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Standard Name	yciT
Gene Synonym(s)	yciT, ECK1279, b1284, JW1276, deoT^[1]^[2], deoT, JW1276
Product Desc.	DNA-binding transcriptional regulator^[2]^[3]
Product Synonyms(s)	predicted DNA-binding transcriptional regulator^[1], B1284^[2]^[1], YciT^[2]^[1], DeoT^[2]^[1] , deoT, ECK1279, JW1276, b1284
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression
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	yciT
Mnemonic	Systematic nomenclature
Synonyms	yciT, ECK1279, b1284, JW1276, deoT^[1]^[2], deoT, JW1276
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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	28.92 minutes	MG1655: 1342370..1341621 <gbrowseImage> name=NC_000913:1341621..1342370 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1342717..1341968 <gbrowseImage> name=NC_012967:1341968..1342717 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1232470..1233219 <gbrowseImage> name=NC_012759:1232470..1233219 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1346060..1345311 <gbrowseImage> name=NC_007779:1345311..1346060 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1431766..1431017 <gbrowseImage> name=NC_010473:1431017..1431766 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔyciT721::kan				PMID:16738554	CGSC:104076
yciT	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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
18B6	Kohara Phage	Genobase	PMID:3038334
E14F6	Kohara Phage	Genobase	PMID:3038334
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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:G6638	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13905	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003233	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945869	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3664	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004312	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	YciT
Synonyms	predicted DNA-binding transcriptional regulator^[1], B1284^[2]^[1], YciT^[2]^[1], DeoT^[2]^[1] , deoT, ECK1279, JW1276, b1284
Product description	DNA-binding transcriptional regulator^[2]^[3]
EC number (for enzymes)
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See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki. <protect></protect>

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. 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:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001034	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018356	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001034	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018356	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACK5	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001034	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018356	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACK5	F	Seeded from EcoCyc (v14.0)	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	fabI	PMID:16606699	Experiment(s):EBI-1139466
Protein	groL	PMID:16606699	Experiment(s):EBI-1139466
Protein	nadE	PMID:16606699	Experiment(s):EBI-1139466
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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki. </protect>

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 MNSRQQTILQ MVIDQGQVSV TDLAKATGVS EVTIRQDLNT LEKLSYLRRA HGFAVSLDSD DVETRMMSNY TLKRELAEFA ASLVQPGETI FIENGSSNAL LARTLGEQKK NVTIITVSSY IAHLLKDAPC EVILLGGVYQ KKSESMVGPL TRQCIQQVHF SKAFIGIDGW QPETGFTGRD MMRTDVVNAV LEKECEAIVL TDSSKFGAVH SYSIGPVERF NRVITDSKIR ASDLMHLEHS KLTIHVVDI
Length	249
Mol. Wt	27.602 kDa
pI	6.4 (calculated)
Extinction coefficient	12,950 - 13,325 (calc based on 5 Y, 1 W, and 3 C residues)
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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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	70..226	PF00455 Bacterial regulatory proteins, deoR family	PMID:19920124
Domain	4..60	PF08220 DeoR-like helix-turn-helix domain	PMID:19920124
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See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

<motif_map/>

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

Structures

<beststructure> gene=yciT taxon=562,83333 </beststructure>

Models

View models at:

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

</protect>

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:16129245	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945869	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004312	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76034	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6638	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13905	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945869	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003233	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3664	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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 MC4100	2.12E+02	molecules/cell	Medium: combined data from rich and minimal media	37
Protein	E. coli K-12 MC4100	2.12E+02	molecules/cell	Medium: combined data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1461	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	304	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	1266	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)
deoT
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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_000913:1342350..1342390 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:b1284 (EcoliWiki Page)	NCBI GEO profiles for deoT
microarray	GenExpDB:b1284 (EcoliWiki Page)	Summary of data for deoT 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 (1342291..1342860) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ17; Well:H6^[4]
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Notes

Accessions Related to yciT Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6638	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3664	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1284
EcoGene	EcoGene:EG13905	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003233	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004312	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	S1371	From SHIGELLACYC
E. coli O157	Z2521	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)	PF00455 Bacterial regulatory proteins, deoR family
Superfamily (EcoliWiki Page)	SUPERFAMILY:46785
Superfamily (EcoliWiki Page)	SUPERFAMILY:100950
Pfam (EcoliWiki Page)	PF08220 DeoR-like helix-turn-helix domain
EcoCyc	EcoCyc:G6638	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13905	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003233	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3664	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004312	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 ^2.9 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
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yciT: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 yciT Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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