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Standard Name	gmr
Gene Synonym(s)	ECK1280, b1285, JW1278, yciR, gem^[1]
Product Desc.	modulator of RNase II stability^[2]^[3] Cyclic-di-GMP phosphodiesterase, csgD regulator; modulates protein stability of RNase II^[4]
Product Synonyms(s)	modulator of Rnase II stability^[1], Gmr^[2]^[1], YciR^[2]^[1], B1285^[2]^[1] , ECK1280, JW1278, yciR, b1285
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gmr^[2]
Regulation/Activity
Quick Links
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Notes

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Gmr has an N-terminal PAS domain, a putative diguanylate cyclase GGDEF domain, then a C-terminal cyclic-di-GMP phosphodiesterase EAL domain. AFMB Structural Genomics target No. 68 (http://afmb.cnrs-mrs.fr/article171.html). gmr is a non-essential gene. RpoS regulon (Weber, 2006). Gmr(YciR) has cyclic-di-GMP phosphodiesterase activity in vitro (Weber, 2006). YdaM/Gmr(YciR) constitute an RpoS-regulated c-di-GMP synthesis/degradation module inversely regulated by Hns and controlling the expression of curli genes (Weber, 2006).^[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	gmr
Mnemonic	Gene modulating RNase II
Synonyms	ECK1280, b1285, JW1278, yciR, gem^[1]
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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	28.94 minutes	MG1655: 1344766..1342781 <gbrowseImage> name=NC_000913:1342781..1344766 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1343127..1345112 <gbrowseImage> name=NC_012967:1343127..1345112 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1233630..1235615 <gbrowseImage> name=NC_012759:1233630..1235615 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1348456..1346471 <gbrowseImage> name=NC_007779:1346471..1348456 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1434162..1432177 <gbrowseImage> name=NC_010473:1432177..1434162 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
Δgmr (Keio:JW1278)	deletion	deletion	PMID:16738554	Shigen CGSC9149^[5]
Δgmr-722::kan			PMID:16738554	CGSC:101226
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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
JW1278	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAACCGTTAGGGAGTCCAC Primer 2:CCTGCGCGCTTCAGATAGCGTTT
18B6	Kohara Phage	Genobase	PMID:3038334
E14F6	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 39% ^[6] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 37% ^[6] Synonyms:zci-233::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:G6639	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13415	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003234	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945868	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3191	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004317	Escherichia coli str. K-12 substr. MG1655
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Notes

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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	Gmr
Synonyms	modulator of Rnase II stability^[1], Gmr^[2]^[1], YciR^[2]^[1], B1285^[2]^[1] , ECK1280, JW1278, yciR, b1285
Product description	modulator of RNase II stability^[2]^[3] Cyclic-di-GMP phosphodiesterase, csgD regulator; modulates protein stability of RNase II^[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:0004871	signal transducer activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000014	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013767	P	Seeded from EcoCyc (v14.0)	complete
	GO:0007165	signal transduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000014	P	Seeded from EcoCyc (v14.0)	complete
	GO:0010608	posttranscriptional regulation of gene expression	PMID:11260472	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0071111	cyclic-guanylate-specific phosphodiesterase activity	PMID:17010156	IDA: Inferred from Direct Assay		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	sdhA	PMID:16606699	Experiment(s):EBI-1139471
Protein	groL	PMID:16606699	Experiment(s):EBI-1139471
Protein	tldD	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.121030
Protein	ydfU	PMID:19402753	LCMS(ID Probability):99.6
Protein	argR	PMID:19402753	LCMS(ID Probability):99.4
Protein	pmbA	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):39.822271
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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 MKTVRESTTL YNFLGSHNPY WRLTESSDVL RFSTTETTEP DRTLQLSAEQ AARIREMTVI TSSLMMSLTV DESDLSVHLV GRKINKREWA GNASAWHDTP AVARDLSHGL SFAEQVVSEA HSAIVILDSR GNIQRFNRLC EDYTGLKEHD VIGQSVFKLF MSRREAAASR RNNRVFFRSG NAYEVELWIP TCKGQRLFLF RNKFVHSGSG KNEIFLICSG TDITEERRAQ ERLRILANTD SITGLPNRNA MQDLIDHAIN HADNNKVGVV YLDLDNFKKV NDAYGHLFGD QLLRDVSLAI LSCLEHDQVL ARPGGDEFLV LASNTSQSAL EAMASRILTR LRLPFRIGLI EVYTSCSVGI ALSPEHGSDS TAIIRHADTA MYTAKEGGRG QFCVFTPEMN QRVFEYLWLD TNLRKALEND QLVIHYQPKI TWRGEVRSLE ALVRWQSPER GLIPPLDFIS YAEESGLIVP LGRWVILDVV RQVAKWRDKG INLRVAVNIS ARQLADQTIF TALKQVLQEL NFEYCPIDVE LTESCLIEND ELALSVIQQF SQLGAQVHLD DFGTGYSSLS QLARFPIDAI KLDQVFVRDI HKQPVSQSLV RAIVAVAQAL NLQVIAEGVE SAKEDAFLTK NGINERQGFL FAKPMPAVAF ERWYKRYLKR A
Length	661
Mol. Wt	74.665 kDa
pI	6.8 (calculated)
Extinction coefficient	77,350 - 78,350 (calc based on 15 Y, 10 W, and 8 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	237..391	PF00990 GGDEF domain	PMID:19920124
Domain	410..644	PF00563 EAL domain	PMID:19920124
Domain	111..223	PF00989 PAS fold	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=gmr 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:16129246	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945868	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004317	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77334	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6639	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13415	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945868	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003234	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3191	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	36	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	89	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	29	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)
gmr
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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_000913:1344746..1344786 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:b1285 (EcoliWiki Page)	NCBI GEO profiles for gmr
microarray	GenExpDB:b1285 (EcoliWiki Page)	Summary of data for gmr 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 (1344670..1345033) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ16; Well:B2^[7]
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Notes

Accessions Related to gmr Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6639	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3191	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1285
EcoGene	EcoGene:EG13415	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003234	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004317	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF00563 EAL domain
Pfam (EcoliWiki Page)	PF00990 GGDEF domain
Panther (EcoliWiki Page)	PTHR24423:SF315
Superfamily (EcoliWiki Page)	SUPERFAMILY:55073
Superfamily (EcoliWiki Page)	SUPERFAMILY:55785
Superfamily (EcoliWiki Page)	SUPERFAMILY:141868
Pfam (EcoliWiki Page)	PF00989 PAS fold
EcoCyc	EcoCyc:G6639	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13415	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003234	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3191	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004317	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 ^1.9 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 ^2.7 ^2.8 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

gmr: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 gmr Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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