pgaB:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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 Notes References Evidence

Protein

dps

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

narG

PMID:19402753[5]

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[6]

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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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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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