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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	yciM
Gene Synonym(s)	ECK1275, b1280, JW1272^[1], JW1272
Product Desc.	conserved protein^[2]; putative heat shock protein^[3] TPR-repeats protein, function unknown^[4]
Product Synonyms(s)	conserved protein^[1], B1280^[2]^[1], YciM^[2]^[1] , ECK1275, JW1272, b1280
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yciS^[2]
Regulation/Activity
Quick Links
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Notes

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YciM has six tandem TPR repeats that are usually involved in protein-protein interactions. SignalP weakly predicts a 24 aa signal peptide and also indicates a less likely 16 aa signal peptide which is annotated in UniProt; this ambiguiity and uncertainty means that experimental verification is needed.^[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	yciM
Mnemonic	Systematic nomenclature
Synonyms	ECK1275, b1280, JW1272^[1], JW1272
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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	28.85 minutes	MG1655: 1338582..1339751 <gbrowseImage> name=NC_000913:1338582..1339751 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1338930..1340099 <gbrowseImage> name=NC_012967:1338930..1340099 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1229431..1230600 <gbrowseImage> name=NC_012759:1229431..1230600 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1342272..1343441 <gbrowseImage> name=NC_007779:1342272..1343441 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1427978..1429147 <gbrowseImage> name=NC_010473:1427978..1429147 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔyciM (Keio:JW1272)	deletion	deletion			PMID:16738554	Shigen CGSC9144^[5]
ΔyciM::kan	deletion		Biolog:respiration	unable to respire DL-a-Glycerol	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire Succinate	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire Bromosuccinate	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire L-Alanine	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire L-Alanyl-glycine	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
ΔyciM::kan	deletion		Biolog:respiration	unable to respire L-Serine	PMID:16095938
ΔyciM788::kan					PMID:16738554	CGSC:104066
yciM	deletion		Sensitivity to	increases sensitivity to bicyclomycin	PMID:21357484		fig 2
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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
JW1272	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTGGAGTTGTTGTTTCTGCT Primer 2:CCaAGGCCATCAAGACCGCGAAT
18B6	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 46% ^[6] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 31% ^[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:EG12691	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12691	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002356	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944858	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2554	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004300	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	YciM
Synonyms	conserved protein^[1], B1280^[2]^[1], YciM^[2]^[1] , ECK1275, JW1272, b1280
Product description	conserved protein^[2]; putative heat shock protein^[3] TPR-repeats protein, 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:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011990	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: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	Notes	References	Evidence
Protein	yfeZ		PMID:19402753	LCMS(ID Probability):99.3
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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 MLELLFLLLP VAAAYGWYMG RRSAQQNKQD EANRLSRDYV AGVNFLLSNQ QDKAVDLFLD MLKEDTGTVE AHLTLGNLFR SRGEVDRAIR IHQTLMESAS LTYEQRLLAI QQLGRDYMAA GLYDRAEDMF NQLTDETDFR IGALQQLLQI YQATSEWQKA IDVAERLVKL GKDKQRVEIA HFYCELALQH MASDDLDRAM TLLKKGAAAD KNSARVSIMM GRVFMAKGEY AKAVESLQRV ISQDRELVSE TLEMLQTCYQ QLGKTAEWAE FLQRAVEENT GADAELMLAD IIEARDGSEA AQVYITRQLQ RHPTMRVFHK LMDYHLNEAE EGRAKESLMV LRDMVGEKVR SKPRYRCQKC GFTAYTLYWH CPSCRAWSTI KPIRGLDGL
Length	389
Mol. Wt	44.531 kDa
pI	6.5 (calculated)
Extinction coefficient	49,850 - 50,600 (calc based on 15 Y, 5 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	Notes	References
motif	1-16	UniProt Manual:Signal Peptides	UniProt:P0AB58
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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=yciM 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:16129241	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944858	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004300	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AB58	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12691	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12691	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944858	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002356	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2554	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	Ecoli K-12	13.589+/-0.223	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.048759624	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	147	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	93	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	103	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)
yciS
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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_000913:1338562..1338602 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:b1280 (EcoliWiki Page)	NCBI GEO profiles for yciM
microarray	GenExpDB:b1280 (EcoliWiki Page)	Summary of data for yciM 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 yciM Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12691	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2554	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1280
EcoGene	EcoGene:EG12691	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002356	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004300	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	YCIM	From SHIGELLACYC
E. coli O157	YCIM	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:48452
EcoCyc	EcoCyc:EG12691	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12691	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002356	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2554	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004300	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).

yciM: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 yciM Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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