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Standard Name	ygiF
Gene Synonym(s)	ECK3044, b3054, JW3026, orfXE^[1]^[2]
Product Desc.	predicted adenylate cyclase^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted adenylate cyclase^[1], B3054^[2]^[1], YgiF^[2]^[1] , ECK3044, JW3026, b3054
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): glnE^[2]
Regulation/Activity
Quick Links
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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	ygiF
Mnemonic	Systematic nomenclature
Synonyms	ECK3044, b3054, JW3026, orfXE^[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	68.92 minutes	MG1655: 3198987..3197686 <gbrowseImage> name=NC_000913:3197686..3198987 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3133799..3132498 <gbrowseImage> name=NC_012967:3132498..3133799 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3084834..3086135 <gbrowseImage> name=NC_012759:3084834..3086135 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3199621..3198320 <gbrowseImage> name=NC_007779:3198320..3199621 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3296732..3295431 <gbrowseImage> name=NC_010473:3295431..3296732 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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)	Reference	Availability
ΔygiF (Keio:JW3026)	deletion	deletion	PMID:16738554	Shigen CGSC10312^[5]
ΔygiF747::kan			PMID:16738554	CGSC:105042
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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
JW3026	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTCAGGAAATCGAATTAAA Primer 2:CCACGTTTTCCGCTGTGCAACCA
9F9	Kohara Phage	Genobase	PMID:3038334
tolC210::Tn10	Linked marker	CAG12184 = CGSC7437^[5]	est. P1 cotransduction: 49% ^[6]
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 53% ^[6] Synonyms:zgh-3075::Tn10, zgj-3075::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:EG11603	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001551	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947554	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1560	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010020	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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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	YgiF
Synonyms	predicted adenylate cyclase^[1], B3054^[2]^[1], YgiF^[2]^[1] , ECK3044, JW3026, b3054
Product description	predicted adenylate cyclase^[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
	GO:0004016	adenylate cyclase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008172	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006171	cAMP biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008172	P	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	References	Evidence
Protein	aceE	PMID:15690043	Experiment(s):EBI-880398
Protein	aceF	PMID:15690043	Experiment(s):EBI-880398
Protein	ompA	PMID:15690043	Experiment(s):EBI-880398, EBI-885823
Protein	ompC	PMID:15690043	Experiment(s):EBI-880398
Protein	phoE	PMID:15690043	Experiment(s):EBI-880398
Protein	rpmB	PMID:15690043	Experiment(s):EBI-885823
Protein	lacZ	PMID:16606699	Experiment(s):EBI-1144655
Protein	rhsA	PMID:16606699	Experiment(s):EBI-1144655
Protein	ycbY	PMID:16606699	Experiment(s):EBI-1144655
Protein	nadE	PMID:16606699	Experiment(s):EBI-1144655
Protein	ompA	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):39.031252
Protein	rpmB	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 MAQEIELKFI VNHSAVEALR DHLNTLGGEH HDPVQLLNIY YETPDNWLRG HDMGLRIRGE NGRYEMTMKV AGRVTGGLHQ RPEYNVALSE PTLDLAQLPT EVWPNGELPA DLASRVQPLF STDFYREKWL VAVDGSQIEI ALDQGEVKAG EFAEPICELE LELLSGDTRA VLKLANQLVS QTGLRQGSLS KAARGYHLAQ GNPAREIKPT TILHVAAKAD VEQGLEAALE LALAQWQYHE ELWVRGNDAA KEQVLAAISL VRHTLMLFGG IVPRKASTHL RDLLTQCEAT IASAVSAVTA VYSTETAMAK LALTEWLVSK AWQPFLDAKA QGKISDSFKR FADIHLSRHA AELKSVFCQP LGDRYRDQLP RLTRDIDSIL LLAGYYDPVV AQAWLENWQG LHHAIATGQR IEIEHFRNEA NNQEPFWLHS GKR
Length	433
Mol. Wt	48.389 kDa
pI	6.1 (calculated)
Extinction coefficient	71,390 - 71,765 (calc based on 11 Y, 10 W, and 3 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	2..202	PF01928 CYTH domain		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=ygiF 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:16130950	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947554	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010020	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P30871	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11603	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11603	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947554	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001551	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1560	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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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

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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	20.325+/-0.192	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.032667179	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	1003	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	370	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	918	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		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.

Transcription unit(s)
glnE
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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_000913:3198967..3199007 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
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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:b3054 (EcoliWiki Page)	NCBI GEO profiles for ygiF
microarray	GenExpDB:b3054 (EcoliWiki Page)	Summary of data for ygiF 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
	GFP Fusion	Intergenic region (3198525..3198918) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:D12^[7]
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Notes

Accessions Related to ygiF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11603	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1560	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3054
EcoGene	EcoGene:EG11603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001551	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010020	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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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
Shigella flexneri	YGIF	From SHIGELLACYC
E. coli O157	YGIF	From ECOO157CYC
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Do-It-Yourself Web Tools

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)	PF01928 CYTH domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:55154
EcoCyc	EcoCyc:EG11603	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001551	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1560	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010020	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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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 ^2.7 ^2.8 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 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ygiF:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ygiF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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