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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	usg
Gene Synonym(s)	ECK2313, b2319, JW2316, usg-1^[1]^[2]
Product Desc.	predicted semialdehyde dehydrogenase^[2]^[3] Gene in pdxB operon, function unknown^[4]
Product Synonyms(s)	predicted semialdehyde dehydrogenase^[1], B2319^[2]^[1], Usg^[2]^[1] , ECK2313, JW2316, b2319
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): usg-truA-dedA^[2], pdxB-usg-truA-dedA^[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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HT_Cmplx38_Cyt: Usg+YbbN. HT_Cmplx50_Mem: Pgk+Usg.^[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	usg
Mnemonic	Upstream gene
Synonyms	ECK2313, b2319, JW2316, usg-1^[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	52.45 minutes	MG1655: 2434671..2433658 <gbrowseImage> name=NC_000913:2433658..2434671 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2380241..2379228 <gbrowseImage> name=NC_012967:2379228..2380241 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2319463..2320476 <gbrowseImage> name=NC_012759:2319463..2320476 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2442095..2441082 <gbrowseImage> name=NC_007779:2441082..2442095 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2526436..2525423 <gbrowseImage> name=NC_010473:2525423..2526436 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	2433658	Edman degradation	PMID:2681152
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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
Δusg (Keio:JW2316)	deletion	deletion	PMID:16738554	Shigen CGSC9858^[5]
Δusg-728::kan			PMID:16738554	CGSC:103330
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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
JW2316	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCTGAAGGCTGGAACATTGC Primer 2:CCGTACAGATACTCCTGCACCAG
12F12	Kohara Phage	Genobase	PMID:3038334
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[5]	est. P1 cotransduction: 14% ^[6] Synonyms:zej-223::Tn10
zfd-1::Tn10	Linked marker	CAG18467 = CGSC7408^[5]	est. P1 cotransduction: 5% ^[6] Synonyms:zfb-1::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:EG11059	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11059	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001048	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946797	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1052	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007660	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	Usg
Synonyms	predicted semialdehyde dehydrogenase^[1], B2319^[2]^[1], Usg^[2]^[1] , ECK2313, JW2316, b2319
Product description	predicted semialdehyde dehydrogenase^[2]^[3] Gene in pdxB operon, function unknown^[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
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004073	aspartate-semialdehyde dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012080	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000534	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012280	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000534	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008652	cellular amino acid biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012080	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008652	cellular amino acid biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012280	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000534	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012280	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046983	protein dimerization activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012280	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050661	NADP or NADPH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012080	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000534	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012080	P	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	rpoC	PMID:15690043	Experiment(s):EBI-879802, EBI-884632
Protein	rpsC	PMID:15690043	Experiment(s):EBI-879802
Protein	tufA	PMID:15690043	Experiment(s):EBI-879802, EBI-884632
Protein	nusG	PMID:16606699	Experiment(s):EBI-1142543
Protein	yibA	PMID:16606699	Experiment(s):EBI-1142543
Protein	rpoC	PMID:16606699	Experiment(s):EBI-1142543
Protein	uidR	PMID:16606699	Experiment(s):EBI-1142543
Protein	yjcC	PMID:16606699	Experiment(s):EBI-1142543
Protein	cusA	PMID:16606699	Experiment(s):EBI-1142543
Protein	rpoA	PMID:15690043	Experiment(s):EBI-884632
Protein	rpoB	PMID:15690043	Experiment(s):EBI-884632
Protein	ygfZ	PMID:15690043	Experiment(s):EBI-884632
Protein	nusG	PMID:15690043	Experiment(s):EBI-884632
Protein	pykA	PMID:15690043	Experiment(s):EBI-884632
Protein	rplL	PMID:15690043	Experiment(s):EBI-884632
Protein	ygfZ	PMID:19402753	LCMS(ID Probability):99.0
Protein	rpoC	PMID:19402753	LCMS(ID Probability):99.0 MALDI(Z-score):10.607685
Protein	rplL	PMID:19402753	LCMS(ID Probability):99.6
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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 MSEGWNIAVL GATGAVGEAL LETLAERQFP VGEIYALARN ESAGEQLRFG GKTITVQDAA EFDWTQAQLA FFVAGKEATA AWVEEATNSG CLVIDSSGLF ALEPDVPLVV PEVNPFVLTD YRNRNVIAVP DSLTSQLLAA LKPLIDQGGL SRISVTSLIS ASAQGKKAVD ALAGQSAKLL NGIPIDEEDF FGRQLAFNML PLLPDSEGSV REERRIVDEV RKILQDEGLM ISASVVQAPV FYGHAQMVNF EALRPLAAEE ARDAFVQGED IVLSEENEFP TQVGDASGTP HLSVGCVRND YGMPEQVQFW SVADNVRFGG ALMAVKIAEK LVQEYLY
Length	337
Mol. Wt	36.363 kDa
pI	4.2 (calculated)
Extinction coefficient	30,940 - 31,190 (calc based on 6 Y, 4 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	References
Domain	6..121	PF01118 Semialdehyde dehydrogenase, NAD binding domain	PMID:19920124
Domain	141..318	PF02774 Semialdehyde dehydrogenase, dimerisation 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=usg 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:16130254	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946797	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007660	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P08390	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11059	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11059	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946797	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001048	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1052	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	2.68E+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	2191	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	578	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	1176	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)
usg-truA-dedA
pdxB-usg-truA-dedA
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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_000913:2434651..2434691 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:b2319 (EcoliWiki Page)	NCBI GEO profiles for usg
microarray	GenExpDB:b2319 (EcoliWiki Page)	Summary of data for usg 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 (2434588..2434790) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:B11^[7]
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Notes

Accessions Related to usg Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11059	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1052	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2319
EcoGene	EcoGene:EG11059	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001048	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007660	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	AT1G14810 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDR158W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	USG	From SHIGELLACYC
E. coli O157	USG	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:51735
Panther (EcoliWiki Page)	PTHR10174:SF2
Superfamily (EcoliWiki Page)	SUPERFAMILY:55347
Pfam (EcoliWiki Page)	PF01118 Semialdehyde dehydrogenase, NAD binding domain
Pfam (EcoliWiki Page)	PF02774 Semialdehyde dehydrogenase, dimerisation domain
EcoCyc	EcoCyc:EG11059	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11059	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001048	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1052	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007660	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 ^2.7 ^2.8 ^2.9 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

usg: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 usg Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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