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Gene |

Product(s) |

Expression|

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Standard Name	csiD
Gene Synonym(s)	ygaT, ECK2653, b2659, JW5427, csi-12^[1]^[2], csi-12
Product Desc.	predicted protein^[2]^[3] Carbon starvation induced gene, function unknown; first gene in csiD-ygaF-gabDTP operon; tetrameric; structural homolog of 2-oxoglutarate Fe(II)-dependent oxygenases^[4]
Product Synonyms(s)	predicted protein^[1], B2659^[2]^[1], YgaT^[2]^[1], CsiD^[2]^[1] , csi-12, ECK2653, JW5427, ygaT, b2659
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): csiD-ygaF-gabDTP^[2], csiD
Regulation/Activity
Quick Links
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Notes

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RpoS, cAMP-CRP, HN-S and Lrp regulons.^[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	csiD
Mnemonic	Carbon starvation induced
Synonyms	ygaT, ECK2653, b2659, JW5427, csi-12^[1]^[2], csi-12
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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	60.07 minutes	MG1655: 2787007..2787984 <gbrowseImage> name=NC_000913:2787007..2787984 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2683666..2684643 <gbrowseImage> name=NC_012967:2683666..2684643 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2672819..2673796 <gbrowseImage> name=NC_012759:2672819..2673796 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2787641..2788618 <gbrowseImage> name=NC_007779:2787641..2788618 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
Coding Start (SO:0000323)	MG1655	2787007	Edman degradation	PMID:9512707
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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
ΔcsiD740::kan					PMID:16738554	CGSC:106152
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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:

12G12

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:G7394	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13523	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003961	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948076	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3295	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008754	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	YgaT
Synonyms	predicted protein^[1], B2659^[2]^[1], YgaT^[2]^[1], CsiD^[2]^[1] , csi-12, ECK2653, JW5427, ygaT, b2659
Product description	predicted protein^[2]^[3] Carbon starvation induced gene, function unknown; first gene in csiD-ygaF-gabDTP operon; tetrameric; structural homolog of 2-oxoglutarate Fe(II)-dependent oxygenases^[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:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	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
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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 MSLLCAFFRN VDIFRLWLRN EHRHVTLHLI RGSLLMNALT AVQNNAVDSG QDYSGFTLTP SAQSPRLLEL TFTEQTTKQF LEQVAEWPVQ ALEYKSFLRF RVAKILDDLC ANQLQPLLLK TLLNRAEGAL LINAVGVDDV KQADEMVKLA TAVAHLIGRS NFDAMSGQYY ARFVVKNVDN SDSYLRQPHR VMELHNDGTY VEEITDYVLM MKIDEQNMQG GNSLLLHLDD WEHLDNYFRH PLARRPMRFA APPSKNVSKD VFHPVFDVDQ QGRPVMRYID QFVQPKDFEE GVWLSELSDA IETSKGILSV PVPVGKFLLI NNLFWLHGRD RFTPHPDLRR ELMRQRGYFA YASNHYQTHQ
Length	360
Mol. Wt	41.62 kDa
pI	6.8 (calculated)
Extinction coefficient	45,380 - 45,630 (calc based on 12 Y, 5 W, and 2 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	20..315	PF08943 CsiD		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=csiD 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:90111476	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948076	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008754	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76621	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7394	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13523	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948076	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003961	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3295	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	E. coli K-12 MG1655	1^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	111	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)
csiD-ygaF-gabDTP
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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_000913:2786987..2787027 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:b2659 (EcoliWiki Page)	NCBI GEO profiles for csiD
microarray	GenExpDB:b2659 (EcoliWiki Page)	Summary of data for csiD 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 (2786576..2786966) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ17; Well:C8^[5]
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Notes

Accessions Related to csiD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7394	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3295	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2659
EcoGene	EcoGene:EG13523	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003961	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008754	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	S2871	From SHIGELLACYC
E. coli O157	Z3956	From ECOO157CYC
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Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF08943 CsiD
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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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

csiD: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 csiD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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