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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	tdcD
Gene Synonym(s)	ECK3104, b3115, JW5806, yhaA^[1], yhaA
Product Desc.	Propionate kinase, anaerobic; non-essential gene^[2]
Product Synonyms(s)	propionate kinase/acetate kinase C, anaerobic^[1], B3115^[3]^[1], YhaA^[3]^[1], TdcD^[3]^[1] , ECK3104, JW5806, yhaA, b3115
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): tdcABCDEFG^[3], OP00167, tdcABC
Regulation/Activity
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Notes

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otherPDB (S. typhimurium): 1X3M, 1X3N.^[2]

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	tdcD
Mnemonic	Threonine dehydratase, catabolic
Synonyms	ECK3104, b3115, JW5806, yhaA^[1], yhaA
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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	70.27 minutes	MG1655: 3261694..3260474 <gbrowseImage> name=NC_000913:3260474..3261694 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3196706..3195486 <gbrowseImage> name=NC_012967:3195486..3196706 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3147622..3148830 <gbrowseImage> name=NC_012759:3147622..3148830 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3263515..3262220 <gbrowseImage> name=NC_007779:3262220..3263515 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3359439..3358219 <gbrowseImage> name=NC_010473:3358219..3359439 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: Type	Phenotype: Description	Reference	Availability	Comments
ΔtdcD (Keio:JW5806)	deletion	deletion			PMID:16738554	Shigen
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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
JW5806	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATGAATTTCCGGTTGTTTT Primer 2:CCAATAGGCTGATTCAAGGCATT
8F8	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[4]	est. P1 cotransduction: 14% ^[5] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[4]	est. P1 cotransduction: 1% ^[5] Synonyms:zgj-203::Tn10, zha-203::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:EG11172	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11172	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001154	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947635	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1159	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010245	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	TdcD
Synonyms	propionate kinase/acetate kinase C, anaerobic^[1], B3115^[3]^[1], YhaA^[3]^[1], TdcD^[3]^[1] , ECK3104, JW5806, yhaA, b3115
Product description	Propionate kinase, anaerobic; non-essential gene^[2]
EC number (for enzymes)	2.7.2.1^[1] 2.7.2.-^[1]
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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: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:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000890	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00020	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008776	acetate kinase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00020	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008980	propionate kinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.2.15	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016310	phosphorylation	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00020	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016310	phosphorylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000890	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	lysS	PMID:15690043	Experiment(s):EBI-886684, EBI-890312
Protein	tufA	PMID:15690043	Experiment(s):EBI-886684
Protein	glf	PMID:15690043	Experiment(s):EBI-893053
Protein	glf	PMID:19402753	LCMS(ID Probability):99.6
Protein	tufB	PMID:19402753	MALDI(Z-score):23.149329
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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 MRKEMNEFPV VLVINCGSSS IKFSVLDASD CEVLMSGIAD GINSENAFLS VNGGEPAPLA HHSYEGALKA IAFELEKRNL NDSVALIGHR IAHGGSIFTE SAIITDEVID NIRRVSPLAP LHNYANLSGI ESAQQLFPGV TQVAVFDTSF HQTMAPEAYL YGLPWKYYEE LGVRRYGFHG TSHRYVSQRA HSLLNLAEDD SGLVVAHLGN GASICAVRNG QSVDTSMGMT PLEGLMMGTR SGDVDFGAMS WVASQTNQSL GDLERVVNKE SGLLGISGLS SDLRVLEKAW HEGHERAQLA IKTFVHRIAR HIAGHAASLR RLDGIIFTGG IGENSSLIRR LVMEHLAVLG LEIDTEMNNR SNSCGERIVS SENARVICAV IPTNEEKMIA LDAIHLGKVN APAEFA
Length	406
Mol. Wt	43.928 kDa
pI	5.9 (calculated)
Extinction coefficient	28,420 - 29,045 (calc based on 8 Y, 3 W, and 5 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	6..387	PF00871 Acetokinase 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=tdcD 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:145698313	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947635	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010245	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P11868	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11172	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11172	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947635	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001154	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1159	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	Ecoli K-12	0.222+/-0.043	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	30	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	8	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	15^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)
tdcABCDEFG
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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_000913:3261674..3261714 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:b3115 (EcoliWiki Page)	NCBI GEO profiles for tdcD
microarray	GenExpDB:b3115 (EcoliWiki Page)	Summary of data for tdcD 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 tdcD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11172	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1159	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3115
EcoGene	EcoGene:EG11172	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001154	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010245	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
Xenopus tropicalis	ENSXETP00000023519 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	TDCD	From SHIGELLACYC
E. coli O157	TDCD	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)	PF00871 Acetokinase family
Panther (EcoliWiki Page)	PTHR21060:SF9
Superfamily (EcoliWiki Page)	SUPERFAMILY:53067
Superfamily (EcoliWiki Page)	SUPERFAMILY:53067
EcoCyc	EcoCyc:EG11172	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11172	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001154	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1159	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010245	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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

tdcD: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 tdcD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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