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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	patA
Gene Synonym(s)	ECK3063, b3073, JW5510, oat, pat, patA, ygjG^[1], ygjG
Product Desc.	G7596^[2]^[3] Putrescine:2-oxoglutaric acid aminotransferase; sigma 54-dependent^[4]
Product Synonyms(s)	putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent^[1], B3073^[2]^[1], YgjG^[2]^[1], Oat^[2]^[1], Pat^[2]^[1] , ECK3063, JW5510, ygjG, b3073
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): patA^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 29 (http://afmb.cnrs-mrs.fr/article171.html). The pat gene, mapped to 89.1 minutes, was thought to encode this activity. No ORF in the metB-argH region is a candidate. perhaps the pat mutation is a ygjG regulatory mutation and ygjG is the pat structural gene. YgjG also transaminates cadaverine and spermidine.YdcW couples with YgjG to convert putrescine to gamma-aminobutyric acid.^[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	patA
Mnemonic	Putrescine aminotransferase
Synonyms	ECK3063, b3073, JW5510, oat, pat, patA, ygjG^[1], ygjG
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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	69.35 minutes	MG1655: 3217489..3218895 <gbrowseImage> name=NC_000913:3217489..3218895 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3104664..3106043 <gbrowseImage> name=NC_012759:3104664..3106043 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3218123..3219529 <gbrowseImage> name=NC_007779:3218123..3219529 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3315234..3316640 <gbrowseImage> name=NC_010473:3315234..3316640 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)	Reference	Availability
ΔygjG (Keio:JW5510)	deletion	deletion	PMID:16738554	Shigen CGSC11435^[5]
ΔygjG763::kan			PMID:16738554	CGSC:105058
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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
JW5510	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATACGCGAGCCTCCGGAGCA Primer 2:CCtGCTTCTTCGACACTTACTCG
19F2	Kohara Phage	Genobase	PMID:3038334
17E4	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 93% ^[6] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[5]	est. P1 cotransduction: % ^[6] 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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3073
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3828
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YGJG
EcoCyc (EcoliWiki Page)	ECOCYC:G7596	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947120	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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	PatA
Synonyms	putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent^[1], B3073^[2]^[1], YgjG^[2]^[1], Oat^[2]^[1], Pat^[2]^[1] , ECK3063, JW5510, ygjG, b3073
Product description	G7596^[2]^[3] Putrescine:2-oxoglutaric acid aminotransferase; sigma 54-dependent^[4]
EC number (for enzymes)	2.6.1.29^[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:0030288	outer membrane-bounded periplasmic space				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008483	transaminase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01276	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008483	transaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005814	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008483	transaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010164	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008483	transaminase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0032	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009447	putrescine catabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01276	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009447	putrescine catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017747	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01276	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005814	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010164	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017747	F	Seeded from EcoCyc (v14.0)	complete
	GO:0033094	butane-1,4-diamine:2-oxoglutarate aminotransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017747	F	Seeded from EcoCyc (v14.0)	complete
	GO:0033094	butane-1,4-diamine:2-oxoglutarate aminotransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.6.1.82	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	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	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 MITEFVFIPI FAIAAGVAQS LQYLNRYHVI REPPEHILNR LPSSASALAC SAHALNLIEK RTLDHEEMKA LNREVIEYFK EHVNPGFLEY RKSVTAGGDY GAVEWQAGSL NTLVDTQGQE FIDCLGGFGI FNVGHRNPVV VSAVQNQLAK QPLHSQELLD PLRAMLAKTL AALTPGKLKY SFFCNSGTES VEAALKLAKA YQSPRGKFTF IATSGAFHGK SLGALSATAK STFRKPFMPL LPGFRHVPFG NIEAMRTALN ECKKTGDDVA AVILEPIQGE GGVILPPPGY LTAVRKLCDE FGALMILDEV QTGMGRTGKM FACEHENVQP DILCLAKALG GGVMPIGATI ATEEVFSVLF DNPFLHTTTF GGNPLACAAA LATINVLLEQ NLPAQAEQKG DMLLDGFRQL AREYPDLVQE ARGKGMLMAI EFVDNEIGYN FASEMFRQRV LVAGTLNNAK TIRIEPPLTL TIEQCELVIK AARKALAAMR VSVEEA
Length	496
Mol. Wt	53.911 kDa
pI	6.5 (calculated)
Extinction coefficient	20,400 - 21,525 (calc based on 10 Y, 1 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	68..397	PF00202 Aminotransferase class-III		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=ygjG 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:145698310	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947120	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P42588	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947120	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	12.881+/-0.131	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.277382646	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	8	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	789	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	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)
ygjG
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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

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<protect><gbrowseImage> name=NC_000913:3217469..3217509 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:b3073 (EcoliWiki Page)	NCBI GEO profiles for ygjG
microarray	GenExpDB:b3073 (EcoliWiki Page)	Summary of data for ygjG 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 (3216638..3217043) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:B10^[7]
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Notes

Accessions Related to patA Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3073
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	AT5G46180 (score: 1.000; bootstrap: 95%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000015623 (score: 1.000; bootstrap: 56%) ENSMMUP00000005330 (score: 0.444)	From Inparanoid:20070104
Oryza gramene	Q60DP3 (score: 1.000; bootstrap: 90%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC27F15c (score: 1.000; bootstrap: 86%)	From Inparanoid:20070104
Shigella flexneri	YGJG	From SHIGELLACYC
E. coli O157	YGJG	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)	PF00202 Aminotransferase class-III
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
Panther (EcoliWiki Page)	PTHR11986:SF30
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 ^1.12 ^1.13 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 ^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

patA: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 patA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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