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View Structure Prediction Details

Protein: NMD2
Organism: Saccharomyces cerevisiae
Length: 1089 amino acids
Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076



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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for NMD2.

Description E-value Query
Range		 Subject
Range
NMD2 - Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; ...
NMD2_YEAST - Nonsense-mediated mRNA decay protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=N...
 0.0 [1..1089] [1..1089]
upf2 - nonsense-mediated decay protein Upf2
NMD2_SCHPO - Nonsense-mediated mRNA decay protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=upf...
 0.0 [10..974] [17..1046]
gi|7243197 - gi|7243197|dbj|BAA92646.1| KIAA1408 protein [Homo sapiens]
 0.0 [6..810] [167..1032]
smg-3 - status:Confirmed UniProt:Q95XD2 protein_id:AAK68590.2
 0.0 [30..1022] [44..1112]
gi|16117302 - gi|16117302|dbj|BAB16725.2| hypothetical protein [Macaca fascicularis]
 3.0E-96 [397..810] [1..418]
Upf2-PA - The gene Upf2 is referred to in FlyBase by the symbol Dmel\Upf2 (CG2253, FBgn0029992). It is a prote...
 3.0E-95 [6..392] [79..450]

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Predicted Domain #1
Region A:
Residues: [1-272] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDDGRKKELH DLNTRAWNGE EVFPLKSKKL DSSIKRNTGF IKKLKKGFVK GSESSLLKDL  60
   61 SEASLEKYLS EIIVTVTECL LNVLNKNDDV IAAVEIISGL HQRFNGRFTS PLLGAFLQAF 120
  121 ENPSVDIESE RDELQRITRV KGNLRVFTEL YLVGVFRTLD DIESKDAIPN FLQKKTGRKD 180
  181 PLLFSILREI LNYKFKLGFT TTIATAFIKK FAPLFRDDDN SWDDLIYDSK LKGALQSLFK 240
  241 NFIDATFARA TELHKKVNKL QREHQKCQIR TG

[Run NCBI BLAST on this sequence.]

Detection Method: Pfam
Confidence: 28.070581
Match: PF02854
Description: MIF4G domain

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2
Region A:
Residues: [273-336] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KLRDEYVEEY DKLLPIFIRF KTSAITLGEF FKLEIPELEG ASNDDLKETA SPMITNQILP  60
   61 PNQR

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

    MCM
Score		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.871 0.025 mRNA catabolic process a.60.3 C-terminal domain of RNA polymerase alpha subunit

Predicted Domain #3
Region A:
Residues: [337-589] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LWENEDTRKF YEILPDISKT VEESQSSKTE KDSNVNSKNI NLFFTDLEMA DCKDIIDDLS  60
   61 NRYWSSYLDN KATRNRILKF FMETQDWSKL PVYSRFIATN SKYMPEIVSE FINYLDNGFR 120
  121 SQLHSNKINV KNIIFFSEMI KFQLIPSFMI FHKIRTLIMY MQVPNNVEIL TVLLEHSGKF 180
  181 LLNKPEYKEL MEKMVQLIKD KKNDRQLNMN MKSALENIIT LLYPPSVKSL NVTVKTITPE 240
  241 QQFYRILIRS ELS

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 13.8
Match: 1h2vC
Description: CBP80, 80KDa nuclear cap-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 4.05046860305563 bayes_pls_golite062009
mRNA binding 2.35042158577052 bayes_pls_golite062009
binding 1.72811847650743 bayes_pls_golite062009
protein binding 1.3800948965226 bayes_pls_golite062009
nucleic acid binding 0.916304573557693 bayes_pls_golite062009
structural molecule activity 0.867897004862886 bayes_pls_golite062009
RNA cap binding 0.357520253345298 bayes_pls_golite062009
hydrolase activity 0.33256091835104 bayes_pls_golite062009
transcription regulator activity 0.0462205765670426 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [590-944] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SLDFKHIVKL VRKAHWDDVA IQKVLFSLFS KPHKISYQNI PLLTKVLGGL YSYRRDFVIR  60
   61 CIDQVLENIE RGLEINDYGQ NMHRISNVRY LTEIFNFEMI KSDVLLDTIY HIIRFGHINN 120
  121 QPNPFYLNYS DPPDNYFRIQ LVTTILLNIN RTPAAFTKKC KLLLRFFEYY TFIKEQPLPK 180
  181 ETEFRVSSTF KKYENIFGNT KFERSENLVE SASRLESLLK SLNAIKSKDD RVKGSSASIH 240
  241 NGKESAVPIE SITEDDEDED DENDDGVDLL GEDEDAEIST PNTESAPGKH QAKQDESEDE 300
  301 DDEDDDEDDD DDDDDDDDDG EEGDEDDDED DDDEDDDDEE EEDSDSDLEY GGDLD

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 48.522879
Match: 1i84S_
Description: Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 4.20683443264388 bayes_pls_golite062009
mRNA binding 2.49094746544717 bayes_pls_golite062009
binding 1.83406697369076 bayes_pls_golite062009
protein binding 1.50566694420704 bayes_pls_golite062009
nucleic acid binding 0.967597910409065 bayes_pls_golite062009
structural molecule activity 0.868289396026548 bayes_pls_golite062009
RNA cap binding 0.66277586901495 bayes_pls_golite062009
hydrolase activity 0.29428275639657 bayes_pls_golite062009
transcription regulator activity 0.022274123463527 bayes_pls_golite062009

Predicted Domain #5
Region A:
Residues: [945-1089] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ADRDIEMKRM YEEYERKLKD EEERKAEEEL ERQFQKMMQE SIDARKSEKV VASKIPVISK  60
   61 PVSVQKPLLL KKSEEPSSSK ETYEELSKPK KIAFTFLTKS GKKTQSRILQ LPTDVKFVSD 120
  121 VLEEEEKLKT ERNKIKKIVL KRSFD

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 17.221849
Match: 2tmaA_
Description: Tropomyosin
Matching Structure (courtesy of the PDB):
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle