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View Structure Prediction Details

Protein: NRD1
Organism: Saccharomyces cerevisiae
Length: 575 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 NRD1.

Description E-value Query
Range		 Subject
Range
NRD1 - RNA-binding protein that interacts with the C-terminal domain of the RNA polymerase II large subunit...
NRD1_YEAST - Protein NRD1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NRD1 PE=1 SV=1
gi|190409225 - gi|190409225|gb|EDV12490.1| protein NRD1 [Saccharomyces cerevisiae RM11-1a]
 0.0 [1..566] [1..566]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
 7.0E-70 [179..573] [76..480]
gi|13560783 - gi|13560783|gb|AAK30205.1|AF349964_1 poly(A)-binding protein [Daucus carota]
 2.0E-68 [184..565] [87..482]
PABPC4 - poly(A) binding protein, cytoplasmic 4 (inducible form)
 6.0E-68 [179..574] [55..459]
PAB5_ARATH, PABP... - Polyadenylate-binding protein 5 OS=Arabidopsis thaliana GN=PAB5 PE=1 SV=2, (Q05196) Polyadenylate-bi...
 7.0E-68 [180..574] [81..499]
gi|126540996, gi... - gi|22507391|ref|NP_683717.1| poly(A) binding protein, cytoplasmic 4 isoform 2 [Mus musculus], gi|163...
 2.0E-67 [179..574] [55..459]

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Predicted Domain #1
Region A:
Residues: [1-200] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQQDDDFQNF VATLESFKDL KSGISGSRIK KLTTYALDHI DIESKIISLI IDYSRLCPDS  60
   61 HKLGSLYIID SIGRAYLDET RSNSNSSSNK PGTCAHAINT LGEVIQELLS DAIAKSNQDH 120
  121 KEKIRMLLDI WDRSGLFQKS YLNAIRSKCF AMDISNNTAN TASQQLSLDP KQRSKQILSN 180
  181 LKKSPPLNLN ISLPTDLTST

[Run NCBI BLAST on this sequence.]

Detection Method: MSA

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: [201-301] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DPAKQQAALF QVIAALQKHF KTLPSHTSVG TVAPPQAHTI TEYGSRRERE RERERYNSRR  60
   61 NRSRSPPAPF SQPSTGRKDR YPSVAQDQYS IGAPNTTFGT N

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 52.69897
Match: 2up1A_
Description: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
nucleic acid binding 4.50398990564944 bayes_pls_golite062009
binding 4.16717332578111 bayes_pls_golite062009
RNA binding 2.92438188845619 bayes_pls_golite062009
transcription regulator activity 2.18211199677674 bayes_pls_golite062009
mRNA binding 1.94495589345842 bayes_pls_golite062009
DNA binding 1.73925834998328 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 1.59667241219553 bayes_pls_golite062009
protein binding 1.32954276279597 bayes_pls_golite062009
transcription factor activity 0.873765500321315 bayes_pls_golite062009
0.84116054461637 bayes_pls_golite062009
RNA polymerase II transcription factor activity 0.632534695085793 bayes_pls_golite062009
hydrolase activity 0.520121701073354 bayes_pls_golite062009
sequence-specific DNA binding 0.294937517750882 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.100880394187931 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [302-413] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NHHLYPDELN VSNNPHYRPK PVSYDSTLPP DHIKVYSRTL FIGGVPLNMK EWDLANVLKP  60
   61 FAEVQSVILN NSRKHAFVKV YSRHEAENVL QNFNKDGALP LRTRWGVGFG PR

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 52.69897
Match: 2up1A_
Description: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
nucleic acid binding 4.50398990564944 bayes_pls_golite062009
binding 4.16717332578111 bayes_pls_golite062009
RNA binding 2.92438188845619 bayes_pls_golite062009
transcription regulator activity 2.18211199677674 bayes_pls_golite062009
mRNA binding 1.94495589345842 bayes_pls_golite062009
DNA binding 1.73925834998328 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 1.59667241219553 bayes_pls_golite062009
protein binding 1.32954276279597 bayes_pls_golite062009
transcription factor activity 0.873765500321315 bayes_pls_golite062009
0.84116054461637 bayes_pls_golite062009
RNA polymerase II transcription factor activity 0.632534695085793 bayes_pls_golite062009
hydrolase activity 0.520121701073354 bayes_pls_golite062009
sequence-specific DNA binding 0.294937517750882 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.100880394187931 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [414-508] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DCCDYQHGYS IIPMHRLTDA DKKWSVSAQW GGTSGQPLVT GIVFEEPDII VGEGVSSKAI  60
   61 SQKMPTDSGR NGPRSGKPNK SGSISSISPV PYGNA

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 36.69897
Match: 1fxlA_
Description: Hu antigen D (Hud)
Matching Structure (courtesy of the PDB):

Predicted Domain #5
Region A:
Residues: [509-575] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PLASPPPQQY VQPMMQQPYG YAPNQPLPSQ GPAAAAPPVP QQQFDPTAQL NSLMNMLNQQ  60
   61 QQQQQQS

[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.

Found no confident structure predictions for this domain.

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle