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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	ttdT
Gene Synonym(s)	ygjE, ECK3053, b3063, JW3035, ygjC^[1]^[2], ygjC
Product Desc.	YgjE tartrate/succinate DASS transporter^[3]; TtdT tartrate/succinate DASS transporter^[2] L-tartrate/succinate antiporter; needed for L-tatrate uptake and tartrate induction of ttdAB^[4]
Product Synonyms(s)	predicted tartrate:succinate antiporter^[1], B3063^[3]^[1], YgjC^[3]^[1], YgjE^[3]^[1], TtdT^[3]^[1] , ECK3053, JW3035, ygjC, ygjE, b3063
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ygjE^[3], ttdAB^[3]
Regulation/Activity
Quick Links
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Notes

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TtdT does not transport D-tartrate and can uptake succinate, although excretion of succinate is favored. IT (Ion Transporter) superfamily (Prakash, 2003). ST(3) structural class based on hydropathy profile (Lolkema, 2003). YgjE was mistakenly identified as both ygjE and YgiE in the abstract for Oshima (2006), and thus ygiE is listed as a synonym for ygjE in TCDB. The real YgiE is now called ZupT.^[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	ttdT
Mnemonic	Tartrate dehydratase
Synonyms	ygjE, ECK3053, b3063, JW3035, ygjC^[1]^[2], ygjC
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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	69.1 minutes	MG1655: 3206046..3207509 <gbrowseImage> name=NC_000913:3206046..3207509 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3140841..3142304 <gbrowseImage> name=NC_012967:3140841..3142304 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3093194..3094657 <gbrowseImage> name=NC_012759:3093194..3094657 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3206680..3208143 <gbrowseImage> name=NC_007779:3206680..3208143 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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: Type	Phenotype: Description	Reference	Availability	Comments
ΔttdT755::kan					PMID:16738554	CGSC:106368
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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

19F2

Kohara Phage

Genobase

PMID:3038334

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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:EG12393	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12393	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002256	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947576	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2294	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010056	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	TtdT
Synonyms	predicted tartrate:succinate antiporter^[1], B3063^[3]^[1], YgjC^[3]^[1], YgjE^[3]^[1], TtdT^[3]^[1] , ECK3053, JW3035, ygjC, ygjE, b3063
Product description	YgjE tartrate/succinate DASS transporter^[3]; TtdT tartrate/succinate DASS transporter^[2] L-tartrate/succinate antiporter; needed for L-tatrate uptake and tartrate induction of ttdAB^[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:0015297	antiporter activity	PMID:17172328	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	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:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006814	sodium ion transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001898	P	Seeded from EcoCyc (v14.0)	complete
	GO:0015297	antiporter activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0050	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001898	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:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0055085	transmembrane transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001898	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
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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
plasma membrane	C-terminus localized to the periplasm with 13 predicted transmembrane domains	Daley et al. (2005) ^[5]
plasma membrane			From EcoCyc^[2]
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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 MKPSTEWWRY LAPLAVIAII ALLPVPAGLE NHTWLYFAVF TGVIVGLILE PVPGAVVAMV GISIIAILSP WLLFSPEQLA QPGFKFTAKS LSWAVSGFSN SVIWLIFAAF MFGTGYEKTG LGRRIALILV KKMGHRTLFL GYAVMFSELI LAPVTPSNSA RGAGIIYPII RNLPPLYQSQ PNDSSSRSIG SYIMWMGIVA DCVTSAIFLT AMAPNLLLIG LMKSASHATL SWGDWFLGML PLSILLVLLV PWLAYVLYPP VLKSGDQVPR WAETELQAMG PLCSREKRML GLMVGALVLW IFGGDYIDAA MVGYSVVALM LLLRIISWDD IVSNKAAWNV FFWLASLITL ATGLNNTGFI SWFGKLLAGS LSGYSPTMVM VALIVVFYLL RYFFASATAY TSALAPMMIA AALAMPEIPL PVFCLMVGAA IGLGSILTPY ATGPSPIYYG SGYLPTADYW RLGAIFGLIF LVLLVITGLL WMPVVLL
Length	487
Mol. Wt	52.909 kDa
pI	9.2 (calculated)
Extinction coefficient	128,800 - 129,175 (calc based on 20 Y, 18 W, and 3 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	4..487	PF00939 Sodium:sulfate symporter transmembrane region		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=ttdT 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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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:16130959	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947576	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010056	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39414	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12393	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12393	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947576	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002256	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2294	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	0^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^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)
ygjE
ttdAB
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File:.jpg

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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_000913:3206026..3206066 source=MG1655 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

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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:b3063 (EcoliWiki Page)	NCBI GEO profiles for ttdT
microarray	GenExpDB:b3063 (EcoliWiki Page)	Summary of data for ttdT 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 ttdT Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12393	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2294	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3063
EcoGene	EcoGene:EG12393	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002256	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010056	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
Bos taurus	ENSBTAP00000001161 (score: 1.000; bootstrap: 100%) ENSBTAP00000031644 (score: 1.000; bootstrap: 100%) ENSBTAP00000006144 (score: 1.000; bootstrap: 100%) ENSBTAP00000035160 (score: 0.440) ENSBTAP00000005040 (score: 0.374)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00003517 (score: 1.000; bootstrap: 100%) WBGene00007138 (score: 0.263) WBGene00003518 (score: 0.223)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000015478 (score: 1.000; bootstrap: 100%) ENSCAFP00000022664 (score: 0.383) ENSCAFP00000027595 (score: 0.366) ENSCAFP00000004912 (score: 0.332) ENSCAFP00000005317 (score: 0.328)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000000383 (score: 1.000; bootstrap: 100%) ENSCINP00000019736 (score: 0.314) ENSCINP00000007638 (score: 0.240) ENSCINP00000017616 (score: 0.190) ENSCINP00000019733 (score: 0.144)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-2486 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-3433 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-3336 (score: 0.384) ZDB-GENE-040426-2389 (score: 0.384) ZDB-CDNA-040425-3750 (score: 0.383) ZDB-CDNA-040425-846 (score: 0.334) ZDB-CDNA-040425-845 (score: 0.334) ZDB-GENE-031222-3 (score: 0.334)	From Inparanoid:20070104
Homo sapiens	ENSP00000279027 (score: 1.000; bootstrap: 100%) ENSP00000194130 (score: 1.000; bootstrap: 100%) ENSP00000297282 (score: 0.461) ENSP00000293800 (score: 0.416) ENSP00000316202 (score: 0.402)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000012550 (score: 1.000; bootstrap: 100%) ENSMMUP00000028937 (score: 0.446) ENSMMUP00000022045 (score: 0.410) ENSMMUP00000022249 (score: 0.398) ENSMMUP00000021519 (score: 0.253)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000019234 (score: 1.000; bootstrap: 100%) ENSMODP00000020288 (score: 1.000; bootstrap: 100%) ENSMODP00000017491 (score: 0.438) ENSMODP00000024030 (score: 0.361) ENSMODP00000020748 (score: 0.097)	From Inparanoid:20070104
Mus musculus	MGI:1859937 (score: 1.000; bootstrap: 100%) MGI:1276558 (score: 0.361) MGI:3037150 (score: 0.353) MGI:2149635 (score: 0.334)	From Inparanoid:20070104
Oryza gramene	Q768R3 (score: 1.000; bootstrap: 100%) Q768R2 (score: 0.991) Q6Z229 (score: 0.823) Q6K4A2 (score: 0.709) Q768R4 (score: 0.696) Q8L801 (score: 0.668)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000023355 (score: 1.000; bootstrap: 100%) ENSPTRP00000033801 (score: 0.328) ENSPTRP00000014757 (score: 0.179) ENSPTRP00000015222 (score: 0.159) ENSPTRP00000040805 (score: 0.091)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000025843 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNR013C (score: 1.000; bootstrap: 100%) YCR037C (score: 0.305) YJL198W (score: 0.282)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000180927 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000179051 (score: 0.503) NEWSINFRUP00000181759 (score: 0.322)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00029948001 (score: 1.000; bootstrap: 100%) GSTENP00030073001 (score: 1.000; bootstrap: 100%) GSTENP00029947001 (score: 0.795) GSTENP00014690001 (score: 0.641) GSTENP00023460001 (score: 0.394) GSTENP00019703001 (score: 0.351) GSTENP00009235001 (score: 0.289) GSTENP00030074001 (score: 0.117)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000017162 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGJE	From SHIGELLACYC
E. coli O157	YGJE	From ECOO157CYC
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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)	PF00939 Sodium:sulfate symporter transmembrane region
EcoCyc	EcoCyc:EG12393	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12393	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002256	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2294	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010056	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 EcoCyc (release 10.6; 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.
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

ttdT: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 ttdT Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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