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Product(s) |

Expression|

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Standard Name	yjdA
Gene Synonym(s)	ECK4102, b4109, JW4070^[1], JW4070
Product Desc.	conserved protein with nucleoside triphosphate hydrolase domain^[2]^[3] Function unknown^[4]
Product Synonyms(s)	conserved protein with nucleoside triphosphate hydrolase domain product^[1], B4109 product^[2]^[1], YjdA product^[2]^[1] , ECK4102, JW4070, b4109
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yjdA^[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	yjdA
Mnemonic	Systematic nomenclature
Synonyms	ECK4102, b4109, JW4070^[1], JW4070
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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	93.22 minutes	MG1655: 4325158..4327386 <gbrowseImage> name=NC_000913:4325158..4327386 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4305849..4308077 <gbrowseImage> name=NC_012967:4305849..4308077 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4263893..4266121 <gbrowseImage> name=NC_012759:4263893..4266121 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4331813..4334041 <gbrowseImage> name=NC_007779:4331813..4334041 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4425520..4427748 <gbrowseImage> name=NC_010473:4425520..4427748 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)	Phenotype: Description	Reference	Availability	Comments
ΔyjdA (Keio:JW4070)	deletion	deletion		PMID:16738554	Shigen CGSC10929^[5]
yjdAI516M		I516M	(in strain: B)			Strain variation; seeded from UniProt:P16694
yjdAE594A		E594A	(in strain: B)			Strain variation; seeded from UniProt:P16694
yjdAY346H		Y346H	(in strain: B)			Strain variation; seeded from UniProt:P16694
yjdAP356A		P356A	(in strain: B)			Strain variation; seeded from UniProt:P16694
yjdAKV499NA		KV499NA	(in strain: B)			Strain variation; seeded from UniProt:P16694
yjdAI458V		I458V	(in strain: B)			Strain variation; seeded from UniProt:P16694
yjdAE600D		E600D	(in strain: B)			Strain variation; seeded from UniProt:P16694
ΔyjdA735::kan				PMID:16738554	CGSC:105490
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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
JW4070	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTACACACAGACCCTGTATGA Primer 2:CCATATCGTTCTGCCGTGAAAAG
12H2	Kohara Phage	Genobase	PMID:3038334
2C12	Kohara Phage	Genobase	PMID:3038334
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 49% ^[6]
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 29% ^[6] Synonyms:zjd-2231::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:EG11210	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11210	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001190	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948620	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1195	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013456	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	YjdA product
Synonyms	conserved protein with nucleoside triphosphate hydrolase domain product^[1], B4109 product^[2]^[1], YjdA product^[2]^[1] , ECK4102, JW4070, b4109
Product description	conserved protein with nucleoside triphosphate hydrolase domain^[2]^[3] Function unknown^[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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003924	GTPase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001401	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005525	GTP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001401	F	Seeded from EcoCyc (v14.0)	complete
	GO:0015716	phosphonate transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0019	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	References	Evidence
Protein	dnaE	PMID:16606699	Experiment(s):EBI-1147464
Protein	metH	PMID:16606699	Experiment(s):EBI-1147464
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1147464
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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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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 MYTQTLYELS QEAERLLQLS RQQLQLLEKM PLSVPGDDAP QLALPWSQPN IAERHAMLNN ELRKISRLEM VLAIVGTMKA GKSTTINAIV GTEVLPNRNR PMTALPTLIR HTPGQKEPVL HFSHVAPIDC LIQQLQQRLR DCDIKHLTDV LEIDKDMRAL MQRIENGVAF EKYYLGAQPI FHCLKSLNDL VRLAKALDVD FPFSAYAAIE HIPVIEVEFV HLAGLESYPG QLTLLDTPGP NEAGQPHLQK MLNQQLARAS AVLAVLDYTQ LKSISDEEVR EAILAVGQSV PLYVLVNKFD QQDRNSDDAD QVRALISGTL MKGCITPQQI FPVSSMWGYL ANRARYELAN NGKLPPPEQQ RWVEDFAHAA LGRRWRHADL ADLEHIRHAA DQLWEDSLFA QPIQALLHAA YANASLYALR SAAHKLLNYA QQAREYLDFR AHGLNVACEQ LRQNIHQIEE SLQLLQLNQA QVSGEIKHEI ELALTSANHF LRQQQDALKV QLAALFQDDS EPLSEIRTRC ETLLQTAQNT ISRDFTLRFA ELESTLCRVL TDVIRPIEQQ VKMELSESGF RPGFHFPVFH GVVPHFNTRQ LFSEVISRQE ATDEQSTRLG VVRETFSRWL NQPDWGRGNE KSPTETVDYS VLQRALSAEV DLYCQQMAKV LAEQVDESVT AGMNTFFAEF ASCLTELQTR LRESLALRQQ NESVVRLMQQ QLQQTVMTHG WIYTDAQLLR DDIQTLFTAE RY
Length	742
Mol. Wt	84.371 kDa
pI	5.7 (calculated)
Extinction coefficient	70,820 - 71,945 (calc based on 18 Y, 8 W, and 9 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
Domain	72..300	PF00350 Dynamin family		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=yjdA 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:16131935	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948620	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013456	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P16694	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11210	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11210	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948620	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001190	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1195	Escherichia coli str. K-12 substr. MG1655
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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 MG1655	27	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	20	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	25	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)
yjdA
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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_000913:4325138..4325178 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:b4109 (EcoliWiki Page)	NCBI GEO profiles for yjdA
microarray	GenExpDB:b4109 (EcoliWiki Page)	Summary of data for yjdA 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 yjdA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11210	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1195	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4109
EcoGene	EcoGene:EG11210	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001190	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013456	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	YJDA	From SHIGELLACYC
E. coli O157	YJDA	From ECOO157CYC
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Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00350 Dynamin family
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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).

yjdA: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 yjdA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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