ada:Gene Product(s): Difference between revisions

Standard name	Ada
Synonyms	fused DNA-binding transcriptional dual regulator^[1], O6-methylguanine-DNA methyltransferase^[1], B2213^[2]^[1], Ada^[2]^[1] , ECK2205, JW2201, b2213
Product description	Ada transcriptional dual regulator^[2]^[3] O6-methylguanine-DNA methyltransferase, transcription factor; inducible; DNA repair against methylating and alkylating agents; binds Zn(II)^[4]
EC number (for enzymes)	2.1.1.63^[1]
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Notes

Function

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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:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004026	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014048	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003908	methylated-DNA-(protein)-cysteine S-methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001497	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003908	methylated-DNA-(protein)-cysteine S-methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008332	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003908	methylated-DNA-(protein)-cysteine S-methyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.1.1.63	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001497	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004026	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008332	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014048	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0234	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004026	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0227	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	PMID:1581309^[5]	IDA: Inferred from Direct Assay		F	N-terminal domain binds Zn	complete
	GO:0008168	methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004026	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008168	methyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0489	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004026	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	PMID:1581309^[5]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003908	methylated-DNA-(protein)-cysteine S-methyltransferase activity	PMID:6754717^[6]	IDA: Inferred from Direct Assay		F		complete
	GO:0005625	soluble fraction	PMID:6754717^[6]	IDA: Inferred from Direct Assay		C		complete
	GO:0006307	DNA dealkylation involved in DNA repair	PMID:6754717^[6]	IDA: Inferred from Direct Assay		P		complete
	GO:0006307	DNA dealkylation involved in DNA repair	PMID:282622^[7]	IDA: Inferred from Direct Assay		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	References	Evidence
Protein	rplB	PMID:16606699^[8]	Experiment(s):EBI-1142195
Protein	rpsC	PMID:16606699^[8]	Experiment(s):EBI-1142195
Protein	moeB	PMID:16606699^[8]	Experiment(s):EBI-1142195
Protein	fur	PMID:16606699^[8]	Experiment(s):EBI-1142195
Protein	rpsG	PMID:16606699^[8]	Experiment(s):EBI-1142195
Protein	ybiA	PMID:16606699^[8]	Experiment(s):EBI-1142195
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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
membrane			From EcoCyc^[3]
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Notes

Structure and Physical Properties

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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 MKKATCLTDD QRWQSVLARD PNADGEFVFA VRTTGIFCRP SCRARHALRE NVSFYANASE ALAAGFRPCK RCQPEKANAQ QHRLDKITHA CRLLEQETPV TLEALADQVA MSPFHLHRLF KATTGMTPKA WQQAWRARRL RESLAKGESV TTSILNAGFP DSSSYYRKAD ETLGMTAKQF RHGGENLAVR YALADCELGR CLVAESERGI CAILLGDDDA TLISELQQMF PAADNAPADL MFQQHVREVI ASLNQRDTPL TLPLDIRGTA FQQQVWQALR TIPCGETVSY QQLANAIGKP KAVRAVASAC AANKLAIIIP CHRVVRGDGT LSGYRWGVSR KAQLLRREAE NEER
Length	354
Mol. Wt	39.323 kDa
pI	8.8 (calculated)
Extinction coefficient	36,440 - 37,940 (calc based on 6 Y, 5 W, and 12 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	10..75	PF02805 Metal binding domain of Ada	PMID:19920124^[9]
Domain	95..133	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124^[9]
Domain	140..182	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124^[9]
Domain	269..353	PF01035 6-O-methylguanine DNA methyltransferase, DNA binding domain	PMID:19920124^[9]
Domain	188..266	PF02870 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain	PMID:19920124^[9]
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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=ada taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:16130150	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946710	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007311	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P06134	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10029	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10029	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946710	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000026	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0028	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 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
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 Myers, LC et al. (1992) Zinc binding by the methylation signaling domain of the Escherichia coli Ada protein. Biochemistry 31 4541-7 PubMed
↑ ^6.0 ^6.1 ^6.2 Demple, B et al. (1982) Repair of alkylated DNA in Escherichia coli. Physical properties of O6-methylguanine-DNA methyltransferase. J. Biol. Chem. 257 13776-80 PubMed
↑ Schendel, PF & Robins, PE (1978) Repair of O6-methylguanine in adapted Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 75 6017-20 PubMed
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 ^8.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^9.0 ^9.1 ^9.2 ^9.3 ^9.4 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

@@ Line 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
-fused DNA-binding transcriptional dual regulator<ref name='LIB:Riley_2006'/>, O6-methylguanine-DNA methyltransferase<ref name='LIB:Riley_2006'/>, B2213<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Ada<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''fused DNA-binding transcriptional dual regulator<ref name='LIB:Riley_2006'/>, O6-methylguanine-DNA methyltransferase<ref name='LIB:Riley_2006'/>, B2213<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Ada<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2205, JW2201, b2213''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 71: / Line 71: @@
 ******************************************************************************************
 *
-*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="Z46aa98cac84ca"  class=" tableEdit GO_table_product dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46aa98cac84ca"  class=" tableEdit GO_table_product dataTable"
 |- {{table_heading_style}}
-!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
+!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
 |-
 |
@@ Line 590: / Line 590: @@
 |
 complete
+|-
+|
+|
+GO:0006307
+|
+DNA dealkylation involved in DNA repair
+|
+PMID:6754717
+|
+IDA: Inferred from Direct Assay
+|
+|
+P
+|
+|
+complete
+|-
+|
+|
+GO:0006307
+|
+DNA dealkylation involved in DNA repair
+|
+PMID:
+|
+IDA: Inferred from Direct Assay
+|
+|
+P
+|
+|
+<div class="mw-parser-output"><p>complete
+</p></div>
 |- class="tableEdit_footer"
-|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24595.Z46aa98cac84ca&page=24595&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</span> || || || || || || || ||
+|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24595.Z46aa98cac84ca&page=24595&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</div> || || || || || || || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.24595.Z46aa98cac84ca-->
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 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="G46aa98ec716d5"  class=" tableEdit Product_interactions_table dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aa98ec716d5"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 691: / Line 731: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="U46aa98ed35ea6"  class=" tableEdit Product_localization_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46aa98ed35ea6"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |-
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@@ Line 728: / Line 768: @@
 ****************************************************************************************** -->{{Product_physical_properties_help}}
 {|   id="N46aa98eec4384"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 771: / Line 815: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="Z46aa98ef3d7e3"  class=" tableEdit Product_motif_table dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46aa98ef3d7e3"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
@@ Line 864: / Line 908: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P06134 Protein Model Portal]
-* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
+* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P06134 PSI-PRED (P06134)]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P06134 Genomes TO Protein (P06134)] (GTOP)
-* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
-* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
 |- class="tableEdit_footer"
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 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="K46aa98f0046e8"  class=" tableEdit Product_resource_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aa98f0046e8"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 931: / Line 973: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="L46aa98f06149e"  class=" tableEdit Gene_accessions_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46aa98f06149e"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|Database!!Accession!!Notes
 |-
 |
-[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/protein/16130150 GI:16130150]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/protein/NP_416717.1 GeneID:946710]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0007311
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P06134 UniProtKB/Swiss-Prot:P06134]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
 |
-[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=PD00230 EcoCyc:PD00230]
+EcoCyc:EG10029
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:EG10029
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
 |
-[http://www.uniprot.org/uniprot/P06134 UniProt:P06134]
+[http://www.ncbi.nlm.nih.gov/gene?term=946710 GeneID:946710]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.janelia.org/protein/P06134 Pfam:P06134]
+RegulonDB:ECK120000026
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
+[[EchoBASE]]
 |
-[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416717 RefSeq:NP_416717]
+EchoBASE:EB0028
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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-{|   id="A46a82cfd89960"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a82cfd89960"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments

ada:Gene Product(s): Difference between revisions

Latest revision as of 19:15, 6 June 2024

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

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ada:Gene Product(s): Difference between revisions

Latest revision as of 19:15, 6 June 2024

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

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