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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	yhgF
Gene Synonym(s)	ECK3394, b3407, JW3370^[1], JW3370
Product Desc.	predicted transcriptional accessory protein^[2]^[3] Putative transcription accessory factor; contains S1 RNA-binding domain; low abundance protein^[4]
Product Synonyms(s)	predicted transcriptional accessory protein^[1], B3407^[2]^[1], YhgF^[2]^[1] , ECK3394, JW3370, b3407
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yhgF^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 16 (http://afmb.cnrs-mrs.fr/article171.html). The yhfG gene is homologous to B. pertussis Tex transcription factor. Repressed during biofilm formation.^[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	yhgF
Mnemonic	Systematic nomenclature
Synonyms	ECK3394, b3407, JW3370^[1], JW3370
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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	76.2 minutes	MG1655: 3535407..3537728 <gbrowseImage> name=NC_000913:3535407..3537728 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3466072..3468390 <gbrowseImage> name=NC_012967:3466072..3468390 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3422564..3424885 <gbrowseImage> name=NC_012759:3422564..3424885 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4103031..4100710 <gbrowseImage> name=NC_007779:4100710..4103031 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3633152..3635473 <gbrowseImage> name=NC_010473:3633152..3635473 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	Comments
ΔyhgF (Keio:JW3370)	deletion	deletion	PMID:16738554	Shigen CGSC10512^[5]
yhgF::Tn5KAN-I-SceI (FB21171)	Insertion at nt 976 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21171	contains pKD46
ΔyhgF741::kan			PMID:16738554	CGSC:105206
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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
JW3370	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATGAATGATTCGTTCTGCCG Primer 2:CCACGTTTTTTGCCCATTGCCGC
2F6	Kohara Phage	Genobase	PMID:3038334
1C9	Kohara Phage	Genobase	PMID:3038334
zhf-3084::Tn10	Linked marker	CAG18456 = CGSC7576^[5]	est. P1 cotransduction: 27% ^[6] Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).
glgP721::Tn10	Linked marker	CAG18638 = CGSC7451^[5]	est. P1 cotransduction: 34% ^[6] Synonyms:zhg-3086::Tn10, zhh-21::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:G7746	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12932	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004289	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947911	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2768	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011120	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	YhgF
Synonyms	predicted transcriptional accessory protein^[1], B3407^[2]^[1], YhgF^[2]^[1] , ECK3394, JW3370, b3407
Product description	predicted transcriptional accessory protein^[2]^[3] Putative transcription accessory factor; contains S1 RNA-binding domain; low abundance protein^[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:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003029	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006641	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016788	hydrolase activity, acting on ester bonds	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006641	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	References	Evidence
Protein	dnaC	PMID:16606699	Experiment(s):EBI-1145821
Protein	gltX	PMID:16606699	Experiment(s):EBI-1145821
Protein	rpsT	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 MPFIARYRKE ITGGLDDTQL RNLETRLSYL RELEERRQAI LKSISEQGKL TDDLAKAINA TLSKTELEDL YLPYKPKRRT RGQIAIEAGL EPLADLLWSD PSHTPEVAAA QYVYADKGVA DTKAALDGAR YILMERFAED AALLAKVRDY LWKNAHLVST VVSGKEEEGA KFRDYFDHHE PLSTVPSHRA LAMFRGRNEG VLQLSLNADP QFDEPPKESY CEQIIMDHLG LRLNNAPADS WRKGVVSWTW RIKVLMHLET ELMGTVRERA EDEAINVFAR NLHDLLMAAP AGLRATMGLD PGLRTGVKVA VVDATGKLVA TDTIYPHTGQ AAKAAMTVAA LCEKHNVELV AIGNGTASRE TERFYLDVQK QFPKVTAQKV IVSEAGASVY SASELAAQEF PDLDVSLRGA VSIARRLQDP LAELVKIDPK SIGVGQYQHD VSQTQLARKL DAVVEDCVNA VGVDLNTASV PLLTRVAGLT RMMAQNIVAW RDENGQFQNR QQLLKVSRLG PKAFEQCAGF LRINHGDNPL DASTVHPEAY PVVERILAAT QQALKDLMGN SSELRNLKAS DFTDEKFGVP TVTDIIKELE KPGRDPRPEF KTAQFADGVE TMNDLQPGMI LEGAVTNVTN FGAFVDIGVH QDGLVHISSL SNKFVEDPHT VVKAGDIVKV KVLEVDLQRK RIALTMRLDE QPGETNARRG GGNERPQNNR PAAKPRGREA QPAGNSAMMD ALAAAMGKKR
Length	740
Mol. Wt	81.506 kDa
pI	6.5 (calculated)
Extinction coefficient	55,350 - 55,850 (calc based on 15 Y, 6 W, and 4 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	References
Domain	647..720	PF00575 S1 RNA binding domain	PMID:19920124
Domain	10..202	PF09371 Tex-like protein N-terminal 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=yhgF 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:90111588	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947911	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011120	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P46837	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7746	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12932	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947911	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004289	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2768	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	Reference(s)
Protein	E. coli K-12 MC4100	4.10E+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	3198	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	825	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	1681	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)
yhgF
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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_000913:3535387..3535427 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:b3407 (EcoliWiki Page)	NCBI GEO profiles for yhgF
microarray	GenExpDB:b3407 (EcoliWiki Page)	Summary of data for yhgF 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 (3534855..3535202) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:E4^[7]
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Notes

Accessions Related to yhgF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7746	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2768	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3407
EcoGene	EcoGene:EG12932	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004289	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011120	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
Anopheles gambiae	ENSANGP00000000001 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000000619 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G65440 (score: 1.000; bootstrap: 100%) AT1G63210 (score: 0.523)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000009881 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00042160 (score: 1.000; bootstrap: 90%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00022830 (score: 1.000; bootstrap: 95%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000003722 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000012297 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0051156 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA16052-PA (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000016215 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Homo sapiens	ENSP00000263736 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000004654 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000024080 (score: 1.000; bootstrap: 66%)	From Inparanoid:20070104
Mus musculus	MGI:1925836 (score: 1.000; bootstrap: 68%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000020409 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000019895 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC1F71c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000148064 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00014324001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000004445 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YHGF	From SHIGELLACYC
E. coli O157	YHGF	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:50249
Panther (EcoliWiki Page)	PTHR10724:SF0
Pfam (EcoliWiki Page)	PF00575 S1 RNA binding domain
Pfam (EcoliWiki Page)	PF09371 Tex-like protein N-terminal domain
EcoCyc	EcoCyc:G7746	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12932	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004289	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2768	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011120	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 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yhgF: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 yhgF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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