yfiN: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 |
yfiN |
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Gene Synonym(s) |
ECK2601, b2604, JW2585[1], JW2585 |
Product Desc. |
predicted diguanylate cyclase[2][3] Probable diguanylate cyclase, function unknown[4] |
Product Synonyms(s) |
predicted diguanylate cyclase[1], B2604[2][1], YfiN[2][1] , ECK2601, JW2585, b2604 |
Function from GO |
<GO_nr /> |
Knock-Out Phenotype | |
Regulation/Expression | |
Regulation/Activity | |
Quick Links | |
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>
Notes
YfiN has a C-terminal putative diguanylate cyclase GGDEF domain.[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
Standard name |
yfiN |
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Mnemonic |
Systematic nomenclature |
Synonyms |
ECK2601, b2604, JW2585[1], JW2585 |
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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 |
59.06 minutes |
MG1655: 2740405..2741631 |
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NC_012967: 2663790..2665016 |
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NC_012759: 2626217..2627443 |
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W3110 |
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W3110: 2741039..2742265 |
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DH10B: 2832170..2833396 |
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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 |
---|---|---|---|---|---|
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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 |
---|---|---|---|---|---|---|---|
ΔyfiN (Keio:JW2585) |
deletion |
deletion |
PMID:16738554 |
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ΔyfiN767::kan |
PMID:16738554 |
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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
See Help:Gene_resources for help entering information into the Genetic Resources table.
Resource | Resource Type | Source | Notes/Reference |
---|---|---|---|
Plasmid clone |
PMID:16769691 Status: Primer 1: Primer 2: | ||
Kohara Phage |
PMID:3038334 | ||
Kohara Phage |
PMID:3038334 | ||
Linked marker |
est. P1 cotransduction: 91% [6] | ||
Linked marker |
est. P1 cotransduction: % [6] | ||
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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:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120002419 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EchoBASE:EB2718 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0008570 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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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 |
YfiN |
---|---|
Synonyms |
predicted diguanylate cyclase[1], B2604[2][1], YfiN[2][1] , ECK2601, JW2585, b2604 |
Product description |
predicted diguanylate cyclase[2][3] Probable diguanylate cyclase, function unknown[4] |
EC number (for enzymes) |
|
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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:0004871 |
signal transducer activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR003660 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005886 |
plasma membrane |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0997 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005886 |
plasma membrane |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-1003 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0007165 |
signal transduction |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR003660 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016020 |
membrane |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0472 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016021 |
integral to membrane |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR003660 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016021 |
integral to membrane |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0812 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016021 |
integral to membrane |
GO_REF:0000023 |
IEA: Inferred from Electronic Annotation |
SP_SL:SL-9909 |
C |
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 |
---|---|---|---|---|
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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 |
---|---|---|---|---|
plasma membrane |
C-terminus localized in the cytoplasm with 2 predicted transmembrane domains |
Daley et al. (2005) [7] |
| |
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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 |
MMDNDNSLNK RPTFKRALRN ISMTSIFITM MLIWLLLSVT SVLTLKQYAQ KNLALTAATM TYSLEAAVVF ADGPAATETL AALGQQGQFS TAEVRDKQQN ILASWHYTRK DPGDTFSNFI SHWLFPAPII QPIRHNGETI GEVRLTARDS SISHFIWFSL AVLTGCILLA SGIAITLTRH LHNGLVEALK NITDVVHDVR SNRNFSRRVS EERIAEFHRF ALDFNSLLDE MEEWQLRLQA KNAQLLRTAL HDPLTGLANR AAFRSGINTL MNNSDARKTS ALLFLDGDNF KYINDTWGHA TGDRVLIEIA KRLAEFGGLR HKAYRLGGDE FAMVLYDVQS ESEVQQICSA LTQIFNLPFD LHNGHQTTMT LSIGYAMTIE HASAEKLQEL ADHNMYQAKH QRAEKLVR |
Length |
408 |
Mol. Wt |
45.99 kDa |
pI |
7.5 (calculated) |
Extinction coefficient |
44,920 - 45,170 (calc based on 8 Y, 6 W, and 2 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.
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<motif_map/> |
Structure
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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 |
---|---|---|
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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-0008570 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EcoCyc:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
RegulonDB:ECK120002419 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB2718 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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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
Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
---|---|---|---|---|---|---|---|
Protein |
E. coli K-12 MG1655 |
27 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
Protein |
E. coli K-12 MG1655 |
25 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
Protein |
E. coli K-12 MG1655 |
8a |
molecules/cell/generation |
|
Ribosome Profiling |
Low confidence in the sequencing data set. |
PMID: 24766808 |
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Notes
Transcription and Transcriptional Regulation
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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
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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
<protect><gbrowseImage>
name=NC_000913:2740385..2740425
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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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 |
NCBI GEO profiles for yfiN | |
microarray |
Summary of data for yfiN 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 yfiN Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB2718 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120002419 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0008570 |
Escherichia coli str. K-12 substr. MG1655 | |
edit table |
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Notes
Links
Name | URL | Comments |
---|---|---|
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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 |
---|---|---|
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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:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG12880 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120002419 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB2718 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0008570 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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References
See Help:References for how to manage references in EcoliWiki.
- ↑ 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)
- ↑ 2.0 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
- ↑ 3.0 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).
- ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
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