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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	gcvP
Gene Synonym(s)	ECK2898, b2903, JW2871^[1], JW2871
Product Desc.	GcvP^[2]; glycine decarboxylase^[3]; Component of glycine dehydrogenase (decarboxylating)^[2]; glycine decarboxylase^[3]; gcv system^[2]^[3] Glycine dehydrogenase (decarboxylating)^[4]
Product Synonyms(s)	glycine decarboxylase, PLP-dependent, subunit (protein P) of glycine cleavage complex^[1], B2903^[2]^[1], GcvP^[2]^[1], P-protein^[3]^[1] , ECK2898, JW2871, b2903
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gcvTHP^[2], OP00232, gcv
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

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	gcvP
Mnemonic	Glycine cleavage
Synonyms	ECK2898, b2903, JW2871^[1], JW2871
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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	65.61 minutes	MG1655: 3047063..3044190 <gbrowseImage> name=NC_000913:3044190..3047063 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2934793..2931920 <gbrowseImage> name=NC_012967:2931920..2934793 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2931338..2934211 <gbrowseImage> name=NC_012759:2931338..2934211 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3047697..3044824 <gbrowseImage> name=NC_007779:3044824..3047697 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3140933..3138060 <gbrowseImage> name=NC_010473:3138060..3140933 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
Coding Start (SO:0000323)	MG1655	3044193	Edman degradation	PMID:8375392
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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	Comments
ΔgcvP (Keio:JW2871)	deletion	deletion	PMID:16738554	Shigen CGSC10227^[5]
gcvP::Tn5KAN-I-SceI (FB20967)	Insertion at nt 377 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20967	does not contain pKD46
gcvP::Tn5KAN-I-SceI (FB20968)	Insertion at nt 377 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20968	contains pKD46
ΔgcvP754::kan			PMID:16738554	CGSC:101120
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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
JW2871	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACACAGACGTTAAGCCAGCT Primer 2:CCtTGGTATTCGCTAATCGGTAC
22H4	Kohara Phage	Genobase	PMID:3038334
5E11	Kohara Phage	Genobase	PMID:3038334
10B4	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: % ^[6]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: 17% ^[6] Synonyms:zgd-210::Tn10, zgf-210::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:EG11810	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11810	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001744	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947394	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1758	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009531	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	GcvP
Synonyms	glycine decarboxylase, PLP-dependent, subunit (protein P) of glycine cleavage complex^[1], B2903^[2]^[1], GcvP^[2]^[1], P-protein^[3]^[1] , ECK2898, JW2871, b2903
Product description	GcvP^[2]; glycine decarboxylase^[3]; Component of glycine dehydrogenase (decarboxylating)^[2]; glycine decarboxylase^[3]; gcv system^[2]^[3] Glycine dehydrogenase (decarboxylating)^[4]
EC number (for enzymes)	1.4.4.2^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0004375	glycine dehydrogenase (decarboxylating) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003437	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004375	glycine dehydrogenase (decarboxylating) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.4.4.2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006544	glycine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003437	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019464	glycine decarboxylation via glycine cleavage system	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00711	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003437	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	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
Protein	Subunits of glycine dehydrogenase (decarboxylating)	could be indirect
Protein	pbpC		PMID:16606699	Experiment(s):EBI-1144247
Protein	yhbJ		PMID:16606699	Experiment(s):EBI-1144247
Protein	rpmE		PMID:16606699	Experiment(s):EBI-1144247
Protein	rpoB		PMID:16606699	Experiment(s):EBI-1144247
Protein	purU		PMID:16606699	Experiment(s):EBI-1144247
Protein	nadE		PMID:16606699	Experiment(s):EBI-1144247
Protein	matC		PMID:16606699	Experiment(s):EBI-1144247
Protein	secA		PMID:16606699	Experiment(s):EBI-1144247
Protein	yfhM		PMID:16606699	Experiment(s):EBI-1144247
Protein	gltI		PMID:19402753	LCMS(ID Probability):99.6
Protein	gabD		PMID:19402753	LCMS(ID Probability):99.6
Protein	Subunits of gcv system	could be indirect
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Notes

Localization

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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 MTQTLSQLEN SGAFIERHIG PDAAQQQEML NAVGAQSLNA LTGQIVPKDI QLATPPQVGA PATEYAALAE LKAIASRNKR FTSYIGMGYT AVQLPPVILR NMLENPGWYT AYTPYQPEVS QGRLEALLNF QQVTLDLTGL DMASASLLDE ATAAAEAMAM AKRVSKLKNA NRFFVASDVH PQTLDVVRTR AETFGFEVIV DDAQKVLDHQ DVFGVLLQQV GTTGEIHDYT ALISELKSRK IVVSVAADIM ALVLLTAPGK QGADIVFGSA QRFGVPMGYG GPHAAFFAAK DEYKRSMPGR IIGVSKDAAG NTALRMAMQT REQHIRREKA NSNICTSQVL LANIASLYAV YHGPVGLKRI ANRIHRLTDI LAAGLQQKGL KLRHAHYFDT LCVEVADKAG VLTRAEAAEI NLRSDILNAV GITLDETTTR ENVMQLFNVL LGDNHGLDID TLDKDVAHDS RSIQPAMLRD DEILTHPVFN RYHSETEMMR YMHSLERKDL ALNQAMIPLG SCTMKLNAAA EMIPITWPEF AELHPFCPPE QAEGYQQMIA QLADWLVKLT GYDAVCMQPN SGAQGEYAGL LAIRHYHESR NEGHRDICLI PASAHGTNPA SAHMAGMQVV VVACDKNGNI DLTDLRAKAE QAGDNLSCIM VTYPSTHGVY EETIREVCEV VHQFGGQVYL DGANMNAQVG ITSPGFIGAD VSHLNLHKTF CIPHGGGGPG MGPIGVKAHL APFVPGHSVV QIEGMLTRQG AVSAAPFGSA SILPISWMYI RMMGAEGLKK ASQVAILNAN YIASRLQDAF PVLYTGRDGR VAHECILDIR PLKEETGISE LDIAKRLIDY GFHAPTMSFP VAGTLMVEPT ESESKVELDR FIDAMLAIRA EIDQVKAGVW PLEDNPLVNA PHIQSELVAE WAHPYSREVA VFPAGVADKY WPTVKRLDDV YGDRNLFCSC VPISEYQ
Length	957
Mol. Wt	104.376 kDa
pI	5.9 (calculated)
Extinction coefficient	81,710 - 83,335 (calc based on 29 Y, 7 W, and 13 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
Initiator Methionine	1	Removed	UniProt:P33195
Domain	16..440	PF02347 Glycine cleavage system P-protein		PMID:19920124
Domain	456..808	PF02347 Glycine cleavage system P-protein		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=gcvP 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:16130805	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947394	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009531	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P33195	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11810	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11810	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947394	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001744	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1758	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 MC4100	6.33E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	89.275+/-0.849	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.058997564	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	397	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	836	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	780	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)
gcvTHP
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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_000913:3047043..3047083 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:b2903 (EcoliWiki Page)	NCBI GEO profiles for gcvP
microarray	GenExpDB:b2903 (EcoliWiki Page)	Summary of data for gcvP 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 (3046961..3047260) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:B5^[7]
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Notes

Accessions Related to gcvP Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11810	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1758	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2903
EcoGene	EcoGene:EG11810	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001744	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009531	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	ENSANGP00000014378 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000005712 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G26080 (score: 1.000; bootstrap: 100%) AT4G33010 (score: 0.810)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000036556 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00025598 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00020022 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000002033 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000012269 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030131-340 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-1077 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231130 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0037801 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000024228 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000019020 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1341155 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6V9T1 (score: 1.000; bootstrap: 100%) Q69X42 (score: 0.938) O22575 (score: 0.865) Q38766 (score: 0.865) Q6RS61 (score: 0.629)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000015456 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YMR189W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC13G66c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000180377 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00028986001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000001204 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	GCVP	From SHIGELLACYC
E. coli O157	GCVP	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)	PF02347 Glycine cleavage system P-protein
Pfam (EcoliWiki Page)	PF02347 Glycine cleavage system P-protein
Panther (EcoliWiki Page)	PTHR11773:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
EcoCyc	EcoCyc:EG11810	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11810	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001744	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1758	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009531	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 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 ^3.7 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

gcvP: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 gcvP Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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