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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	dsdA
Gene Synonym(s)	ECK2362, b2366, JW2363^[1], JW2363
Product Desc.	D-Serine deaminase^[2]
Product Synonyms(s)	D-serine ammonia-lyase^[1], B2366^[3]^[1], DsdA^[3]^[1] , ECK2362, JW2363, b2366
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dsdA^[3], dsdXA^[3], OP00199, dsd
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	dsdA
Mnemonic	D-Serine deaminase
Synonyms	ECK2362, b2366, JW2363^[1], JW2363
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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	53.39 minutes	MG1655: 2477224..2478552 <gbrowseImage> name=NC_000913:2477224..2478552 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2413429..2414757 <gbrowseImage> name=NC_012967:2413429..2414757 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2363029..2364357 <gbrowseImage> name=NC_012759:2363029..2364357 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2484648..2485976 <gbrowseImage> name=NC_007779:2484648..2485976 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2568989..2570317 <gbrowseImage> name=NC_010473:2568989..2570317 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	2477224	Edman degradation	PMID:795658 PMID:9222324
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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
ΔdsdA (Keio:JW2363)	deletion	deletion	PMID:16738554	Shigen CGSC9887^[4]
dsdA1				CGSC:8899
dsdA7				CGSC:9615
ΔdsdA775::kan			PMID:16738554	CGSC:100656
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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
JW2363	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAAAACGCTAAAATGAACTC Primer 2:CCACGGCCTTTTGCCAGATATTG
3A11	Kohara Phage	Genobase	PMID:3038334
6B9	Kohara Phage	Genobase	PMID:3038334
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[4]	est. P1 cotransduction: % ^[5] Synonyms:zej-223::Tn10
zfd-1::Tn10	Linked marker	CAG18467 = CGSC7408^[4]	est. P1 cotransduction: 61% ^[5] 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:EG10249	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10249	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000243	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946837	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0245	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007804	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	DsdA
Synonyms	D-serine ammonia-lyase^[1], B2366^[3]^[1], DsdA^[3]^[1] , ECK2362, JW2363, b2366
Product description	D-Serine deaminase^[2]
EC number (for enzymes)	4.3.1.18^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001926	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000634	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001926	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008721	D-serine ammonia-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011780	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008721	D-serine ammonia-lyase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.3.1.18	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016836	hydro-lyase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01030	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000634	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001926	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011780	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046416	D-amino acid metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01030	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046416	D-amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011780	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
	GO:0008721	D-serine ammonia-lyase activity	PMID:5327100	IDA: Inferred from Direct Assay		F		complete
	GO:0070178	D-serine metabolic process	PMID:5327100	IDA: Inferred from Direct Assay		P		complete
	GO:0016836	hydro-lyase activity	PMID:4917239	IDA: Inferred from Direct Assay		F		complete
	GO:0030170	pyridoxal phosphate binding	PMID:789365	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0005737	cytoplasm	PMID:4917239	IDA: Inferred from Direct Assay		C		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	yhbZ	PMID:16606699	Experiment(s):EBI-1142657
Protein	yagA	PMID:16606699	Experiment(s):EBI-1142657
Protein	nadE	PMID:16606699	Experiment(s):EBI-1142657
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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 MENAKMNSLI AQYPLVKDLV ALKETTWFNP GTTSLAEGLP YVGLTEQDVQ DAHARLSRFA PYLAKAFPET AATGGIIESE LVAIPAMQKR LEKEYQQPIS GQLLLKKDSH LPISGSIKAR GGIYEVLAHA EKLALEAGLL TLDDDYSKLL SPEFKQFFSQ YSIAVGSTGN LGLSIGIMSA RIGFKVTVHM SADARAWKKA KLRSHGVTVV EYEQDYGVAV EEGRKAAQSD PNCFFIDDEN SRTLFLGYSV AGQRLKAQFA QQGRIVDADN PLFVYLPCGV GGGPGGVAFG LKLAFGDHVH CFFAEPTHSP CMLLGVHTGL HDQISVQDIG IDNLTAADGL AVGRASGFVG RAMERLLDGF YTLSDQTMYD MLGWLAQEEG IRLEPSALAG MAGPQRVCAS VSYQQMHGFS AEQLRNTTHL VWATGGGMVP EEEMNQYLAK GR
Length	442
Mol. Wt	47.9 kDa
pI	5.8 (calculated)
Extinction coefficient	44,350 - 44,975 (calc based on 15 Y, 4 W, and 5 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	73..409	PF00291 Pyridoxal-phosphate dependent enzyme		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=dsdA 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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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:16130298	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946837	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007804	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P00926	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10249	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10249	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946837	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000243	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0245	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	1.47E+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	1.887+/-0.07	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.00753012	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	474	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	131	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	405	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)
dsdA
dsdXA
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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_000913:2477204..2477244 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:b2366 (EcoliWiki Page)	NCBI GEO profiles for dsdA
microarray	GenExpDB:b2366 (EcoliWiki Page)	Summary of data for dsdA 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 dsdA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10249	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0245	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2366
EcoGene	EcoGene:EG10249	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000243	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007804	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
Shigella flexneri	DSDA	From SHIGELLACYC
E. coli O157	DSDA	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)	PF00291 Pyridoxal-phosphate dependent enzyme
Panther (EcoliWiki Page)	PTHR10314:SF9
Superfamily (EcoliWiki Page)	SUPERFAMILY:53686
EcoCyc	EcoCyc:EG10249	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10249	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000243	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0245	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007804	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

dsdA:On One Page

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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 dsdA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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