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Gene |

Product(s) |

Expression|

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Standard Name	yciG
Gene Synonym(s)	ECK1253, b1259, JW1251^[1], JW1251
Product Desc.	predicted protein^[2]^[3] Required for swarming phenotype^[4], function unknown^[5]
Product Synonyms(s)	predicted protein^[1], B1259^[2]^[1], YciG^[2]^[1] , ECK1253, JW1251, b1259
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yciGFE^[2]
Regulation/Activity
Quick Links
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Notes

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ymdF and yciG are paralogs. YciG and YmdF may be related to small stress proteins (shares COG3729 with GsiB of B. subtilis).^[5] yciG is regulated by RpoS.^[6]

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	yciG
Mnemonic	Systematic nomenclature
Synonyms	ECK1253, b1259, JW1251^[1], JW1251
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Notes

Location(s) and DNA Sequence

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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	28.32 minutes	MG1655: 1314059..1313880 <gbrowseImage> name=NC_000913:1313880..1314059 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1313629..1313450 <gbrowseImage> name=NC_012967:1313450..1313629 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1204729..1204908 <gbrowseImage> name=NC_012759:1204729..1204908 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1317749..1317570 <gbrowseImage> name=NC_007779:1317570..1317749 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1403455..1403276 <gbrowseImage> name=NC_010473:1403276..1403455 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
ΔyciG (Keio:JW1251)	deletion	deletion			PMID:16738554	Shigen CGSC9128^[7]
ΔyciG::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
ΔyciG767::kan					PMID:16738554	CGSC:104058
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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
JW1251	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCCGAACATCGTGGTGGTTC Primer 2:CCGGATTTGCCTGATTTATTACC
14C4	Kohara Phage	Genobase	PMID:3038334
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[7]	est. P1 cotransduction: 71% ^[8] Synonyms:zch-506::Tn10, zci-506::Tn10
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[7]	est. P1 cotransduction: 88% ^[8] Synonyms:trpB83::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:EG11127	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11127	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001111	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947489	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1117	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004229	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	YciG
Synonyms	predicted protein^[1], B1259^[2]^[1], YciG^[2]^[1] , ECK1253, JW1251, b1259
Product description	predicted protein^[2]^[3] Required for swarming phenotype^[4], function unknown^[5]
EC number (for enzymes)
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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:0071978

bacterial-type flagellum-dependent swarming motility

PMID:17122336^[4]

IMP: Inferred from Mutant Phenotype

P

Supplemental Table S1

no significant defects in swimming motility

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	yciH	PMID:16606699^[9]	Experiment(s):EBI-1139338
Protein	pepD	PMID:16606699^[9]	Experiment(s):EBI-1139338
Protein	rpsI	PMID:16606699^[9]	Experiment(s):EBI-1139338
Protein	nadE	PMID:16606699^[9]	Experiment(s):EBI-1139338
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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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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 MSTHNTHINE TMQRNGRNNM AEHRGGSGNF AEDREKASDA GRKGGQHSGG NFKNDPQRAS EAGKKGGQQS GGNKSGKS
Length	78
Mol. Wt	8.239 kDa
pI	12.3 (calculated)
Extinction coefficient	0 (calc based on 0 Y, 0 W, and 0 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..31	PF10685 Stress-induced bacterial acidophilic repeat motif	PMID:19920124^[10]
Domain	32..53	PF10685 Stress-induced bacterial acidophilic repeat motif	PMID:19920124^[10]
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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=yciG taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

Gene Product Resources

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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:90111238	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947489	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004229	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P21361	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11127	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11127	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947489	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001111	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1117	Escherichia coli str. K-12 substr. MG1655
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Notes

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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	2^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	519	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)
yciGFE
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Notes

yciG is regulated by RpoS.^[6]

Translation and Regulation of Translation

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<gbrowseImage> name=NC_000913:1314039..1314079 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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

</protect>

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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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:b1259 (EcoliWiki Page)	NCBI GEO profiles for yciG
microarray	GenExpDB:b1259 (EcoliWiki Page)	Summary of data for yciG 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 (1314045..1314476) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ12; Well:E9^[11]
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Notes

Accessions Related to yciG Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11127	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1117	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1259
EcoGene	EcoGene:EG11127	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001111	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004229	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	YCIG	From SHIGELLACYC
E. coli O157	YCIG	From ECOO157CYC
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Notes

Families

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See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF10685 Stress-induced bacterial acidophilic repeat motif
Pfam (EcoliWiki Page)	PF10685 Stress-induced bacterial acidophilic repeat motif
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Notes

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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 Inoue, T et al. (2007) Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. J. Bacteriol. 189 950-7 PubMed
↑ ^5.0 ^5.1 ^5.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^6.0 ^6.1 Van Dyk, TK et al. (1998) Constricted flux through the branched-chain amino acid biosynthetic enzyme acetolactate synthase triggers elevated expression of genes regulated by rpoS and internal acidification. J. Bacteriol. 180 785-92 PubMed
↑ ^7.0 ^7.1 ^7.2 CGSC: The Coli Genetics Stock Center
↑ ^8.0 ^8.1 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).
↑ ^9.0 ^9.1 ^9.2 ^9.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^10.0 ^10.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yciG:On One Page

Quickview

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 yciG Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

Categories

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