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Q6P2Q9

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    Q6P2Q9 Annotations

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    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

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    reference to undefined name 'queryReturn' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'queryReturn' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'ebiQuery' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'queryReturn' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'queryReturn' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'queryReturn' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'queryReturn' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Resources: GeneCardsLocal Structure PredictionUNIPROTPFAM, Interpro
     

    Q6P2Q9 210-357 Putative Domain Summary

    Comment from Janusz Bujnicki:

    Dlakic and Mushegian published a prediction that a bromodomain spans residues 127-242. I cannot confirm their prediction, their alignment includes a part of a conserved domain and a part is missing from Prp8 orthologs. A model based on their alignment scores very poorly with MQAPs.

    I believe there is a true conserved domain roughly within the region 210-357, but we failed to predict its relationship to any known domains. An interesting target for crystallization!!!

    References:

    Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase.
    Dlakić M, Mushegian A.
    RNA. 2011 May;17(5):799-808.

    Structural bioinformatics of the human spliceosomal proteome: 252 proteins, 464 ordered domains, and comparison with Giardia lamblia
    Korneta I, Magnus M, Bujnicki JM,
    manuscript to be published

     

    Your annotation here.

    Q6P2Q9 210-357 Domain Information
    Sequence Length: 148 Sequence Local Structure Prediction # Uniprot Refs: 13
    N-terminal boundary: pfamA domain C-terminal boundary: disordered region
    Is region cluster seed?: Yes   Cluster Size: 1  
    HMMER:
      # sequence matches: 307 # architectures: 30 # taxonomy ids: 250
    FFAS:
      No significant hits in PDB.
      No significant hits in Pfam.
    GRDB


    Q6P2Q9 802-985 Putative Domain Summary

    Comment from Janusz Bujnicki:

    Domain boundaries are messed up in a region spaning this "domain" and its neighbors.  

    RRM_4 from PFAM-A is probably not a real RRM.

    I agree with a prediction published by Dlakić and Mushegian that this region contains a domain homologous to the reverse transcriptase domain. We predict that the region 857-1304 corresponds to an "RT module", which is composed of several structural subdomains. Possibly re-anotate as PF00078 RVT_1 Reverse transcriptase (RNA-dependent DNA polymerase) Family?

    References:

    Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase.
    Dlakić M, Mushegian A.
    RNA. 2011 May;17(5):799-808.

    Structural bioinformatics of the human spliceosomal proteome: 252 proteins, 464 ordered domains, and comparison with Giardia lamblia
    Korneta I, Magnus M, Bujnicki JM,
    manuscript to be published

     

    Your annotation here.

    Q6P2Q9 802-985 Domain Information
    Sequence Length: 184 Sequence Local Structure Prediction # Uniprot Refs: 13
    N-terminal boundary: pfamA domain C-terminal boundary: pfamA domain
    Is region cluster seed?: Yes   Cluster Size: 1  
    HMMER:
      # sequence matches: 233 # architectures: 36 # taxonomy ids: 176
    FFAS:
      Top FFAS hit in PDB: Epidermal growth factor receptor kinase subst
      No significant hits in Pfam.
    GRDB
    Comments: Remote similarity to SAM domain.  


    Q6P2Q9 1078-1208 Putative Domain Summary

    Comment from Janusz Bujnicki:

    Domain boundaries are messed up in a region spaning this "domain" and its neighbors.  

    RRM_4 from PFAM-A is probably not a real RRM.

    I agree with a prediction published by Dlakić and Mushegian that this region contains a domain homologous to the reverse transcriptase domain. We predict that the region 857-1304 corresponds to an "RT module", which is composed of several structural subdomains. Possibly re-anotate as PF00078 RVT_1 Reverse transcriptase (RNA-dependent DNA polymerase) Family?

    References:

    Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase.
    Dlakić M, Mushegian A.
    RNA. 2011 May;17(5):799-808.

    Structural bioinformatics of the human spliceosomal proteome: 252 proteins, 464 ordered domains, and comparison with Giardia lamblia
    Korneta I, Magnus M, Bujnicki JM,
    manuscript to be published

     

    Your annotation here.

    Q6P2Q9 1078-1208 Domain Information
    Sequence Length: 131 Sequence Local Structure Prediction # Uniprot Refs: 13
    N-terminal boundary: pfamA domain C-terminal boundary: pfamA domain
    Is region cluster seed?: Yes   Cluster Size: 1  
    HMMER:
      # sequence matches: 225 # architectures: 41 # taxonomy ids: 171
    FFAS:
      No significant hits in PDB.
      No significant hits in Pfam.
    GRDB


    Q6P2Q9 1602-1749 Putative Domain Summary

    Comment from Janusz Bujnicki:

    Probably a novel, strutured alpha/beta domain. We failed to detect its homology to anything known.

    Reference:
    Structural bioinformatics of the human spliceosomal proteome: 252 proteins, 464 ordered domains, and comparison with Giardia lamblia
    Korneta I, Magnus M, Bujnicki JM,
    manuscript to be published

     

    Your annotation here.

    Q6P2Q9 1602-1749 Domain Information
    Sequence Length: 148 Sequence Local Structure Prediction # Uniprot Refs: 13
    N-terminal boundary: pfamA domain C-terminal boundary: psi-blast hit in PDB
    Is region cluster seed?: Yes   Cluster Size: 1  
    HMMER:
      # sequence matches: 243 # architectures: 37 # taxonomy ids: 189
    FFAS:
      No significant hits in PDB.
      No significant hits in Pfam.
    GRDB


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