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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	gfcD
Gene Synonym(s)	ymcA, ECK0975, b0984, JW0967^[1]^[2]^[3], JW0967
Product Desc.	conserved protein^[3]; putative lipoprotein^[2] Required for formation of the O-antigen capsule; silenced by IS1D insertion in promoter region^[4]
Product Synonyms(s)	conserved protein^[1], B0984^[3]^[1], YmcA^[3]^[1], GfcD^[3]^[1] , ECK0975, JW0967, ymcA, b0984
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ymcA^[3]
Regulation/Activity
Quick Links
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Notes

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Function characterized in enteropathogenic E. coli (EPEC). gfcD and yjbH are paralogs. GfcD has both type I (21 aa) and (slightly better) type II (17 aa) signal peptide predictions by SignalP/LipoP. GfcD is not likely to be a lipoprotein because the lipobox Cys is poorly conserved. Part of the gfcABCDE-etp-etk operon.^[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	gfcD
Mnemonic	Group 4 Capsule
Synonyms	ymcA, ECK0975, b0984, JW0967^[1]^[2]^[3], JW0967
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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	22.52 minutes	MG1655: 1047168..1045072 <gbrowseImage> name=NC_000913:1045072..1047168 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1062940..1065036 <gbrowseImage> name=NC_012967:1062940..1065036 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 948040..950136 <gbrowseImage> name=NC_012759:948040..950136 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1048367..1046271 <gbrowseImage> name=NC_007779:1046271..1048367 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1101096..1099000 <gbrowseImage> name=NC_010473:1099000..1101096 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
ΔgfcD728::kan					PMID:16738554	CGSC:106196
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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:
4H11	Kohara Phage	Genobase	PMID:3038334
2F1	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:G6505	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13729	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003105	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945588	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3493	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003319	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	YmcA
Synonyms	conserved protein^[1], B0984^[3]^[1], YmcA^[3]^[1], GfcD^[3]^[1] , ECK0975, JW0967, ymcA, b0984
Product description	conserved protein^[3]; putative lipoprotein^[2] Required for formation of the O-antigen capsule; silenced by IS1D insertion in promoter region^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0031225	anchored to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9901	C	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 MKKNSYLLSC LAIAVSSACH AEVLTYPDPL GSSQSDFGGT GLLQMPNARI APEGEFSVNY RDNDQYRFYS TSVALFPWLE GTIRYTDVRT RKYSQWEDFS GDQSYKDKSF DFKLRLWEEG YWLPQVAFGK RDIAGTGLFD GEYLVASKQA GPFDFTLGMA WGYAGNAGNI TNPFCRVSDK YCHRAESHDA GDISFSDIFR GPASIFGGIE YQTPWNPLRL KLEYDGNNYQ NDFAGKLPQA SHFNVGAVYR AASWADLNLS YERGNTLMFG FTLRTNFNDL RPALRDTPKP AYQPAPESEG LQYTTVANQL TALKYNAGFD APEIQLRDKT LYMSGQQYKY RDSREAVDRA NRILVNNLPQ GVEKISVTQK REHMAMVTTE TDVASLRKQL AGTAPGQSEP LQQQRVEAED LSAFGRGYRI REDRFSYSFN PTLSQSLGGP EDFYMFQLGL MSSARYWFTD HLLLDGGIFT NIYNNYDKFK SSLLPADSTL PRVRTHIRDY VRNDVYLNNL QANYFADLGN GFYGQVYGGY LETMYAGVGS ELLYRPLDAC WALGVDVNYV KQRDWDNMMR FTDYSTPTGF VTAYWNPPTL NGVLMKLSVG QYLAKDKGAT IDVAKRFDSG VAVGVWAAIS NVSKDDYGEG GFSKGFYISI PFDLMTIGPN RNRAVVSWTP LTRDGGQMLS RKYQLYPMTA EREVPVGQ
Length	698
Mol. Wt	78.689 kDa
pI	6.1 (calculated)
Extinction coefficient	138,550 - 139,175 (calc based on 45 Y, 13 W, and 5 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
motif	1-18	UniProt Manual:Signal Peptides	UniProt:P75882
Domain	32..692	PF06082 Bacterial putative lipoprotein (DUF940)		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=gfcD taxon=562,83333 </beststructure>

Models

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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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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:16128950	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945588	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003319	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75882	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6505	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13729	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945588	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003105	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3493	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	12	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	4	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)
ymcA
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File:.jpg

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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_000913:1047148..1047188 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:b0984 (EcoliWiki Page)	NCBI GEO profiles for gfcD
microarray	GenExpDB:b0984 (EcoliWiki Page)	Summary of data for gfcD 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 gfcD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6505	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3493	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0984
EcoGene	EcoGene:EG13729	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003105	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003319	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	YMCA	From SHIGELLACYC
E. coli O157	YMCA	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)	PF06082 Bacterial putative lipoprotein (DUF940)
EcoCyc	EcoCyc:G6505	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13729	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003105	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3493	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003319	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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 EcoCyc (release 10.6; 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.

gfcD: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 gfcD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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