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Expression|

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Standard Name	hybA
Gene Synonym(s)	ECK2990, b2996, JW2964, hydC, hydL^[1], hydL
Product Desc.	hydrogenase 2 4Fe-4S ferredoxin-type component^[2]^[3]; Component of hydrogenase 2^[2]^[3] Hydrogenase 2 component, periplasmic; possibly electron acceptor for hydrogenase 2 small subunit; probably binds 4 4Fe-4S clusters^[4]
Product Synonyms(s)	hydrogenase 2 4Fe-4S ferredoxin-type component^[1], B2996^[2]^[1], HydL^[2]^[1], HybA^[2]^[1] , ECK2990, hydL, JW2964, b2996
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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Upregulated in biofilms; biofilm microarray result was validated with RT-PCR. Verified Tat substrate: HybA has a predicted Tat-only (Class I) 26 aa signal peptide.^[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	hybA
Mnemonic	Hydrogenase 2
Synonyms	ECK2990, b2996, JW2964, hydC, hydL^[1], hydL
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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	67.72 minutes	MG1655: 3143162..3142176 <gbrowseImage> name=NC_000913:3142176..3143162 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3079227..3078241 <gbrowseImage> name=NC_012967:3078241..3079227 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3029324..3030310 <gbrowseImage> name=NC_012759:3029324..3030310 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3143796..3142810 <gbrowseImage> name=NC_007779:3142810..3143796 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3240907..3239921 <gbrowseImage> name=NC_010473:3239921..3240907 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
ΔhybA (Keio:JW2964)	deletion	deletion	PMID:16738554	Shigen
hybA::Tn5KAN-I-SceI (FB21007)	Insertion at nt 342 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21007	does not contain pKD46
hybA::Tn5KAN-I-SceI (FB21008)	Insertion at nt 342 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21008	contains pKD46
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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
JW2964	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACAGACGTAATTTTATTAA Primer 2:CCTGACTCATGATCGTCTCCTCC
5C10	Kohara Phage	Genobase	PMID:3038334
nupG511::Tn10	Linked marker	CAG18472 = CGSC7433^[5]	est. P1 cotransduction: 20% ^[6]
metC162::Tn10	Linked marker	CAG18475 = CGSC7435^[5]	est. P1 cotransduction: 76% ^[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:EG11799	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11799	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001733	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944842	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1747	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009832	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	HybA
Synonyms	hydrogenase 2 4Fe-4S ferredoxin-type component^[1], B2996^[2]^[1], HydL^[2]^[1], HybA^[2]^[1] , ECK2990, hydL, JW2964, b2996
Product description	hydrogenase 2 4Fe-4S ferredoxin-type component^[2]^[3]; Component of hydrogenase 2^[2]^[3] Hydrogenase 2 component, periplasmic; possibly electron acceptor for hydrogenase 2 small subunit; probably binds 4 4Fe-4S clusters^[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:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	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:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	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
	GO:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0411	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0004	F	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
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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 2	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1144524
Protein	dinG		PMID:16606699	Experiment(s):EBI-1144524
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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
Periplasm		PMID:9738917	EchoLocation:hybA
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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 MNRRNFIKAA SCGALLTGAL PSVSHAAAEN RPPIPGSLGM LYDSTLCVGC QACVTKCQDI NFPERNPQGE QTWSNNDKLS PYTNNIIQVW TSGTGVNKDQ EENGYAYIKK QCMHCVDPNC VSVCPVSALK KDPKTGIVHY DKDVCTGCRY CMVACPYNVP KYDYNNPFGA LHKCELCNQK GVERLDKGGL PGCVEVCPAG AVIFGTREEL MAEAKKRLAL KPGSEYHYPR QTLKSGDTYL HTVPKYYPHL YGEKEGGGTQ VLVLTGVPYE NLDLPKLDDL STGARSENIQ HTLYKGMMLP LAVLAGLTVL VRRNTKNDHH DGGDDHES
Length	328
Mol. Wt	36.002 kDa
pI	7.4 (calculated)
Extinction coefficient	36,330 - 38,455 (calc based on 17 Y, 2 W, and 17 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
motif	1-27	UniProt Manual:Signal Peptides	UniProt:P0AAJ8
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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=hybA 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:16130896	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944842	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009832	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AAJ8	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11799	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11799	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944842	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001733	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1747	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	114	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	10	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	46^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_000913:3143142..3143182 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:b2996 (EcoliWiki Page)	NCBI GEO profiles for hybA
microarray	GenExpDB:b2996 (EcoliWiki Page)	Summary of data for hybA 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 hybA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11799	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1747	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2996
EcoGene	EcoGene:EG11799	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001733	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009832	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	HYBA	From SHIGELLACYC
E. coli O157	HYBA	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:54862
EcoCyc	EcoCyc:EG11799	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11799	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001733	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1747	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009832	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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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 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 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).

hybA: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 hybA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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