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Gene |

Product(s) |

Expression|

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Standard Name	ydgH
Gene Synonym(s)	ECK1599, b1604, JW1596^[1], JW1596
Product Desc.	conserved hypothetical protein^[2]^[3] Predicted periplasmic protein, YhcN family, function unknown; contains 3 tandem YhcN domains^[4]
Product Synonyms(s)	predicted protein^[1], B1604^[2]^[1], YdgH^[2]^[1] , ECK1599, JW1596, b1604
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydgH^[2]
Regulation/Activity
Quick Links
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Notes

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The first 22 aa are predicted to be a type I signal peptide.^[4]

YdgH is a member of the YhcN_Family of paralogs.^[5]

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	ydgH
Mnemonic	Systematic nomenclature
Synonyms	ECK1599, b1604, JW1596^[1], JW1596
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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	36.13 minutes	MG1655: 1676451..1677395 <gbrowseImage> name=NC_000913:1676451..1677395 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1655622..1656566 <gbrowseImage> name=NC_012967:1655622..1656566 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1568510..1569454 <gbrowseImage> name=NC_012759:1568510..1569454 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1680141..1681085 <gbrowseImage> name=NC_007779:1680141..1681085 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1767412..1768356 <gbrowseImage> name=NC_010473:1767412..1768356 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
ΔydgH (Keio:JW1596)	deletion	deletion	PMID:16738554	Shigen CGSC9357^[6]
ΔydgH752::kan			PMID:16738554	CGSC:104270
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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
JW1596	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGCTTAAGAACACCCTCCT Primer 2:CCTTTATACAGATCTGCGCTGAC
11H12	Kohara Phage	Genobase	PMID:3038334
6A3	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[6]	est. P1 cotransduction: % ^[7] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[6]	est. P1 cotransduction: % ^[7] Synonyms:zdh-925::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:G6860	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13929	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003449	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945117	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3688	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005359	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	YdgH
Synonyms	predicted protein^[1], B1604^[2]^[1], YdgH^[2]^[1] , ECK1599, JW1596, b1604
Product description	conserved hypothetical protein^[2]^[3] Predicted periplasmic protein, YhcN family, function unknown; contains 3 tandem YhcN domains^[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
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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

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 MKLKNTLLAS ALLSAMAFSV NAATELTPEQ AAAVKPFDRV VVTGRFNAIG EAVKAVSRRA DKEGAASFYV VDTSDFGNSG NWRVVADLYK ADAEKAEETS NRVINGVVEL PKDQAVLIEP FDTVTVQGFY RSQPEVNDAI TKAAKAKGAY SFYIVRQIDA NQGGNQRITA FIYKKDAKKR IVQSPDVIPA DSEAGRAALA AGGEAAKKVE IPGVATTASP SSEVGRFFET QSSKGGRYTV TLPDGTKVEE LNKATAAMMV PFDSIKFSGN YGNMTEVSYQ VAKRAAKKGA KYYHITRQWQ ERGNNLTVSA DLYK
Length	314
Mol. Wt	33.902 kDa
pI	9.7 (calculated)
Extinction coefficient	28,880 (calc based on 12 Y, 2 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
motif	1-19	UniProt Manual:Signal Peptides	UniProt:P76177
Domain	24..90	PF07338 Protein of unknown function (DUF1471)		PMID:19920124
Domain	108..174	PF07338 Protein of unknown function (DUF1471)		PMID:19920124
Domain	249..314	PF07338 Protein of unknown function (DUF1471)		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=ydgH taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

NMR and X-ray crystallographic studies of four DUF1471 domains from 3 paralogous DUF1471 subfamilies in Salmonella have been reported, including Salmonella SssB/YdgH and YahO.^[8]

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:16129562	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945117	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005359	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76177	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6860	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13929	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945117	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003449	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3688	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	Reference(s)
Protein	E. coli K-12 MC4100	1.23E+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	E. coli K-12 MG1655	4472	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	2760	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	2263	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)
ydgH
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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_000913:1676431..1676471 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:b1604 (EcoliWiki Page)	NCBI GEO profiles for ydgH
microarray	GenExpDB:b1604 (EcoliWiki Page)	Summary of data for ydgH 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
	GFP Fusion	Intergenic region (1675827..1676525) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:G7^[9]
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Notes

Accessions Related to ydgH Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6860	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3688	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1604
EcoGene	EcoGene:EG13929	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003449	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005359	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	S1757	From SHIGELLACYC
E. coli O157	Z2603	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)	PF07338 Protein of unknown function (DUF1471)
Pfam (EcoliWiki Page)	PF07338 Protein of unknown function (DUF1471)
Pfam (EcoliWiki Page)	PF07338 Protein of unknown function (DUF1471)
EcoCyc	EcoCyc:G6860	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13929	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003449	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3688	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005359	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.
↑ Rudd, KE et al. (1998) Low molecular weight proteins: a challenge for post-genomic research. Electrophoresis 19 536-44 PubMed
↑ ^6.0 ^6.1 ^6.2 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 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).
↑ Eletsky, A et al. (2014) Structural and functional characterization of DUF1471 domains of Salmonella proteins SrfN, YdgH/SssB, and YahO. PLoS ONE 9 e101787 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ydgH: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 ydgH Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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