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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	hpf
Gene Synonym(s)	yhbH, ECK3192, b3203, JW3170, rp5M^[1]^[2]
Product Desc.	probable sigma-54 modulation protein^[3]; predicted ribosome-associated, sigma 54 modulation protein^[2] Ribosome hibernation promoting factor HPF; stabilizes 70S dimers (100S); induced in stationary phase; raiA paralog has opposite effect on 70S dimers^[4]
Product Synonyms(s)	predicted ribosome-associated, sigma 54 modulation protein^[1], B3203^[3]^[1], YhbH^[3]^[1], Hpf^[2]^[1] , ECK3192, JW3170, yhbH, b3203
Function from GO	<GO_nr />
Knock-Out Phenotype	Non-essential ^[5]
Regulation/Expression	transcription unit(s): lptB-rpoN-yhbH-ptsN-yhbJ^[3], yhbG-rpoN-yhbH-ptsN-yhbJ, rpoN-yhbH-ptsN-yhbJ-npr^[3], rpoN-ORFII-ORF-III-ORF-IV-ORFV, rpoN-yhbH-ptsN-yhbJ-ptsO
Regulation/Activity
Quick Links
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Notes

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Homologous to RpoN modulators. Induced by AI-2 pheromone. The rpoN operon contains rpoN-hpf-ptsN-yhbJ-npr.^[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	hpf
Mnemonic	Hibernation promoting factor
Synonyms	yhbH, ECK3192, b3203, JW3170, rp5M^[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	72.08 minutes	MG1655: 3344195..3344482 <gbrowseImage> name=NC_000913:3344195..3344482 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3231343..3231630 <gbrowseImage> name=NC_012759:3231343..3231630 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3346028..3346315 <gbrowseImage> name=NC_007779:3346028..3346315 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3441940..3442227 <gbrowseImage> name=NC_010473:3441940..3442227 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
Coding Start (SO:0000323)	MG1655	3344195	Edman degradation	PMID:11168583
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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
ΔyhbH731::kan					PMID:16738554	CGSC:105100
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
7E3	Kohara Phage	Genobase	PMID:3038334
3G10	Kohara Phage	Genobase	PMID:3038334
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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:EG11681	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11681	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001624	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947718	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1632	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010516	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	YhbH
Synonyms	predicted ribosome-associated, sigma 54 modulation protein^[1], B3203^[3]^[1], YhbH^[3]^[1], Hpf^[2]^[1] , ECK3192, JW3170, yhbH, b3203
Product description	probable sigma-54 modulation protein^[3]; predicted ribosome-associated, sigma 54 modulation protein^[2] Ribosome hibernation promoting factor HPF; stabilizes 70S dimers (100S); induced in stationary phase; raiA paralog has opposite effect on 70S dimers^[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:0044238	primary metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003489	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	dnaN	PMID:15690043	Experiment(s):EBI-881763
Protein	yraI	PMID:16606699	Experiment(s):EBI-1145153
Protein	yhbY	PMID:16606699	Experiment(s):EBI-1145153
Protein	dnaN	PMID:19402753	MALDI(Z-score):39.063809
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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
cytoplasm			From EcoCyc^[2]
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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 MQLNITGNNV EITEALREFV TAKFAKLEQY FDRINQVYVV LKVEKVTHTS DATLHVNGGE IHASAEGQDM YAAIDGLIDK LARQLTKHKD KLKQH
Length	95
Mol. Wt	10.749 kDa
pI	7.0 (calculated)
Extinction coefficient	4,470 (calc based on 3 Y, 0 W, and 0 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..95	PF02482 Sigma 54 modulation protein / S30EA ribosomal protein		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=hpf 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:16131093	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947718	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010516	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFX0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11681	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11681	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947718	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001624	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1632	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	E. coli K-12 MC4100	1.68E+03	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	Ecoli K-12	273.582+/-2.034	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.44954+/-0.05245	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.731707317	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	1006	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	2917	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	768	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)
lptB-rpoN-yhbH-ptsN-yhbJ
rpoN-yhbH-ptsN-yhbJ-npr
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File:.jpg

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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_000913:3344175..3344215 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:b3203 (EcoliWiki Page)	NCBI GEO profiles for hpf
microarray	GenExpDB:b3203 (EcoliWiki Page)	Summary of data for hpf 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 hpf Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11681	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1632	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3203
EcoGene	EcoGene:EG11681	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001624	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010516	Escherichia coli str. K-12 substr. MG1655
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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	YHBH	From SHIGELLACYC
E. coli O157	YHBH	From ECOO157CYC
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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)	PF02482 Sigma 54 modulation protein / S30EA ribosomal protein
Superfamily (EcoliWiki Page)	SUPERFAMILY:69754
EcoCyc	EcoCyc:EG11681	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11681	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001624	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1632	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010516	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 ^1.8 ^1.9 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 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 ^3.7 EcoCyc (release 10.6; 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.
↑ Bubunenko, M et al. (2007) Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J. Bacteriol. 189 2844-53 PubMed

hpf:On One Page

Quickview

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 hpf Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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