYGQRLGMG GGFYDRTLQN WQHYKTQPVG YAHDCQLVEK LPVEEWDIPL PAVVTPSKVW EW
Length

182

Mol. Wt

21.104 kDa

pI

6.9 (calculated)

Extinction coefficient

37,930 - 38,055 (calc based on 7 Y, 5 W, and 1 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

1..176

PF01812 5-formyltetrahydrofolate cyclo-ligase family

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=ygfA 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

EcoCyc

EcoCyc:EG11158

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11158

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001141

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1147

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009559

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

Ecoli K-12

3.221+/-0.052

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.015510949

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

144

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

41

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

40a

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

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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)

ygfA

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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_000913:3054243..3054283 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
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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:b2912 (EcoliWiki Page)

NCBI GEO profiles for ygfA

microarray

GenExpDB:b2912 (EcoliWiki Page)

Summary of data for ygfA 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 ygfA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11158

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1147

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2912

EcoGene

EcoGene:EG11158

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001141

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009559

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

  • ENSANGP00000013275 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000022655 (score: 1.000; bootstrap: 64%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G13050 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000026669 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000022735 (score: 0.872)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00013708 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000020604 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0034851 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA10745-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000010514 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000258874 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000019960 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000024242 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1340032 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q7F102 (score: 1.000; bootstrap: 100%)
  • Q7F101 (score: 0.597)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000012576 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000017879 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YER183C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC17038c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000146660 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000052456 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000052459 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YGFA

From SHIGELLACYC

E. coli O157

YGFA

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)

PF01812 5-formyltetrahydrofolate cyclo-ligase family

Panther (EcoliWiki Page)

PTHR23407:SF1

Superfamily (EcoliWiki Page)

SUPERFAMILY:100950

EcoCyc

EcoCyc:EG11158

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11158

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001141

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1147

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009559

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 4.2 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).

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