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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	gcp
Gene Synonym(s)	ECK3054, b3064, JW3036, gcp^[1], ygjD
Product Desc.	predicted peptidase^[2]^[3] Function unknown, Gcp glycoprotease homolog, essential gene^[4]
Product Synonyms(s)	predicted peptidase^[1], B3064^[2]^[1], YgjD^[2]^[1], Gcp^[2]^[1] , Gcp, ECK3054, JW3036, ygjD, b3064
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ygjD^[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	gcp
Mnemonic	Systematic nomenclature
Synonyms	ECK3054, b3064, JW3036, gcp^[1], ygjD
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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	69.13 minutes	MG1655: 3208565..3207552 <gbrowseImage> name=NC_000913:3207552..3208565 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3143360..3142347 <gbrowseImage> name=NC_012967:3142347..3143360 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3094700..3095713 <gbrowseImage> name=NC_012759:3094700..3095713 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3209199..3208186 <gbrowseImage> name=NC_007779:3208186..3209199 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3306310..3305297 <gbrowseImage> name=NC_010473:3305297..3306310 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
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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
JW3036	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTGTACTGGGTATTGAAAC Primer 2:CCgGCAGCCGGTAACTCCGCCAG
tolC210::Tn10	Linked marker	CAG12184 = CGSC7437^[5]	est. P1 cotransduction: 32% ^[6]
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 77% ^[6] Synonyms:zgh-3075::Tn10, zgj-3075::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
NCBI (EcoliWiki Page)	GeneID:947578	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	Gcp
Synonyms	predicted peptidase^[1], B3064^[2]^[1], YgjD^[2]^[1], Gcp^[2]^[1] , Gcp, ECK3054, JW3036, ygjD, b3064
Product description	predicted peptidase^[2]^[3] Function unknown, Gcp glycoprotease homolog, essential gene^[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:0004175	endopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009180	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004222	metalloendopeptidase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01445	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004222	metalloendopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000905	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004222	metalloendopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017860	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004222	metalloendopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017861	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:19376873	IPI: Inferred from Physical Interaction	UniProtKB:P76256	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000905	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017860	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017861	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008233	peptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0645	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008237	metallopeptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0482	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009180	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:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	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	References	Evidence
Protein	aceE	PMID:15690043	Experiment(s):EBI-885224
Protein	tufA	PMID:15690043	Experiment(s):EBI-885224
Protein	yeaZ	PMID:15690043	Experiment(s):EBI-885224, EBI-881680
Protein	hybG	PMID:15690043	Experiment(s):EBI-891983
Protein	rplL	PMID:15690043	Experiment(s):EBI-891983
Protein	rpoA	PMID:15690043	Experiment(s):EBI-891983
Protein	rpoB	PMID:15690043	Experiment(s):EBI-891983
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-891983
Protein	ligB	PMID:16606699	Experiment(s):EBI-1144688
Protein	groL	PMID:16606699	Experiment(s):EBI-1144688
Protein	hybG	PMID:19402753	LCMS(ID Probability):99.0
Protein	metK	PMID:19402753	MALDI(Z-score):25.830797
Protein	tufB	PMID:19402753	MALDI(Z-score):22.984140
Protein	rpsJ	PMID:19402753	LCMS(ID Probability):99.6
Protein	yeaZ	PMID:19402753	LCMS(ID Probability):97.9 MALDI(Z-score):39.653697
Protein	rplL	PMID:19402753	LCMS(ID Probability):99.6
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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 MRVLGIETSC DETGIAIYDD EKGLLANQLY SQVKLHADYG GVVPELASRD HVRKTVPLIQ AALKESGLTA KDIDAVAYTA GPGLVGALLV GATVGRSLAF AWDVPAIPVH HMEGHLLAPM LEDNPPEFPF VALLVSGGHT QLISVTGIGQ YELLGESIDD AAGEAFDKTA KLLGLDYPGG PLLSKMAAQG TAGRFVFPRP MTDRPGLDFS FSGLKTFAAN TIRDNGTDDQ TRADIARAFE DAVVDTLMIK CKRALDQTGF KRLVMAGGVS ANRTLRAKLA EMMKKRRGEV FYARPEFCTD NGAMIAYAGM VRFKAGATAD LGVSVRPRWP LAELPAA
Length	337
Mol. Wt	36.008 kDa
pI	6.3 (calculated)
Extinction coefficient	22,920 - 23,295 (calc based on 8 Y, 2 W, and 3 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	23..307	PF00814 Glycoprotease 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=ygjD 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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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:16130960	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947578	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P05852	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947578	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	1.454+/-0.948	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.03751234	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	1968	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	493	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	974	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)
ygjD
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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_000913:3208545..3208585 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:b3064 (EcoliWiki Page)	NCBI GEO profiles for ygjD
microarray	GenExpDB:b3064 (EcoliWiki Page)	Summary of data for ygjD 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 (3208113..3208494) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ20; Well:A2^[7]
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Notes

Accessions Related to ygjD Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3064
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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
Anopheles gambiae	ENSANGP00000010411 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000034603 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G45270 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000016671 (score: 1.000; bootstrap: 76%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00032676 (score: 1.000; bootstrap: 67%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007237 (score: 1.000; bootstrap: 67%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000013815 (score: 1.000; bootstrap: 95%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030616-532 (score: 1.000; bootstrap: 83%) ZDB-CDNA-051120-5 (score: 1.000; bootstrap: 84%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0183804 (score: 1.000; bootstrap: 90%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0031060 (score: 1.000; bootstrap: 70%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA12844-PA (score: 1.000; bootstrap: 84%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000003745 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000264151 (score: 1.000; bootstrap: 66%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000018798 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000014319 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Mus musculus	MGI:1919335 (score: 1.000; bootstrap: 79%)	From Inparanoid:20070104
Oryza gramene	Q6L4N8 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000021771 (score: 1.000; bootstrap: 65%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000049478 (score: 1.000; bootstrap: 74%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDL104C (score: 1.000; bootstrap: 85%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC12590 (score: 1.000; bootstrap: 76%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000150388 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00029225001 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000050666 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGJD	From SHIGELLACYC
E. coli O157	YGJD	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)	PF00814 Glycoprotease family
Superfamily (EcoliWiki Page)	SUPERFAMILY:53067
Panther (EcoliWiki Page)	PTHR11735:SF6
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

gcp: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 ygjD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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