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Expression|

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Standard Name	yajL
Gene Synonym(s)	ECK0418, b0424, JW5057, thiJ^[1](incorrect), thiJ
Product Desc.	conserved protein^[2]^[3] Function unknown, PfpI/HchA protease/chaperone family; not involved in thiamine metabolism^[4]
Product Synonyms(s)	conserved protein^[1], B0424^[2]^[1], YajL^[2]^[1], ThiJ^[2]^[1] , ECK0418, JW5057, thiJ, b0424
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yajL^[2]
Regulation/Activity
Quick Links
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Notes

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From EcoGene^[4]:

YajL has been mistakenly described as ThiJ, involved in thiamine metabolism. This phenotype is now attributed to the adjacent thiI gene. This error is acknowledged by T. Begley in a personal communication cited in the discussion section of Mueller et al., NAR 26:2606-10 (1998).^[5] C56 peptidase family; DJ-1/PARK7 superfamily.^[6]

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	yajL
Mnemonic	Systematic nomenclature
Synonyms	ECK0418, b0424, JW5057, thiJ^[1](incorrect), thiJ
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Notes

"YajL was mistakenly identified as ThiJ and was implicated in thiamine biosynthesis. However, later experiments showed that the original complementation phenotype was due to the neighboring gene, thiI ^[5]. The biochemical function of YajL is therefore unclear." (from EcoCyc)

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	9.53 minutes	MG1655: 442865..442275 <gbrowseImage> name=NC_000913:442275..442865 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 411473..412063 <gbrowseImage> name=NC_012967:411473..412063 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 345034..345624 <gbrowseImage> name=NC_012759:345034..345624 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 442865..442275 <gbrowseImage> name=NC_007779:442275..442865 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 382196..381606 <gbrowseImage> name=NC_010473:381606..382196 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
yajL(del) (Keio:JW5057)	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
JW5057	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGCATCGGCACTGGTTTG Primer 2:CCtTCGTAATAATTATAAATCCC
19F6	Kohara Phage	Genobase	PMID:3038334
2H5	Kohara Phage	Genobase	PMID:3038334
tsx-247::Tn10	Linked marker	CAG12148 = CGSC7337^[7]	est. P1 cotransduction: 69% ^[8]
zaj-3054::Tn10	Linked marker	CAG12017 = CGSC7339^[7]	est. P1 cotransduction: 54% ^[8] Synonyms:zba-3054::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:G198	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002673	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945066	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3057	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001472	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	YajL
Synonyms	conserved protein^[1], B0424^[2]^[1], YajL^[2]^[1], ThiJ^[2]^[1] , ECK0418, JW5057, thiJ, b0424
Product description	conserved protein^[2]^[3] Function unknown, PfpI/HchA protease/chaperone family; not involved in thiamine metabolism^[4]
EC number (for enzymes)
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Notes

"YajL was mistakenly identified as ThiJ and was implicated in thiamine biosynthesis. However, later experiments showed that the original complementation phenotype was due to the neighboring gene, thiI ^[5]. The biochemical function of YajL is therefore unclear." (from EcoCyc)

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	Aspect	Notes	Status
NOT	GO:0016301	kinase activity	PMID:2540841		F	Activity later shown to be associated with thiI, not yajL.^[5]	Missing: evidence
	GO:0042026	protein refolding	PMID:20124404	IMP: Inferred from Mutant Phenotype	P	From EcoCyc	complete
NOT	GO:0008972	phosphomethylpyrimidine kinase activity	PMID:2540841		F	Activity later shown to be associated with thiI, not yajL.^[5]	Missing: evidence
Deprecated	GO:0005737	cytoplasm	PMID:2540841		C	The protein purified in the cited paper was later shown not to be YajL.^[5]	Missing: evidence
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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 MNMSASALVC LAPGSEETEA VTTIDLLVRG GIKVTTASVA SDGNLAITCS RGVKLLADAP LVEVADGEYD VIVLPGGIKG AECFRDSTLL VETVKQFHRS GRIVAAICAA PATVLVPHDI FPIGNMTGFP TLKDKIPAEQ WLDKRVVWDA RVKLLTSQGP GTAIDFGLKI IDLLVGREKA HEVASQLVMA AGIYNYYE
Length	198
Mol. Wt	21.022 kDa
pI	5.1 (calculated)
Extinction coefficient	16,960 - 17,460 (calc based on 4 Y, 2 W, and 4 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	31..173	PF01965 DJ-1/PfpI 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=yajL 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:90111131	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945066	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001472	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q46948	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G198	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13272	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945066	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002673	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3057	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 MC4100	3.48E+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	E. coli K-12 MG1655	1096	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	540	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	550	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)
yajL
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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_000913:442845..442885 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:b0424 (EcoliWiki Page)	NCBI GEO profiles for yajL
microarray	GenExpDB:b0424 (EcoliWiki Page)	Summary of data for yajL 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 yajL Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G198	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3057	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0424
EcoGene	EcoGene:EG13272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002673	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001472	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	ENSANGP00000011918 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000023021 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G53280 (score: 1.000; bootstrap: 100%) AT3G14990 (score: 0.690) AT4G34020 (score: 0.271)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000027339 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00029190 (score: 1.000; bootstrap: 100%) WBGene00029191 (score: 0.397)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00015184 (score: 1.000; bootstrap: 100%) WBGene00016789 (score: 0.473)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029113 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000007455 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-041010-5 (score: 1.000; bootstrap: 100%) ZDB-CDNA-041010-5 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0186988 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0039802 (score: 1.000; bootstrap: 100%) FBgn0033885 (score: 0.394)	From Inparanoid:20070104
Drosophila pseudoobscura	GA12322-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000000741 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000234912 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000025846 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000011989 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:2135637 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5Z790 (score: 1.000; bootstrap: 100%) Q5QNE8 (score: 0.568) Q5QNF2 (score: 0.440) Q6F2Y9 (score: 0.344)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000024711 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC22E123c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000147408 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00027576001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000013258 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	THIJ	From SHIGELLACYC
E. coli O157	THIJ	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)	PF01965 DJ-1/PfpI family
Superfamily (EcoliWiki Page)	SUPERFAMILY:52317
Panther (EcoliWiki Page)	PTHR11019:SF6
EcoCyc	EcoCyc:G198	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002673	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3057	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001472	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 ^2.7 ^2.8 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 ^5.3 ^5.4 ^5.5 Mueller, EG et al. (1998) Identification of a gene involved in the generation of 4-thiouridine in tRNA. Nucleic Acids Res. 26 2606-10 PubMed
↑ Wei, Y et al. (2007) Identification of functional subclasses in the DJ-1 superfamily proteins. PLoS Comput. Biol. 3 e10 PubMed
↑ ^7.0 ^7.1 CGSC: The Coli Genetics Stock Center
↑ ^8.0 ^8.1 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).

yajL: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 yajL Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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