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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	pgaB
Gene Synonym(s)	ycdR, ECK1013, b1023, JW5142, hmsF^[1]^[2]
Product Desc.	predicted enzyme associated with biofilm formation^[2]^[3] Biofilm adhesin polysaccharide PGA export; lipoprotein; polysaccharide deacetylase activity needed for export^[4]
Product Synonyms(s)	predicted enzyme associated with biofilm formation^[1], B1023^[2]^[1], YcdR^[2]^[1], HmsF^[2]^[1], PgaB^[2]^[1] , ECK1013, JW5142, ycdR, b1023
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pgaABCD^[2]
Regulation/Activity
Quick Links
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Notes

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PGA is a biofilm adhesin polysaccharide. PgaB is homologous to Y. pestis hemin storage protein HmsF, but is unable to complement hmsF mutations. First 20 aa are a type II signal peptide. Codon usage indicates pgaB is an alien (horizontal) gene. CsrA regulon. yadE paralog. PGA is oly-beta-1,6-N-acetyl-D-glucosamine.^[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	pgaB
Mnemonic	Poly--1,6-N-acetyl-d-glucosamine
Synonyms	ycdR, ECK1013, b1023, JW5142, hmsF^[1]^[2]
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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	23.43 minutes	MG1655: 1089080..1087062 <gbrowseImage> name=NC_000913:1087062..1089080 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1104124..1106142 <gbrowseImage> name=NC_012967:1104124..1106142 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 990030..992048 <gbrowseImage> name=NC_012759:990030..992048 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1090279..1088261 <gbrowseImage> name=NC_007779:1088261..1090279 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1143008..1140990 <gbrowseImage> name=NC_010473:1140990..1143008 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
ΔpgaB769::kan					PMID:16738554	CGSC:106282
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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:
1E12	Kohara Phage	Genobase	PMID:3038334
9G7	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:G6530	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13864	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003128	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945604	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3624	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003467	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	YcdR
Synonyms	predicted enzyme associated with biofilm formation^[1], B1023^[2]^[1], YcdR^[2]^[1], HmsF^[2]^[1], PgaB^[2]^[1] , ECK1013, JW5142, ycdR, b1023
Product description	predicted enzyme associated with biofilm formation^[2]^[3] Biofilm adhesin polysaccharide PGA export; lipoprotein; polysaccharide deacetylase activity needed for export^[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:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002509	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011330	P	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:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002509	F	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	References	Evidence
Protein	dps	PMID:19402753	LCMS(ID Probability):99.6
Protein	narG	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):2.538648
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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
Outer membrane		PMID:15174130	EchoLocation:ycdR
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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 MLRNGNKYLL MLVSIIMLTA CISQSRTSFI PPQDRESLLA EQPWPHNGFV AISWHNVEDE AADQRFMSVR TSALREQFAW LRENGYQPVS IAQIREAHRG GKPLPEKAVV LTFDDGYQSF YTRVFPILQA FQWPAVWAPV GSWVDTPADK QVKFGDELVD REYFATWQQV REVARSRLVE LASHTWNSHY GIQANATGSL LPVYVNRAYF TDHARYETAA EYRERIRLDA VKMTEYLRTK VEVNPHVFVW PYGEANGIAI EELKKLGYDM FFTLESGLAN ASQLDSIPRV LIANNPSLKE FAQQIITVQE KSPQRIMHID LDYVYDENLQ QMDRNIDVLI QRVKDMQIST VYLQAFADPD GDGLVKEVWF PNRLLPMKAD IFSRVAWQLR TRSGVNIYAW MPVLSWDLDP TLTRVKYLPT GEKKAQIHPE QYHRLSPFDD RVRAQVGMLY EDLAGHAAFD GILFHDDALL SDYEDASAPA ITAYQQAGFS GSLSEIRQNP EQFKQWARFK SRALTDFTLE LSARVKAIRG PHIKTARNIF ALPVIQPESE AWFAQNYADF LKSYDWTAIM AMPYLEGVAE KSADQWLIQL TNQIKNIPQA KDKSILELQA QNWQKNGQHQ AISSQQLAHW MSLLQLNGVK NYGYYPDNFL HNQPEIDLIR PEFSTAWYPK ND
Length	672
Mol. Wt	77.413 kDa
pI	6.1 (calculated)
Extinction coefficient	153,210 - 153,335 (calc based on 29 Y, 20 W, and 1 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	1-20	UniProt Manual:Signal Peptides	UniProt:P75906
Domain	101..271	PF01522 Polysaccharide deacetylase		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=pgaB 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:16128987	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945604	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003467	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75906	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6530	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13864	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945604	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003128	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3624	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	2	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)
pgaABCD
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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_000913:1089060..1089100 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:b1023 (EcoliWiki Page)	NCBI GEO profiles for pgaB
microarray	GenExpDB:b1023 (EcoliWiki Page)	Summary of data for pgaB 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 pgaB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6530	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3624	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1023
EcoGene	EcoGene:EG13864	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003128	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003467	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF01522 Polysaccharide deacetylase
Superfamily (EcoliWiki Page)	SUPERFAMILY:88713
EcoCyc	EcoCyc:G6530	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13864	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003128	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3624	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003467	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 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.

pgaB: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 pgaB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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