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On One Page

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Expression|

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Standard Name	hybD
Gene Synonym(s)	ECK2987, b2993, JW2961^[1], JW2961
Product Desc.	predicted maturation element for hydrogenase 2^[2]^[3] Maturation endoprotease for Ni-containing hydrogenase 2^[4]
Product Synonyms(s)	predicted maturation element for hydrogenase 2^[1], B2993^[2]^[1], HybD^[2]^[1] , ECK2987, JW2961, b2993
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hybOABCDEFG^[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	hybD
Mnemonic	Hydrogenase 2
Synonyms	ECK2987, b2993, JW2961^[1], JW2961
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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	67.65 minutes	MG1655: 3139308..3138814 <gbrowseImage> name=NC_000913:3138814..3139308 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3075373..3074879 <gbrowseImage> name=NC_012967:3074879..3075373 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3025962..3026456 <gbrowseImage> name=NC_012759:3025962..3026456 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3139942..3139448 <gbrowseImage> name=NC_007779:3139448..3139942 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3237053..3236559 <gbrowseImage> name=NC_010473:3236559..3237053 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
ΔhybD (Keio:JW2961)	deletion	deletion	PMID:16738554	Shigen CGSC10278^[5]
hybD::Tn5KAN-I-SceI (FB21003)	Insertion at nt 63 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21003	does not contain pKD46
hybD::Tn5KAN-I-SceI (FB21004)	Insertion at nt 63 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21004	contains pKD46
ΔhybD766::kan			PMID:16738554	CGSC:101460
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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
JW2961	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTATTTTAGTCTTAGGGGT Primer 2:CCGTCATGAATCGCCTCCCGTGG
2B7	Kohara Phage	Genobase	PMID:3038334
5C10	Kohara Phage	Genobase	PMID:3038334
nupG511::Tn10	Linked marker	CAG18472 = CGSC7433^[5]	est. P1 cotransduction: 24% ^[6]
metC162::Tn10	Linked marker	CAG18475 = CGSC7435^[5]	est. P1 cotransduction: 67% ^[6]
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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:EG11802	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11802	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001736	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948982	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1750	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009826	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	HybD
Synonyms	predicted maturation element for hydrogenase 2^[1], B2993^[2]^[1], HybD^[2]^[1] , ECK2987, JW2961, b2993
Product description	predicted maturation element for hydrogenase 2^[2]^[3] Maturation endoprotease for Ni-containing hydrogenase 2^[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:0004190	aspartic-type endopeptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0064	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008047	enzyme activator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000671	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008233	peptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000671	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008233	peptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0645	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016151	nickel ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0533	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016485	protein processing	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004419	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004419	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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	rplB	PMID:16606699	Experiment(s):EBI-1144514
Protein	yibL	PMID:16606699	Experiment(s):EBI-1144514
Protein	greB	PMID:16606699	Experiment(s):EBI-1144514
Protein	yddH	PMID:16606699	Experiment(s):EBI-1144514
Protein	prfC	PMID:19402753	LCMS(ID Probability):99.0
Protein	wrbA	PMID:19402753	MALDI(Z-score):29.667682
Protein	hybC	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.197872
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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 MRILVLGVGN ILLTDEAIGV RIVEALEQRY ILPDYVEILD GGTAGMELLG DMANRDHLII ADAIVSKKNA PGTMMILRDE EVPALFTNKI SPHQLGLADV LSALRFTGEF PKKLTLVGVI PESLEPHIGL TPTVEAMIEP ALEQVLAALR ESGVEAIPRE AIHD
Length	164
Mol. Wt	17.75 kDa
pI	4.5 (calculated)
Extinction coefficient	2,980 (calc based on 2 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
Modification Site	102	phosphorylation site at S102	probability greater than 75%	PMID:17938405
Domain	20..148	PF01750 Hydrogenase maturation protease		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=hybD 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:16130893	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948982	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009826	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37182	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11802	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11802	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948982	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001736	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1750	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	4.163+/-0.113	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.053643725	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	133	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	26	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	80^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)
hybOABCDEFG
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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_000913:3139288..3139328 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:b2993 (EcoliWiki Page)	NCBI GEO profiles for hybD
microarray	GenExpDB:b2993 (EcoliWiki Page)	Summary of data for hybD 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 hybD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11802	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1750	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2993
EcoGene	EcoGene:EG11802	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001736	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009826	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	HYBD	From SHIGELLACYC
E. coli O157	HYBD	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)	PF01750 Hydrogenase maturation protease
Superfamily (EcoliWiki Page)	SUPERFAMILY:53163
EcoCyc	EcoCyc:EG11802	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11802	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001736	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1750	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009826	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 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).

hybD: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 hybD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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