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Gene |

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Expression|

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Standard Name	asd
Gene Synonym(s)	ECK3419, b3433, JW3396, dap, hom, dap+hom^[1]^[2]
Product Desc.	Asd^[2]^[3]; Component of aspartate semialdehyde dehydrogenase^[2]^[3] Aspartate semialdehyde dehydrogenase^[4]
Product Synonyms(s)	aspartate-semialdehyde dehydrogenase, NAD(P)-binding^[1], B3433^[2]^[1], Dap^[2]^[1], Hom^[2]^[1], Asd^[2]^[1] , dap, ECK3419, hom, JW3396, b3433
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): asd^[2]
Regulation/Activity
Quick Links
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Notes

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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	asd
Mnemonic	Aspartate semialdehyde deHase
Synonyms	ECK3419, b3433, JW3396, dap, hom, dap+hom^[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	76.98 minutes	MG1655: 3572901..3571798 <gbrowseImage> name=NC_000913:3571798..3572901 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3506332..3505229 <gbrowseImage> name=NC_012967:3505229..3506332 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3460292..3461395 <gbrowseImage> name=NC_012759:3460292..3461395 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4065537..4066640 <gbrowseImage> name=NC_007779:4065537..4066640 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3670646..3669543 <gbrowseImage> name=NC_010473:3669543..3670646 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	3571798	Edman degradation	PMID:9298646
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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	AA change(s)	Phenotype: Description	Availability	Comments
asdC135S	C135S	99.7% loss of activity		seeded from UniProt:P0A9Q9
asdC135A	C135A	Complete loss of activity		seeded from UniProt:P0A9Q9
asd-1			CGSC:5115
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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
JW3396	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAATGTTGGTTTTATCGG Primer 2:CCgGCCAGTTGACGAAGCATCCG
10F5	Kohara Phage	Genobase	PMID:3038334
16A5	Kohara Phage	Genobase	PMID:3038334
glgP721::Tn10	Linked marker	CAG18638 = CGSC7451^[5]	est. P1 cotransduction: 75% ^[6] Synonyms:zhg-3086::Tn10, zhh-21::Tn10
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[5]	est. P1 cotransduction: 50% ^[6] Synonyms:zhf-50::Tn10, zhf-5::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:EG10088	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10088	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000084	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947939	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0086	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011211	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	Asd
Synonyms	aspartate-semialdehyde dehydrogenase, NAD(P)-binding^[1], B3433^[2]^[1], Dap^[2]^[1], Hom^[2]^[1], Asd^[2]^[1] , dap, ECK3419, hom, JW3396, b3433
Product description	Asd^[2]^[3]; Component of aspartate semialdehyde dehydrogenase^[2]^[3] Aspartate semialdehyde dehydrogenase^[4]
EC number (for enzymes)	1.2.1.11^[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:0004073	aspartate-semialdehyde dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000319	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004073	aspartate-semialdehyde dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011534	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:0004073	aspartate-semialdehyde dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.2.1.11	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:0009089	lysine biosynthetic process via diaminopimelate	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011534	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019877	diaminopimelate biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0220	P	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:IPR000319	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050661	NADP or NADPH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011534	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:IPR000319	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011534	P	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
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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
Protein	Subunits of aspartate semialdehyde dehydrogenase	could be indirect
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1145894
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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 MKNVGFIGWR GMVGSVLMQR MVEERDFDAI RPVFFSTSQL GQAAPSFGGT TGTLQDAFDL EALKALDIIV TCQGGDYTNE IYPKLRESGW QGYWIDAASS LRMKDDAIII LDPVNQDVIT DGLNNGIRTF VGGNCTVSLM LMSLGGLFAN DLVDWVSVAT YQAASGGGAR HMRELLTQMG HLYGHVADEL ATPSSAILDI ERKVTTLTRS GELPVDNFGV PLAGSLIPWI DKQLDNGQSR EEWKGQAETN KILNTSSVIP VDGLCVRVGA LRCHSQAFTI KLKKDVSIPT VEELLAAHNP WAKVVPNDRE ITMRELTPAA VTGTLTTPVG RLRKLNMGPE FLSAFTVGDQ LLWGAAEPLR RMLRQLA
Length	367
Mol. Wt	40.018 kDa
pI	5.3 (calculated)
Extinction coefficient	51,450 - 51,950 (calc based on 5 Y, 8 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
Modification Site	38	phosphorylation site at S38	probability greater than 75%	PMID:17938405
Domain	3..122	PF01118 Semialdehyde dehydrogenase, NAD binding domain		PMID:19920124
Domain	144..353	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=asd 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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Resource type	Source	Notes/Reference
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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:16131307	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947939	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011211	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9Q9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10088	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10088	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947939	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000084	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0086	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	5.34E+03	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 EMG2	900	molecules/cell	Medium: MOPS glucose minimal Temperature (°C): 37 Doubling time (min): Growth phase: Exponential OD: OD600 = 0.2 to 0.25 other: aerated	Quantitative protein sequencing	Spot ID: M64	PMID: 9298646
Protein	E. coli K-12 MG1655	7060	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	10592	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	6893	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)
asd
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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_000913:3572881..3572921 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:b3433 (EcoliWiki Page)	NCBI GEO profiles for asd
microarray	GenExpDB:b3433 (EcoliWiki Page)	Summary of data for asd 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 (3572434..3572744) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:C9^[7]
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Notes

Accessions Related to asd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10088	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0086	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3433
EcoGene	EcoGene:EG10088	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000084	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011211	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
Xenopus tropicalis	ENSXETP00000014803 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	ASD	From SHIGELLACYC
E. coli O157	ASD	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:55347
Pfam (EcoliWiki Page)	PF01118 Semialdehyde dehydrogenase, NAD binding domain
Pfam (EcoliWiki Page)	PF02774 Semialdehyde dehydrogenase, dimerisation domain
EcoCyc	EcoCyc:EG10088	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10088	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000084	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0086	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011211	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 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 ^2.11 ^2.12 ^2.13 ^2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Alleles and Phenotypes

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Genetic Interactions

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Genetic Resources

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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 asd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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