ybbW:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
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52.46 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
46.684 kDa
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
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8.7 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
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73340 - 73965 (calc based on 16 Y, 9 W, and 5 C residues)  
73,340 - 73,965 (calc based on 16 Y, 9 W, and 5 C residues)


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Revision as of 22:19, 19 June 2009

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
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

YbbW

Synonyms

predicted allantoin transporter[1], B0511[2][1], AllP[2][1], YbbW[2][1]

Product description

YbbW NCS1 Transporter[2][3]

Probable allantoin permease, glyoxylate-inducible or allantoin-inducible (anaerobic)[4]

EC number (for enzymes)


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Notes

Function

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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(s) Evidence Code with/from Aspect Notes Status
GO:0016021

integral to membrane

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc [5]

complete

GO:0016020

membrane

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001248
InterPro:IPR012681
SP_KW:KW-0397
SP_KW:KW-0472

C

Seeded from EcoCyc 12.5 [6]

complete

GO:0015931

nucleobase, nucleoside, nucleotide and nucleic acid transport

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001248
InterPro:IPR012681

P

Seeded from EcoCyc [5]

complete

GO:0015205

nucleobase transmembrane transporter activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001248
InterPro:IPR012681

F

Seeded from EcoCyc [5]

complete

GO:0006810

transport

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc [5]

complete

GO:0006144

purine base metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0659

P

Seeded from EcoCyc [5]

complete

GO:0015292

uniporter activity

F

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005886

plasma membrane

GO_REF:0000004
GO_REF:0000004
GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997
SP_KW:KW-1003
SP_SL:SL-0037

C

Seeded from EcoCyc [5]

complete

GO:0005886

plasma membrane

GO_REF:0000004
GO_REF:0000004
GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997
SP_KW:KW-1003
SP_SL:SL-0037

C

Seeded from EcoCyc

complete

GO:0006144

purine base metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0659

P

Seeded from EcoCyc

complete

GO:0006810

transport

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc

complete

GO:0015205

nucleobase transmembrane transporter activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001248
InterPro:IPR012681

F

Seeded from EcoCyc

complete

GO:0015931

nucleobase, nucleoside, nucleotide and nucleic acid transport

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001248
InterPro:IPR012681

P

Seeded from EcoCyc

complete

GO:0016020

membrane

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001248
InterPro:IPR012681
SP_KW:KW-0472

C

Seeded from EcoCyc

complete

GO:0016021

integral to membrane

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc

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 Notes

plasma membrane

C-terminus localized in the cytoplasm with 12 predicted transmembrane domains

Daley et al. (2005) [7]


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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MVGGFFILGL STFSIMLAII LSAFFIAAVM VLNGAAGSKY GVPFAMILRA SYGVRGALFP
GLLRGGIAAI MWFGLQCYAG SLACLILIGK IWPGFLTLGG DFTLLGLSLP GLITFLIFWL
VNVGIGFGGG KVLNKFTAIL NPCIYIVFGG MAIWAISLVG IGPIFDYIPS GIQKAENGGF
LFLVVINAVV AVWAAPAVSA SDFTQNAHSF REQALGQTLG LVVAYILFAV AGVCIIAGAS
IHYGADTWNV LDIVQRWDSL FASFFAVLVI LMTTISTNAT GNIIPAGYQI AAIAPTKLTY
KNGVLIASII SLLICPWKLM ENQDSIYLFL DIIGGMLGPV IGVMMAHYFV VMRGQINLDE
LYTAPGDYKY YDNGFNLTAF SVTLVAVILS LGGKFIHFME PLSRVSWFVG VIVAFAAYAL
LKKRTTAEKT GEQKTIG
Length

437

Mol. Wt

46.684 kDa

pI

8.7 (calculated)

Extinction coefficient

73,340 - 73,965 (calc based on 16 Y, 9 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

Domain

221 - 243

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

263 - 285

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

298 - 320

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

330 - 352

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

373 - 392

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

402 - 421

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

7 - 29

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

44 - 63

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

70 - 92

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

107 - 129

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

142 - 164

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

Domain

179 - 201

Predicted membrane-spanning helix.

TMD predicted by TMHMM[8]

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<motif_map/>

tmhmm.php?gene=ybbW&show=pic&.jpg
Click the image to view raw output from TMHMM.

Structure See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure>ybbW 562</beststructure>

Models

View models at:

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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

EcoCyc (EcoliWiki Page)

EcoCyc:B0511-MONOMER

UniProt (EcoliWiki Page)

UniProt:P75712

PFAM (EcoliWiki Page)

PFAM:PF02133

RefSeq (EcoliWiki Page)

RefSeq:NP_415044


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Notes

Links

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Name URL Comments
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References

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  1. ↑ 1.0 1.1 1.2 1.3 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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 5.2 5.3 5.4 5.5 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  6. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  7. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 Krogh, A et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 567-80 PubMed


Categories

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