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Expression|

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Standard Name	paoC
Gene Synonym(s)	ECK0283, b0284, JW0278, yagR^[1], JW0278, yagR
Product Desc.	putative molybdemum cofactor-binding oxidoreductase^[2]^[3] PaoCST xanthine dehydrogenase homolog subunit, function unknown^[4]
Product Synonyms(s)	predicted oxidoreductase with molybdenum-binding domain^[1], B0284^[2]^[1], PaoC^[2]^[1], YagR, ECK0283, JW0278, yagR, b0284
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yagQ^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 101 (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	paoC
Mnemonic
Synonyms	ECK0283, b0284, JW0278, yagR^[1], JW0278, yagR
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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	6.42 minutes	MG1655: 300158..297960 <gbrowseImage> name=NC_000913:297960..300158 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 271118..268920 <gbrowseImage> name=NC_012967:268920..271118 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 300158..297960 <gbrowseImage> name=NC_007779:297960..300158 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 275708..273510 <gbrowseImage> name=NC_010473:273510..275708 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)	Reference	Availability	Comments
yagR(del) (Keio:JW0278)	deletion	deletion	PMID:16738554	Shigen CGSC8491^[5]
yagR::Tn5KAN-I-SceI (FB20122)	Insertion at nt 1547 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20123	contains pKD46
yagR728(del)::kan			PMID:16738554	CGSC:103548
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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
JW0278	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAATTTGATAAACCCGCAGG Primer 2:CCAACCACATCCGGCAGCTTATC
21C10	Kohara Phage	Genobase	PMID:3038334
5E5	Kohara Phage	Genobase	PMID:3038334
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[5]	est. P1 cotransduction: 20% ^[6]
lacI3042::Tn10	Linked marker	CAG18439 = CGSC7334^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).
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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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0284
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YAGR
EcoCyc (EcoliWiki Page)	ECOCYC:G6155	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944961	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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	PaoC
Synonyms	predicted oxidoreductase with molybdenum-binding domain^[1], B0284^[2]^[1], PaoC^[2]^[1], YagR, ECK0283, JW0278, yagR, b0284
Product description	putative molybdemum cofactor-binding oxidoreductase^[2]^[3] PaoCST xanthine dehydrogenase homolog subunit, 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:0004854	xanthine dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.17.1.4	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006144	purine base metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0659	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006166	purine ribonucleoside salvage	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0660	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030151	molybdenum ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0500	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000674	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008274	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:0005515	protein binding	PMID:19368556	IPI: Inferred from Physical Interaction	EcoliWiki:yagT EcoliWiki:yagS	F		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	References	Evidence
Protein	pqiA	PMID:16606699	Experiment(s):EBI-1136117
Protein	glpC	PMID:16606699	Experiment(s):EBI-1136117
Protein	deoB	PMID:16606699	Experiment(s):EBI-1136117
Protein	visC	PMID:16606699	Experiment(s):EBI-1136117
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1136117
Protein	rtcB	PMID:16606699	Experiment(s):EBI-1136117
Protein	pgm	PMID:16606699	Experiment(s):EBI-1136117
Protein	intB	PMID:16606699	Experiment(s):EBI-1136117
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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 MKFDKPAGEN PIDQLKVVGR PHDRIDGPLK TTGTARYAYE WHEEAPNAAY GYIVGSAIAK GRLTALDTDA AQKAPGVLAV ITASNAGALG KGDKNTARLL GGPTIEHYHQ AIALVVAETF EQARAAASLV QAHYRRNKGA YSLADEKQAV NQPPEDTPDK NVGDFDGAFT SAAVKIDATY TTPDQSHMAM EPHASMAVWD GNKLTLWTSN QMIDWCRTDL AKTLKVPVEN VRIISPYIGG GFGGKLFLRS DALLAALAAR AVKRPVKVML PRPSIPNNTT HRPATLQHLR IGADQSGKIT AISHESWSGN LPGGTPETAV QQSELLYAGA NRHTGLRLAT LDLPEGNAMR APGEAPGLMA LEIAIDELAE KAGIDPVEFR ILNDTQVDPA DPTRCFSRRQ LIECLRTGAD KFGWKQRNAT PGQVRDGEWL VGHGVAAGFR NNLLEKSGAR VHLEQNGTVT VETDMTDIGT GSYTILAQTA AEMLGVPLEQ VAVHLGDSSF PVSAGSGGQW GANTSTSGVY AACMKLREMI ASAVGFDPEQ SQFADGKITN GTRSATLHEA TAGGRLTAEE SIEFGTLSKE YQQSTFAGHF VEVGVHSATG EVRVRRMLAV CAAGRILNPK TARSQVIGAM TMGMGAALME ELAVDDRLGY FVNHDMAGYE VPVHADIPKQ EVIFLDDTDP ISSPMKAKGV GELGLCGVSA AIANAVYNAT GIRVRDYPIT LDKLLDKLPD VV
Length	732
Mol. Wt	78.088 kDa
pI	6.2 (calculated)
Extinction coefficient	69,330 - 70,080 (calc based on 17 Y, 8 W, and 6 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	34..138	PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain	PMID:19920124
Domain	142..668	PF02738 Molybdopterin-binding domain of aldehyde dehydrogenase	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=yagR 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:16128269	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944961	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77489	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944961	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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 MG1655	1^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	13	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	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
yagQ
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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_000913:300138..300178 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:b0284 (EcoliWiki Page)	NCBI GEO profiles for yagR
microarray	GenExpDB:b0284 (EcoliWiki Page)	Summary of data for yagR 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 paoC Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0284
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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
Monodelphis domestica	ENSMODP00000019349 (score: 1.000; bootstrap: 100%) ENSMODP00000015626 (score: 1.000; bootstrap: 100%) ENSMODP00000015675 (score: 0.597) ENSMODP00000018747 (score: 0.586) ENSMODP00000015728 (score: 0.532)	From Inparanoid:20070104
Mus musculus	MGI:98973 (score: 1.000; bootstrap: 100%) MGI:3529596 (score: 1.000; bootstrap: 100%) MGI:1918974 (score: 0.645) MGI:1919122 (score: 0.625) MGI:88035 (score: 0.594)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000009634 (score: 1.000; bootstrap: 100%) ENSRNOP00000042328 (score: 1.000; bootstrap: 100%) ENSRNOP00000049807 (score: 0.594) ENSRNOP00000021389 (score: 0.557)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00031889001 (score: 1.000; bootstrap: 100%) GSTENP00012569001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	YAGR	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)	PF02738 Molybdopterin-binding domain of aldehyde dehydrogenase
Pfam (EcoliWiki Page)	PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
Panther (EcoliWiki Page)	PTHR11908:SF4
Superfamily (EcoliWiki Page)	SUPERFAMILY:54665
Superfamily (EcoliWiki Page)	SUPERFAMILY:56003
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 ^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).

paoC: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 paoC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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