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Standard Name	ycgM
Gene Synonym(s)	ECK1168, b1180, JW1169^[1], JW1169
Product Desc.	predicted isomerase/hydrolase^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted isomerase/hydrolase^[1], B1180^[2]^[1], YcgM^[2]^[1] , ECK1168, JW1169, b1180
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycgM^[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	ycgM
Mnemonic	Systematic nomenclature
Synonyms	ECK1168, b1180, JW1169^[1], JW1169
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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	26.45 minutes	MG1655: 1227302..1227961 <gbrowseImage> name=NC_000913:1227302..1227961 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1228240..1228899 <gbrowseImage> name=NC_012967:1228240..1228899 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1116023..1116682 <gbrowseImage> name=NC_012759:1116023..1116682 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1229656..1230315 <gbrowseImage> name=NC_007779:1229656..1230315 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1267543..1268202 <gbrowseImage> name=NC_010473:1267543..1268202 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
ΔycgM (Keio:JW1169)	deletion	deletion	PMID:16738554	Shigen CGSC9078^[5]
ΔycgM769::kan			PMID:16738554	CGSC:104026
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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
JW1169	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTATCAACATCACAACTGGCA Primer 2:CCtAAAACGCGAGTTGTCAAAGA
4D1	Kohara Phage	Genobase	PMID:3038334
2A3	Kohara Phage	Genobase	PMID:3038334
11G8	Kohara Phage	Genobase	PMID:3038334
zcf-117::Tn10	Linked marker	CAG18463 = CGSC7363^[5]	est. P1 cotransduction: 56% ^[6]
fadR13::Tn10	Linked marker	CAG18497 = CGSC7365^[5]	est. P1 cotransduction: 79% ^[6]
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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:G6617	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13894	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003212	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946115	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3653	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003957	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	YcgM
Synonyms	predicted isomerase/hydrolase^[1], B1180^[2]^[1], YcgM^[2]^[1] , ECK1168, JW1169, b1180
Product description	predicted isomerase/hydrolase^[2]^[3] 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:IPR002529	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011234	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002529	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011234	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	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	rplB	PMID:16606699	Experiment(s):EBI-1139110
Protein	slyD	PMID:16606699	Experiment(s):EBI-1139110
Protein	rpsD	PMID:16606699	Experiment(s):EBI-1139110
Protein	wcaI	PMID:19402753	LCMS(ID Probability):99.6
Protein	crp	PMID:19402753	LCMS(ID Probability):99.6
Protein	ddpX	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 MYQHHNWQGA LLDYPVSKVV CVGSNYAKHI KEMGSAVPEE PVLFIKPETA LCDLRQPLAI PSDFGSVHHE VELAVLIGAT LRQATEEHVR KAIAGYGVAL DLTLRDVQGK MKKAGQPWEK AKAFDNSCPL SGFIPAAEFT GDPQNTTLSL SVNGEQRQQG TTADMIHKIV PLIAYMSKFF TLKAGDVVLT GTPDGVGPLQ SGDELTVTFD GHSLTTRVL
Length	219
Mol. Wt	23.71 kDa
pI	6.3 (calculated)
Extinction coefficient	18,450 - 18,825 (calc based on 5 Y, 2 W, and 3 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	18..219	PF01557 Fumarylacetoacetate (FAA) hydrolase family		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=ycgM 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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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:16129143	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946115	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003957	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76004	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6617	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13894	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946115	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003212	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3653	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 MG1655	304	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	531	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	392	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)
ycgM
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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_000913:1227282..1227322 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:b1180 (EcoliWiki Page)	NCBI GEO profiles for ycgM
microarray	GenExpDB:b1180 (EcoliWiki Page)	Summary of data for ycgM 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 (1227160..1227326) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:E3^[7]
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Notes

Accessions Related to ycgM Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6617	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3653	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1180
EcoGene	EcoGene:EG13894	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003212	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003957	Escherichia coli str. K-12 substr. MG1655
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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
Anopheles gambiae	ENSANGP00000019158 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000014416 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G15940 (score: 1.000; bootstrap: 100%) AT3G16700 (score: 0.803)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000026637 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00033237 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00022798 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000028815 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000016640 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050522-448 (score: 1.000; bootstrap: 97%) ZDB-CDNA-050522-448 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0167445 (score: 1.000; bootstrap: 88%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0038858 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA19309-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000000719 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000314622 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000000991 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000020117 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Mus musculus	MGI:1915886 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000020939 (score: 1.000; bootstrap: 100%) ENSPTRP00000020997 (score: 0.964) ENSPTRP00000020948 (score: 0.343)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000019767 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL168C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC21C39c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000129219 (score: 1.000; bootstrap: 95%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00028592001 (score: 1.000; bootstrap: 90%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000015691 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	S1257	From SHIGELLACYC
E. coli O157	Z1942	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)	PF01557 Fumarylacetoacetate (FAA) hydrolase family
Panther (EcoliWiki Page)	PTHR11820:SF57
Superfamily (EcoliWiki Page)	SUPERFAMILY:56529
EcoCyc	EcoCyc:G6617	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13894	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003212	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3653	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003957	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 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

ycgM: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 ycgM Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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