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Gene |

Product(s) |

Expression|

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Standard Name	yggS
Gene Synonym(s)	ECK2946, b2951, JW2918^[1], JW2918
Product Desc.	predicted enzyme^[2]^[3] Function unknown; homologous to N-terminal domain of alanine racemase^[4]
Product Synonyms(s)	predicted enzyme^[1], B2951^[2]^[1], YggS^[2]^[1] , ECK2946, JW2918, b2951
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yggS^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 130 (http://afmb.cnrs-mrs.fr/article171.html).^[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	yggS
Mnemonic	Systematic nomenclature
Synonyms	ECK2946, b2951, JW2918^[1], JW2918
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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	66.67 minutes	MG1655: 3093120..3093824 <gbrowseImage> name=NC_000913:3093120..3093824 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2980849..2981553 <gbrowseImage> name=NC_012967:2980849..2981553 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2980268..2980972 <gbrowseImage> name=NC_012759:2980268..2980972 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3093754..3094458 <gbrowseImage> name=NC_007779:3093754..3094458 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3188189..3188893 <gbrowseImage> name=NC_010473:3188189..3188893 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
ΔyggS (Keio:JW2918)	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
JW2918	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACGATATTGCGCATAACCT Primer 2:CCTTTTTTAGAGTAATCACGCGC
23G4S	Kohara Phage	Genobase	PMID:3038334
12C6	Kohara Phage	Genobase	PMID:3038334
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: 77% ^[6] Synonyms:zgd-210::Tn10, zgf-210::Tn10
nupG511::Tn10	Linked marker	CAG18472 = CGSC7433^[5]	est. P1 cotransduction: 69% ^[6]
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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:G7527	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12979	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004088	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947423	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2804	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009681	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	YggS
Synonyms	predicted enzyme^[1], B2951^[2]^[1], YggS^[2]^[1] , ECK2946, JW2918, b2951
Product description	predicted enzyme^[2]^[3] Function unknown; homologous to N-terminal domain of alanine racemase^[4]
EC number (for enzymes)
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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
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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	rpsI	PMID:16606699	Experiment(s):EBI-1144423
Protein	glpK	PMID:16606699	Experiment(s):EBI-1144423
Protein	udk	PMID:16606699	Experiment(s):EBI-1144423
Protein	pepD	PMID:16606699	Experiment(s):EBI-1144423
Protein	rplB	PMID:16606699	Experiment(s):EBI-1144423
Protein	fdnG	PMID:15690043	Experiment(s):EBI-882505
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-882505
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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 MNDIAHNLAQ VRDKISAAAT RCGRSPEEIT LLAVSKTKPA SAIAEAIDAG QRQFGENYVQ EGVDKIRHFQ ELGVTGLEWH FIGPLQSNKS RLVAEHFDWC HTIDRLRIAT RLNDQRPAEL PPLNVLIQIN ISDENSKSGI QLAELDELAA AVAELPRLRL RGLMAIPAPE SEYVRQFEVA RQMAVAFAGL KTRYPHIDTL SLGMSDDMEA AIAAGSTMVR IGTAIFGARD YSKK
Length	234
Mol. Wt	25.787 kDa
pI	6.5 (calculated)
Extinction coefficient	16,960 - 17,210 (calc based on 4 Y, 2 W, and 2 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..230	PF01168 Alanine racemase, N-terminal domain		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=yggS 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:16130852	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947423	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009681	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P67080	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7527	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12979	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947423	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004088	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2804	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	5.46E+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	19.544+/-0.136	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.022727273	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	1053	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	374	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	573	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)
yggS
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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_000913:3093100..3093140 source=MG1655 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:b2951 (EcoliWiki Page)	NCBI GEO profiles for yggS
microarray	GenExpDB:b2951 (EcoliWiki Page)	Summary of data for yggS 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 yggS Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7527	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2804	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2951
EcoGene	EcoGene:EG12979	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004088	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009681	Escherichia coli str. K-12 substr. MG1655
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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	ENSANGP00000018146 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000017762 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G26860 (score: 1.000; bootstrap: 100%) AT1G11930 (score: 0.583)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000039600 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00025436 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00017286 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000009292 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000004257 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231677 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0039751 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000004889 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000333551 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000001271 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000013601 (score: 1.000; bootstrap: 100%) ENSMODP00000018368 (score: 0.631)	From Inparanoid:20070104
Mus musculus	MGI:1891207 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q65XE0 (score: 1.000; bootstrap: 100%) Q5JKX2 (score: 0.626) Q5QT25 (score: 0.603)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000034513 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YBL036C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC6449 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000154212 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00005344001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000052585 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGGS	From SHIGELLACYC
E. coli O157	YGGS	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)	PF01168 Alanine racemase, N-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51419
Panther (EcoliWiki Page)	PTHR10146:SF0
EcoCyc	EcoCyc:G7527	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12979	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004088	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2804	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009681	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 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 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).

yggS:On One Page

Quickview

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 yggS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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