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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	ybdL
Gene Synonym(s)	ECK0594, b0600, JW0593^[1], JW0593
Product Desc.	methionine aminotransferase, PLP-dependent^[2]^[3] Methionine aminotransferase, PLP-dependent^[4]
Product Synonyms(s)	methionine aminotransferase, PLP-dependent^[1], B0600^[2]^[1], YbdL^[2]^[1] , ECK0594, JW0593, b0600
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybdL^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 35 (http://afmb.cnrs-mrs.fr/article171.html). Upregulated by GSNO in defined medium (aerobic). Also an aminotransferase for histidine, and weakly, phenylalanine.^[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	ybdL
Mnemonic	Systematic nomenclature
Synonyms	ECK0594, b0600, JW0593^[1], JW0593
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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	13.64 minutes	MG1655: 632809..633969 <gbrowseImage> name=NC_000913:632809..633969 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 616283..617443 <gbrowseImage> name=NC_012967:616283..617443 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 535569..536729 <gbrowseImage> name=NC_012759:535569..536729 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 632809..633969 <gbrowseImage> name=NC_007779:632809..633969 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 572141..573301 <gbrowseImage> name=NC_010473:572141..573301 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 685401..686561 <gbrowseImage> name=NC_010473:685401..686561 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
ΔybdL (Keio:JW0593)	deletion	deletion	PMID:16738554	Shigen CGSC8709^[5]
ybdL-3			PMID:12142427	CGSC:87226
ΔybdL-4			PMID:12142427	CGSC:87228
ΔybdL-739::kan			PMID:16738554	CGSC:103718
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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
JW0593	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACAAATAACCCTCTGATTCC Primer 2:CCAAGCTGGCGCAGGCGTTCAGC
25A7	Kohara Phage	Genobase	PMID:3038334
4A5	Kohara Phage	Genobase	PMID:3038334
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: % ^[6] Synonyms:purE79::Tn10
dsbG601::Tn10	Linked marker	CAG12149 = CGSC7346^[5]	est. P1 cotransduction: 91% ^[6] Synonyms:zbd-601::Tn10, zbe-601::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:G6329	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13531	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002936	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945211	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3302	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002069	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	YbdL
Synonyms	methionine aminotransferase, PLP-dependent^[1], B0600^[2]^[1], YbdL^[2]^[1] , ECK0594, JW0593, b0600
Product description	methionine aminotransferase, PLP-dependent^[2]^[3] Methionine aminotransferase, PLP-dependent^[4]
EC number (for enzymes)	2.6.1.-^[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:0008152	metabolic process				P	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: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: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:0009058	biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004839	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:0016769	transferase activity, transferring nitrogenous groups	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004839	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004839	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
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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	nadE	PMID:16606699	Experiment(s):EBI-1137336
Protein	groL	PMID:16606699	Experiment(s):EBI-1137336
Protein	htpG	PMID:16606699	Experiment(s):EBI-1137336
Protein	ybdD	PMID:16606699	Experiment(s):EBI-1137336
Protein	zwf	PMID:16606699	Experiment(s):EBI-1137336
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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 MTNNPLIPQS KLPQLGTTIF TQMSALAQQH QAINLSQGFP DFDGPRYLQE RLAHHVAQGA NQYAPMTGVQ ALREAIAQKT ERLYGYQPDA DSDITVTAGA TEALYAAITA LVRNGDEVIC FDPSYDSYAP AIALSGGIVK RMALQPPHFR VDWQEFAALL SERTRLVILN TPHNPSATVW QQADFAALWQ AIAGHEIFVI SDEVYEHINF SQQGHASVLA HPQLRERAVA VSSFGKTYHM TGWKVGYCVA PAPISAEIRK VHQYLTFSVN TPAQLALADM LRAEPEHYLA LPDFYRQKRD ILVNALNESR LEILPCEGTY FLLVDYSAVS TLDDVEFCQW LTQEHGVAAI PLSVFCADPF PHKLIRLCFA KKESTLLAAA ERLRQL
Length	386
Mol. Wt	42.962 kDa
pI	6.2 (calculated)
Extinction coefficient	49,850 - 50,600 (calc based on 15 Y, 5 W, and 6 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	30..383	PF00155 Aminotransferase class I and II		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=ybdL 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:16128583	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945211	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002069	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77806	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6329	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13531	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945211	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002936	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3302	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	Reference(s)
Protein	E. coli K-12 MG1655	105	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	278	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	5802	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)
ybdL
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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_000913:632789..632829 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:b0600 (EcoliWiki Page)	NCBI GEO profiles for ybdL
microarray	GenExpDB:b0600 (EcoliWiki Page)	Summary of data for ybdL 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 (632621..632843) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:G2^[7]
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Notes

Accessions Related to ybdL Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6329	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3302	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0600
EcoGene	EcoGene:EG13531	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002936	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002069	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
Anopheles gambiae	ENSANGP00000022034 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G77670 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000025004 (score: 1.000; bootstrap: 99%) ENSBTAP00000000643 (score: 0.329)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00031645 (score: 1.000; bootstrap: 100%) WBGene00031679 (score: 1.000; bootstrap: 100%) WBGene00029668 (score: 0.507)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00010984 (score: 1.000; bootstrap: 100%) WBGene00009232 (score: 0.515)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029972 (score: 1.000; bootstrap: 100%) ENSCAFP00000029678 (score: 0.363)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1299 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-2233 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-3623 (score: 0.075) ZDB-GENE-040426-2676 (score: 0.075)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231138 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0037955 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA19977-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000007314 (score: 1.000; bootstrap: 99%) ENSGALP00000009970 (score: 0.438)	From Inparanoid:20070104
Homo sapiens	ENSP00000302227 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000028769 (score: 1.000; bootstrap: 100%) ENSMMUP00000024741 (score: 0.100)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000015537 (score: 1.000; bootstrap: 99%) ENSMODP00000008046 (score: 0.375)	From Inparanoid:20070104
Mus musculus	MGI:2677849 (score: 1.000; bootstrap: 99%) MGI:1917516 (score: 0.376)	From Inparanoid:20070104
Oryza gramene	Q67UZ0 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000036664 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000021865 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YJL060W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC6B124c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000158537 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000155898 (score: 0.455)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00014385001 (score: 1.000; bootstrap: 100%) GSTENP00025714001 (score: 0.243)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000044909 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	YBDL	From SHIGELLACYC
E. coli O157	YBDL	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)	PF00155 Aminotransferase class I and II
Panther (EcoliWiki Page)	PTHR11751:SF37
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
EcoCyc	EcoCyc:G6329	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13531	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002936	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3302	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002069	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 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 ^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

ybdL: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 ybdL Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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