{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	yncD
Gene Synonym(s)	ECK1445, b1451, JW1446^[1], JW1446
Product Desc.	probable TonB-dependent receptor^[2]^[3] Putative TonB-dependent outer membrane receptor^[4]
Product Synonyms(s)	predicted iron outer membrane transporter^[1], B1451^[2]^[1], YncD^[2]^[1] , ECK1445, JW1446, b1451
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yncD^[2]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

yncD and fhuA are paralogs.^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	yncD
Mnemonic	Systematic nomenclature
Synonyms	ECK1445, b1451, JW1446^[1], JW1446
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	32.74 minutes	MG1655: 1521089..1518987 <gbrowseImage> name=NC_000913:1518987..1521089 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1493175..1491073 <gbrowseImage> name=NC_012967:1491073..1493175 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1411046..1413148 <gbrowseImage> name=NC_012759:1411046..1413148 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1524779..1522677 <gbrowseImage> name=NC_007779:1522677..1524779 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1611684..1609582 <gbrowseImage> name=NC_010473:1609582..1611684 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability
ΔyncD (Keio:JW1446)	deletion	deletion			PMID:16738554	Shigen CGSC9262^[5]
ΔyncD::kan	deletion		Biolog:respiration	unable to respire Succinate	PMID:16095938
ΔyncD743::kan					PMID:16738554	CGSC:105782
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1446	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGATTTTTTCCGTCCGACA Primer 2:CCtTCAAATCTCCACGCAATATT
5F11	Kohara Phage	Genobase	PMID:3038334
8B7	Kohara Phage	Genobase	PMID:3038334
trg-2::Tn10	Linked marker	CAG12026 = CGSC7376^[5]	est. P1 cotransduction: 39% ^[6]
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: 55% ^[6] Synonyms:zdc-235::Tn10
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6762	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13774	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003351	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946015	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3536	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004839	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name	YncD
Synonyms	predicted iron outer membrane transporter^[1], B1451^[2]^[1], YncD^[2]^[1] , ECK1445, JW1446, b1451
Product description	probable TonB-dependent receptor^[2]^[3] Putative TonB-dependent outer membrane receptor^[4]
EC number (for enzymes)
edit table

Notes

Function

[back to top]

<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:0004872	receptor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000531	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004872	receptor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012910	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004872	receptor activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0675	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005215	transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000531	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005215	transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012910	F	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:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000531	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012910	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009279	cell outer membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0998	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000531	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012910	C	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:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	Seeded from EcoCyc (v14.0)	complete
edit table

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
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
outer membrane			From EcoCyc^[3]
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MKIFSVRQTV LPALLVLSPV VFAADEQTMI VSAAPQVVSE LDTPAAVSVV DGEEMRLATP RINLSESLTG VPGLQVQNRQ NYAQDLQLSI RGFGSRSTYG IRGIRLYVDG IPATMPDGQG QTSNIDLSSV QNVEVLRGPF SALYGNASGG VMNVTTQTGQ QPPTIEASSY YGSFGSWRYG LKATGATGDG TQPGDVDYTV STTRFTTHGY RDHSGAQKNL ANAKLGVRID EASKLSLIFN SVDIKADDPG GLTKAEWKAN PQQAPRAEQY DTRKTIKQTQ AGLRYERSLS SRDDMSVMMY AGERETTQYQ SIPMAPQLNP SHAGGVITLQ RHYQGIDSRW THRGELGVPV TFTTGLNYEN MSENRKGYNN FRLNSGMPEY GQKGELRRDE RNLMWNIDPY LQTQWQLSEK LSLDAGVRYS SVWFDSNDHY VTPGNGDDSG DASYHKWLPA GSLKYAMTDA WNIYLAAGRG FETPTINELS YRADGQSGMN LGLKPSTNDT IEIGSKTRIG DGLLSLALFQ TDTDDEIVVD SSSGGRTTYK NAGKTRRQGA ELAWDQRFAG DFRVNASWTW LDATYRSNVC NEQDCNGNRM PGIARNMGFA SIGYVPEDGW YAGTEARYMG DIMADDENTA KAPSYTLVGL FTGYKYNYHN LTVDLFGRVD NLFDKEYVGS VIVNESNGRY YEPSPGRNYG VGMNIAWRFE
Length	700
Mol. Wt	77.261 kDa
pI	5.2 (calculated)
Extinction coefficient	126,630 - 126,880 (calc based on 37 Y, 13 W, and 2 C residues)
edit table

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	1-23	UniProt Manual:Signal Peptides	UniProt:P76115
Domain	448..696	PF00593 TonB dependent receptor		PMID:19920124
Domain	39..151	PF07715 TonB-dependent Receptor Plug Domain		PMID:19920124
edit table

<motif_map/>

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

Structures

<beststructure> gene=yncD taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129410	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946015	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004839	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76115	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6762	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13774	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946015	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003351	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3536	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	353	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	69	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	163	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
yncD
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:1521069..1521109 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1451 (EcoliWiki Page)	NCBI GEO profiles for yncD
microarray	GenExpDB:b1451 (EcoliWiki Page)	Summary of data for yncD from multiple microarray studies
edit table

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 (1521013..1521344) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ02; Well:H3^[7]
edit table

Notes

Accessions Related to yncD Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6762	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3536	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1451
EcoGene	EcoGene:EG13774	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003351	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004839	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
edit table

</protect>

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:56935
Pfam (EcoliWiki Page)	PF00593 TonB dependent receptor
Pfam (EcoliWiki Page)	PF07715 TonB-dependent Receptor Plug Domain
EcoCyc	EcoCyc:G6762	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13774	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003351	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3536	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004839	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yncD: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 yncD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search