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Expression|

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Standard Name	hyfD
Gene Synonym(s)	ECK2480, b2484, JW2469^[1], JW2469
Product Desc.	hydrogenase 4, component D^[2]^[3]; Component of hydrogenase 4^[3] Putative hydrogenase 4 component D; membrane protein of Hyf electron transfer complex of FHL system^[4]
Product Synonyms(s)	hydrogenase 4, membrane subunit^[1], B2484^[2]^[1], HyfD^[2]^[1] , ECK2480, JW2469, b2484
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hyfABCDEFGHIJR-focB^[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	hyfD
Mnemonic	Hydrogenase
Synonyms	ECK2480, b2484, JW2469^[1], JW2469
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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	56.1 minutes	MG1655: 2602833..2604272 <gbrowseImage> name=NC_000913:2602833..2604272 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2525724..2527073 <gbrowseImage> name=NC_012967:2525724..2527073 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2488638..2490077 <gbrowseImage> name=NC_012759:2488638..2490077 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2603467..2604906 <gbrowseImage> name=NC_007779:2603467..2604906 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2694598..2696037 <gbrowseImage> name=NC_010473:2694598..2696037 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
ΔhyfD (Keio:JW2469)	deletion	deletion	PMID:16738554	Shigen CGSC9970^[5]
ΔhyfD732::kan			PMID:16738554	CGSC:101484
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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
JW2469	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAAAATCTTGCTCTGACGAC Primer 2:CCtTGCAACCAGGTCGCGGCGAT
5A8	Kohara Phage	Genobase	PMID:3038334
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 73% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 4% ^[6] Synonyms:zff-208::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:G7301	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14212	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003873	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947290	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3964	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008185	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	HyfD
Synonyms	hydrogenase 4, membrane subunit^[1], B2484^[2]^[1], HyfD^[2]^[1] , ECK2480, JW2469, b2484
Product description	hydrogenase 4, component D^[2]^[3]; Component of hydrogenase 4^[3] Putative hydrogenase 4 component D; membrane protein of Hyf electron transfer complex of FHL system^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008137	NADH dehydrogenase (ubiquinone) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001516	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008137	NADH dehydrogenase (ubiquinone) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001750	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008137	NADH dehydrogenase (ubiquinone) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003916	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	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
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042773	ATP synthesis coupled electron transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001516	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042773	ATP synthesis coupled electron transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001750	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042773	ATP synthesis coupled electron transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003916	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001516	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001750	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003916	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005887	integral to plasma membrane	PMID:9387241	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P33607	C	Table 2.	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
Protein	Subunits of hydrogenase 4	could be indirect
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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			From EcoCyc^[3]
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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 MENLALTTLL LPFIGALVVS FSPQRRAAEW GVLFAALTTL CMLSLISAFY QADKVAVTLT LVNVGDVALF GLVIDRVSTL ILFVVVFLGL LVTIYSTGYL TDKNREHPHN GTNRYYAFLL VFIGAMAGLV LSSTLLGQLL FFEITGGCSW ALISYYQSDK AQRSALKALL ITHIGSLGLY LAAATLFLQT GTFALSAMSE LHGDARYLVY GGILFAAWGK SAQLPMQAWL PDAMEAPTPI SAYLHAASMV KVGVYIFARA IIDGGNIPHV IGGVGMVMAL VTILYGFLMY LPQQDMKRLL AWSTITQLGW MFFGLSLSIF GSRLALEGSI AYIVNHAFAK SLFFLVAGAL SYSCGTRLLP RLRGVLHTLP LPGVGFCVAA LAITGVPPFN GFFSKFPLFA AGFALSVEYW ILLPAMILLM IESVASFAWF IRWFGRVVPG KPSEAVADAA PLPGSMRLVL IVLIVMSLIS SVIAATWLQ
Length	479
Mol. Wt	51.756 kDa
pI	9.3 (calculated)
Extinction coefficient	80,330 - 80,830 (calc based on 17 Y, 10 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	132..402	PF00361 NADH-Ubiquinone/plastoquinone (complex I), various chains	PMID:19920124
Domain	55..121	PF00662 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus	PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=hyfD 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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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:16130409	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947290	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008185	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77416	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7301	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14212	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947290	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003873	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3964	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	0^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)
hyfABCDEFGHIJR-focB
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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_000913:2602813..2602853 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:b2484 (EcoliWiki Page)	NCBI GEO profiles for hyfD
microarray	GenExpDB:b2484 (EcoliWiki Page)	Summary of data for hyfD 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 hyfD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7301	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3964	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2484
EcoGene	EcoGene:EG14212	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003873	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008185	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
Apis mellifera	ENSAPMP00000001705 (score: 1.000; bootstrap: 100%) ENSAPMP00000031805 (score: 0.293) ENSAPMP00000020683 (score: 0.228) ENSAPMP00000017344 (score: 0.150) ENSAPMP00000028865 (score: 0.126) ENSAPMP00000028230 (score: 0.108)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00042913 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	HYFD	From SHIGELLACYC
E. coli O157	HYFD	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)	PF00361 NADH-Ubiquinone/plastoquinone (complex I), various chains
Pfam (EcoliWiki Page)	PF00662 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
Panther (EcoliWiki Page)	PTHR22773:SF39
EcoCyc	EcoCyc:G7301	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14212	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003873	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3964	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008185	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 ^3.2 ^3.3 ^3.4 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).

hyfD: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 hyfD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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