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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	pth
Gene Synonym(s)	ECK1192, b1204, JW1195, rap, asuA?, G518^[1]^[2]
Product Desc.	peptidyl-tRNA hydrolase^[2]^[3] Peptidyl-tRNA hydrolase; required for phage lambda growth^[4]
Product Synonyms(s)	peptidyl-tRNA hydrolase^[1], B1204^[2]^[1], Rap^[2]^[1], Pth^[2]^[1] , asuA?, ECK1192, JW1195, rap, b1204
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pth-ychF^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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Histidine 20 acts as the catalytic base during hydrolysis.^[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	pth
Mnemonic	Peptidyl tRNA hydrolase, recombination adept with plasmid
Synonyms	ECK1192, b1204, JW1195, rap, asuA?, G518^[1]^[2]
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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	27.1 minutes	MG1655: 1257736..1257152 <gbrowseImage> name=NC_000913:1257152..1257736 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1258663..1258079 <gbrowseImage> name=NC_012967:1258079..1258663 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1145873..1146457 <gbrowseImage> name=NC_012759:1145873..1146457 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1260090..1259506 <gbrowseImage> name=NC_007779:1259506..1260090 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1297977..1297393 <gbrowseImage> name=NC_010473:1297393..1297977 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
Coding Start (SO:0000323)	MG1655	1257152	Edman degradation	PMID:1833189
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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
pth::Tn5KAN-2 (FB20267)	Insertion at nt 551 in Plus orientation			PMID:15262929	E. coli Genome Project:FB20267	does not contain pKD46
pthG101D		G101D	Pth(ts) mutants synthesize thermosensitive PTH and die at 42 degrees Celsius from a defect in protein synthesis			seeded from UniProt:P0A7D1
pthR134H		R134H	Rap mutants do not support vegetative growth of bacteriophage lambda and die upon transcription of lambda DNA bar sites			seeded from UniProt:P0A7D1
pth-1					CGSC:12904
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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
JW1195	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACGATTAAATTGATTGTCGG Primer 2:CCTTGCGCTTTAAAGGCGTGCAA
12A3	Kohara Phage	Genobase	PMID:3038334
4D10	Kohara Phage	Genobase	PMID:3038334
fadR13::Tn10	Linked marker	CAG18497 = CGSC7365^[5]	est. P1 cotransduction: 43% ^[6]
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[5]	est. P1 cotransduction: 12% ^[6] Synonyms:zch-506::Tn10, zci-506::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:EG10785	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10785	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000776	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945765	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0778	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004043	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	Pth
Synonyms	peptidyl-tRNA hydrolase^[1], B1204^[2]^[1], Rap^[2]^[1], Pth^[2]^[1] , asuA?, ECK1192, JW1195, rap, b1204
Product description	peptidyl-tRNA hydrolase^[2]^[3] Peptidyl-tRNA hydrolase; required for phage lambda growth^[4]
EC number (for enzymes)	3.1.1.29^[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:0004045	aminoacyl-tRNA hydrolase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00083	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004045	aminoacyl-tRNA hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001328	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004045	aminoacyl-tRNA hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018171	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004045	aminoacyl-tRNA hydrolase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.1.1.29	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00083	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00083	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001328	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018171	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	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	rpsB	PMID:15690043	Experiment(s):EBI-878620, EBI-881343
Protein	tufA	PMID:15690043	Experiment(s):EBI-878620
Protein	clpS	PMID:15690043	Experiment(s):EBI-878620
Protein	prs	PMID:16606699	Experiment(s):EBI-1139174
Protein	ccmB	PMID:15690043	Experiment(s):EBI-881343
Protein	ispH	PMID:15690043	Experiment(s):EBI-881343
Protein	groL	PMID:15690043	Experiment(s):EBI-881343
Protein	rplD	PMID:15690043	Experiment(s):EBI-881343
Protein	rplK	PMID:15690043	Experiment(s):EBI-881343
Protein	rplL	PMID:15690043	Experiment(s):EBI-881343
Protein	rplM	PMID:15690043	Experiment(s):EBI-881343
Protein	rplV	PMID:15690043	Experiment(s):EBI-881343
Protein	rpmB	PMID:15690043	Experiment(s):EBI-881343
Protein	rpmG	PMID:15690043	Experiment(s):EBI-881343
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-881343
Protein	groL	PMID:19402753	LCMS(ID Probability):99.6
Protein	ispH	PMID:19402753	LCMS(ID Probability):99.0
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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 MTIKLIVGLA NPGAEYAATR HNAGAWFVDL LAERLRAPLR EEAKFFGYTS RVTLGGEDVR LLVPTTFMNL SGKAVAAMAS FFRINPDEIL VAHDELDLPP GVAKFKLGGG HGGHNGLKDI ISKLGNNPNF HRLRIGIGHP GDKNKVVGFV LGKPPVSEQK LIDEAIDEAA RCTEMWFTDG LTKATNRLHA FKAQ
Length	194
Mol. Wt	21.082 kDa
pI	9.3 (calculated)
Extinction coefficient	13,980 - 14,105 (calc based on 2 Y, 2 W, and 1 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	5..189	PF01195 Peptidyl-tRNA hydrolase		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=pth 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:16129167	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945765	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004043	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7D1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10785	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10785	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945765	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000776	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0778	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 MC4100	5.61E+02	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	Ecoli K-12	15.983+/-0.182	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.02739726	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	1966	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	403	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	1030	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)
pth-ychF
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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_000913:1257716..1257756 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

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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:b1204 (EcoliWiki Page)	NCBI GEO profiles for pth
microarray	GenExpDB:b1204 (EcoliWiki Page)	Summary of data for pth 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 (1257650..1258017) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ12; Well:A3^[7]
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Notes

Accessions Related to pth Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10785	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0778	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1204
EcoGene	EcoGene:EG10785	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000776	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004043	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
Arabidopsis thaliana	AT1G18440 (score: 1.000; bootstrap: 100%) AT5G16140 (score: 0.235) AT5G19830 (score: 0.230) AT5G38290 (score: 0.219)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000016930 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029825 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050306-33 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050306-33 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0205243 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000334277 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000021573 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000006808 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1913779 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5N9Q7 (score: 1.000; bootstrap: 100%) Q9M5P4 (score: 0.261) Q5ZCL8 (score: 0.243)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000032989 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YHR189W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC2D105c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000163967 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00031017001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000021973 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PTH	From SHIGELLACYC
E. coli O157	PTH	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:53178
Panther (EcoliWiki Page)	PTHR17224:SF0
Pfam (EcoliWiki Page)	PF01195 Peptidyl-tRNA hydrolase
EcoCyc	EcoCyc:EG10785	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10785	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000776	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0778	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004043	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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.
↑ ^5.0 ^5.1 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

pth: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 pth Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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