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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	citE
Gene Synonym(s)	ECK0609, b0616, JW0608, ybdW^[1], ybdW
Product Desc.	citrate lyase, citryl-ACP lyase β subunit^[2]^[3]; Component of citryl-ACP lyase^[2]^[3]; citrate lyase, inactive^[2]^[3] Putative citrate lyase beta chain^[4]
Product Synonyms(s)	citrate lyase, citryl-ACP lyase (beta) subunit^[1], B0616^[2]^[1], YbdW^[2]^[1], CitE^[2]^[1] , ECK0609, JW0608, ybdW, b0616
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): citG^[2]
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	citE
Mnemonic	Citrate
Synonyms	ECK0609, b0616, JW0608, ybdW^[1], ybdW
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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	13.98 minutes	MG1655: 649713..648805 <gbrowseImage> name=NC_000913:648805..649713 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 632541..631633 <gbrowseImage> name=NC_012967:631633..632541 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 551565..552473 <gbrowseImage> name=NC_012759:551565..552473 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 649713..648805 <gbrowseImage> name=NC_007779:648805..649713 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 589045..588137 <gbrowseImage> name=NC_010473:588137..589045 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 702305..701397 <gbrowseImage> name=NC_010473:701397..702305 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
ΔcitE (Keio:JW0608)	deletion	deletion	PMID:16738554	Shigen CGSC8722^[5]
ΔcitE754::kan			PMID:16738554	CGSC:100324
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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
JW0608	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTTCCGCTTCGCTGCAACA Primer 2:CCTTCTTCGCGGATGCCGGAAAG
3G5	Kohara Phage	Genobase	PMID:3038334
1G6	Kohara Phage	Genobase	PMID:3038334
dsbG601::Tn10	Linked marker	CAG12149 = CGSC7346^[5]	est. P1 cotransduction: 63% ^[6] Synonyms:zbd-601::Tn10, zbe-601::Tn10
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 84% ^[6] Synonyms:zbe-280::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:G6342	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13542	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002949	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945406	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3312	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002122	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	CitE
Synonyms	citrate lyase, citryl-ACP lyase (beta) subunit^[1], B0616^[2]^[1], YbdW^[2]^[1], CitE^[2]^[1] , ECK0609, JW0608, ybdW, b0616
Product description	citrate lyase, citryl-ACP lyase β subunit^[2]^[3]; Component of citryl-ACP lyase^[2]^[3]; citrate lyase, inactive^[2]^[3] Putative citrate lyase beta chain^[4]
EC number (for enzymes)	4.1.3.6^[1] 4.1.3.34^[1]
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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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015813	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006475	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006084	acetyl-CoA metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006475	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006725	cellular aromatic compound metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005000	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008815	citrate (pro-3S)-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011206	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008815	citrate (pro-3S)-lyase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.3.6	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008816	citryl-CoA lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006475	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008816	citryl-CoA lyase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.3.34	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009346	citrate lyase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006475	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009346	citrate lyase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011206	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016830	carbon-carbon lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005000	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
Protein	Subunits of citryl-ACP lyase	could be indirect
Protein	Subunits of citrate lyase, inactive	could be indirect
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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
cytoplasm			From EcoCyc^[3]
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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 MGGLPMISAS LQQRKTRTRR SMLFVPGANA AMVSNSFIYP ADALMFDLED SVALREKDTA RRMVYHALQH PLYRDIETIV RVNALDSEWG VNDLEAVVRG GADVVRLPKT DTAQDVLDIE KEILRIEKAC GREPGSTGLL AAIESPLGIT RAVEIAHASE RLIGIALGAE DYVRNLRTER SPEGTELLFA RCSILQAARS AGIQAFDTVY SDANNEAGFL QEAAHIKQLG FDGKSLINPR QIDLLHNLYA PTQKEVDHAR RVVEAAEAAA REGLGVVSLN GKMVDGPVID RARLVLSRAE LSGIREE
Length	307
Mol. Wt	33.565 kDa
pI	5.6 (calculated)
Extinction coefficient	14,440 - 14,690 (calc based on 6 Y, 1 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	15..234	PF03328 HpcH/HpaI aldolase/citrate lyase family		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=citE taxon=562,83333 </beststructure>

Models

View models at:

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</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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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:90111153	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945406	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002122	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9I1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6342	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13542	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945406	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002949	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3312	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	0^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	0^a	molecules/cell/generation	Medium: MOPS Minimal 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	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)
citG
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Figure courtesy of RegulonDB

</protect>

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_000913:649693..649733 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b0616 (EcoliWiki Page)	NCBI GEO profiles for citE
microarray	GenExpDB:b0616 (EcoliWiki Page)	Summary of data for citE 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 citE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6342	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3312	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0616
EcoGene	EcoGene:EG13542	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002949	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002122	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
Bos taurus	ENSBTAP00000005451 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00032673 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007234 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000008718 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-051120-27 (score: 1.000; bootstrap: 100%) ZDB-CDNA-051120-17 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0185816 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000027213 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000316738 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000004739 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000009624 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1916884 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000044281 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000018918 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000154280 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00027917001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000048236 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	CITE	From SHIGELLACYC
E. coli O157	CITE	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)	PF03328 HpcH/HpaI aldolase/citrate lyase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:51621
Panther (EcoliWiki Page)	PTHR11105:SF0
EcoCyc	EcoCyc:G6342	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13542	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002949	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3312	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002122	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 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 ^2.11 ^2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).

citE: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 citE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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