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On One Page

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Gene |

Product(s) |

Expression|

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References |

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Standard Name	phnF
Gene Synonym(s)	ECK4095, b4102, JW4063^[1], JW4063
Product Desc.	PhnF transcriptional regulator^[2]^[3] Phosphonate utilization, probable regulatory gene^[4]
Product Synonyms(s)	predicted DNA-binding transcriptional regulator of phosphonate uptake and biodegradation^[1], B4102^[2]^[1], PhnF^[2]^[1] , ECK4095, JW4063, b4102
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): phnCDEEFGHIJKLMNOP^[2], OP00283, phnCDE-w4011-phnFGHIJKLMNOP, phnCDE-w4011-phnFGHIJKLMNOPQ, phnCDE-b4103-phnFGHIJKLMNOP
Regulation/Activity
Quick Links
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Notes

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GntR family. Pho regulon. Phosphonate utilization is cryptic in K-12.^[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	phnF
Mnemonic	Phosphonate
Synonyms	ECK4095, b4102, JW4063^[1], JW4063
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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	93.1 minutes	MG1655: 4320445..4319720 <gbrowseImage> name=NC_000913:4319720..4320445 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4301244..4300519 <gbrowseImage> name=NC_012967:4300519..4301244 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4258455..4259180 <gbrowseImage> name=NC_012759:4258455..4259180 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4327100..4326375 <gbrowseImage> name=NC_007779:4326375..4327100 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4420807..4420082 <gbrowseImage> name=NC_010473:4420082..4420807 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
phnF(del) (Keio:JW4063)	deletion	deletion	PMID:16738554	Shigen CGSC10922^[5]
phnF727(del)::kan			PMID:16738554	CGSC:102338
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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
JW4063	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCACTTGTCTACACATCCGAC Primer 2:CCGTGCTCCATAGTGAATTCAAT
10H5	Kohara Phage	Genobase	PMID:3038334
12H2	Kohara Phage	Genobase	PMID:3038334
2C12	Kohara Phage	Genobase	PMID:3038334
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 61% ^[6]
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 22% ^[6] Synonyms:zjd-2231::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:EG10715	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10715	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000707	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948617	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0709	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013435	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	PhnF
Synonyms	predicted DNA-binding transcriptional regulator of phosphonate uptake and biodegradation^[1], B4102^[2]^[1], PhnF^[2]^[1] , ECK4095, JW4063, b4102
Product description	PhnF transcriptional regulator^[2]^[3] Phosphonate utilization, probable regulatory gene^[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:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011663	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000524	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:11756427	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P13669 UniProtKB:P22773 UniProtKB:P22405 UniProtKB:Q07191 UniProtKB:P96061 UniProtKB:Q9F2T4 UniProtKB:Q9X8E2 UniProtKB:Q9K492 UniProtKB:Q54677 UniProtKB:P39796 UniProtKB:Q9ACN8 UniProtKB:O34817	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000524	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000524	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	PMID:11756427	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P13669 UniProtKB:P22773 UniProtKB:P22405 UniProtKB:Q07191 UniProtKB:P96061 UniProtKB:Q9F2T4 UniProtKB:Q9X8E2 UniProtKB:Q9K492 UniProtKB:Q54677 UniProtKB:P39796 UniProtKB:Q9ACN8 UniProtKB:O34817	P	Seeded from EcoCyc (v14.0)	complete
	GO:0015716	phosphonate transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0019	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030528	transcription regulator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011663	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030528	transcription regulator activity	PMID:11756427	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P13669 UniProtKB:P22773 UniProtKB:P22405 UniProtKB:Q07191 UniProtKB:P96061 UniProtKB:Q9F2T4 UniProtKB:Q9X8E2 UniProtKB:Q9K492 UniProtKB:Q54677 UniProtKB:P39796 UniProtKB:Q9ACN8 UniProtKB:O34817	F	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011663	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0805	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	Notes	References	Evidence
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Notes

Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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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 MHLSTHPTSY PTRYQEIAAK LEQELRQHYR CGDYLPAEQQ LAARFEVNRH TLRRAIDQLV EKGWVQRRQG VGVLVLMRPF DYPLNAQARF SQNLLDQGSH PTSEKLLSVL RPASGHVADA LGITEGENVI HLRTLRRVNG VALCLIDHYF ADLTLWPTLQ RFDSGSLHDF LREQTGIALR RSQTRISARR AQAKECQRLE IPNMSPLLCV RTLNHRDGES SPAEYSVSLT RADMIEFTME H
Length	241
Mol. Wt	27.621 kDa
pI	8.6 (calculated)
Extinction coefficient	21,430 - 21,930 (calc based on 7 Y, 2 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	13..75	PF00392 Bacterial regulatory proteins, gntR family	PMID:19920124
Domain	96..236	PF07702 UTRA 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=phnF 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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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:16131928	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948617	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013435	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P16684	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10715	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10715	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948617	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000707	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0709	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 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	1^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
phnCDEEFGHIJKLMNOP
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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_000913:4320425..4320465 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:b4102 (EcoliWiki Page)	NCBI GEO profiles for phnF
microarray	GenExpDB:b4102 (EcoliWiki Page)	Summary of data for phnF 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 phnF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10715	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0709	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4102
EcoGene	EcoGene:EG10715	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000707	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013435	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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<protect> 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

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)	PF00392 Bacterial regulatory proteins, gntR family
Superfamily (EcoliWiki Page)	SUPERFAMILY:46785
Panther (EcoliWiki Page)	PTHR11751:SF174
Superfamily (EcoliWiki Page)	SUPERFAMILY:64288
Pfam (EcoliWiki Page)	PF07702 UTRA domain
EcoCyc	EcoCyc:EG10715	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10715	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000707	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0709	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013435	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).

phnF: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 phnF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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