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View Structure Prediction Details

Protein: MRD1
Organism: Saccharomyces cerevisiae
Length: 887 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 MRD1.

Description E-value Query
Range		 Subject
Range
MRD1 - Essential conserved protein that is part of the 90S preribosome; required for production of 18S rRNA...
MRD1_YEAST - Multiple RNA-binding domain-containing protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S...
 0.0 [1..887] [1..887]
RBM19 - RNA binding motif protein 19
gi|190690741, gi... - gi|190690741|gb|ACE87145.1| RNA binding motif protein 19 protein [synthetic construct], gi|190689379...
 0.0 [1..867] [1..937]
RBM19_MOUSE - Probable RNA-binding protein 19 OS=Mus musculus GN=Rbm19 PE=1 SV=1
 0.0 [1..883] [1..942]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1
 0.0 [341..765] [7..389]

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Predicted Domain #1
Region A:
Residues: [1-113] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSRIIVKGLP VYLTDDNLRE HFTKRLRQKH SHQAVNGSGP DLITDVKILR DRNGESRRFG  60
   61 FIGYRNEEDA FDAVEYFNGS FINTSKIEVS MAKSFADPRV PQPMKEKRRE ALK

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 7.0
Match: 1fj7A_
Description: Nucleolin
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 6.04120049976231 bayes_pls_golite062009
mRNA binding 4.29904003387927 bayes_pls_golite062009
nucleic acid binding 3.81920018903278 bayes_pls_golite062009
binding 3.44552682116509 bayes_pls_golite062009
3.36965439092178 bayes_pls_golite062009
single-stranded RNA binding 2.32565125258004 bayes_pls_golite062009
poly-pyrimidine tract binding 1.99190411806363 bayes_pls_golite062009
structural molecule activity 1.29928829870122 bayes_pls_golite062009
transcription regulator activity 1.07788694919471 bayes_pls_golite062009
protein binding 1.02232785292059 bayes_pls_golite062009
DNA binding 0.978604858165557 bayes_pls_golite062009
snoRNA binding 0.87536768969411 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.764716918216811 bayes_pls_golite062009
snRNA binding 0.45487108214667 bayes_pls_golite062009
transcription factor activity 0.234742017105535 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [114-316] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RFREKEEKLL QEENRKKKKV DENKHSNIDD EIRKNKQLQE FMETMKPSSQ VTSWEKVGID  60
   61 KSIEDEKLKR EEEDSSVQGN SLLAHALALK EENNKDEAPN LVIENESDDE YSALNRNRDE 120
  121 DQEDAGEEEK MISISNLKDT DIGLVNDDAN SDEKENEKRR NLAQDEKVSD LDWFKQRRVR 180
  181 IKESEAETRE KSSSYATEQN ESL

[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 #3
Region A:
Residues: [317-423] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DTKKEEQPER AVPQKTDEEL AIEKINQTGR LFLRNILYTS KEEDFRKLFS PFGELEEVHV  60
   61 ALDTRTGQSK GFAYVLFKDS KNAVNAYVEL DKQIFQGRLL HILPGEE

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 121.232149
Match: 1cvjA_
Description: Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 6.04120049976231 bayes_pls_golite062009
mRNA binding 4.29904003387927 bayes_pls_golite062009
nucleic acid binding 3.81920018903278 bayes_pls_golite062009
binding 3.44552682116509 bayes_pls_golite062009
3.36965439092178 bayes_pls_golite062009
single-stranded RNA binding 2.32565125258004 bayes_pls_golite062009
poly-pyrimidine tract binding 1.99190411806363 bayes_pls_golite062009
structural molecule activity 1.29928829870122 bayes_pls_golite062009
transcription regulator activity 1.07788694919471 bayes_pls_golite062009
protein binding 1.02232785292059 bayes_pls_golite062009
DNA binding 0.978604858165557 bayes_pls_golite062009
snoRNA binding 0.87536768969411 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.764716918216811 bayes_pls_golite062009
snRNA binding 0.45487108214667 bayes_pls_golite062009
transcription factor activity 0.234742017105535 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [424-528] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KKSHRLDEFD LKNMPLKKQK ELKRKAAASR QTFSWNSLYM NQDAVLGSVA AKLGLEKSQL  60
   61 IDAENSSSAV KQALAEAHVI GDVRKYFESK GVDLTKFSQL KSTNQ

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 121.232149
Match: 1cvjA_
Description: Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 6.04120049976231 bayes_pls_golite062009
mRNA binding 4.29904003387927 bayes_pls_golite062009
nucleic acid binding 3.81920018903278 bayes_pls_golite062009
binding 3.44552682116509 bayes_pls_golite062009
3.36965439092178 bayes_pls_golite062009
single-stranded RNA binding 2.32565125258004 bayes_pls_golite062009
poly-pyrimidine tract binding 1.99190411806363 bayes_pls_golite062009
structural molecule activity 1.29928829870122 bayes_pls_golite062009
transcription regulator activity 1.07788694919471 bayes_pls_golite062009
protein binding 1.02232785292059 bayes_pls_golite062009
DNA binding 0.978604858165557 bayes_pls_golite062009
snoRNA binding 0.87536768969411 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.764716918216811 bayes_pls_golite062009
snRNA binding 0.45487108214667 bayes_pls_golite062009
transcription factor activity 0.234742017105535 bayes_pls_golite062009

Predicted Domain #5
Region A:
Residues: [529-627] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RDDKVILVKN FPFGTTREEL GEMFLPYGKL ERLLMPPAGT IAIVQFRDTT SARAAFTKLS  60
   61 YKRFKDGIIY LERGPKDCFT KPAEADDLIN NTSAKEEEN

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 41.980454
Match: 1fjeB_
Description: Nucleolin
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 6.04120049976231 bayes_pls_golite062009
mRNA binding 4.29904003387927 bayes_pls_golite062009
nucleic acid binding 3.81920018903278 bayes_pls_golite062009
binding 3.44552682116509 bayes_pls_golite062009
3.36965439092178 bayes_pls_golite062009
single-stranded RNA binding 2.32565125258004 bayes_pls_golite062009
poly-pyrimidine tract binding 1.99190411806363 bayes_pls_golite062009
structural molecule activity 1.29928829870122 bayes_pls_golite062009
transcription regulator activity 1.07788694919471 bayes_pls_golite062009
protein binding 1.02232785292059 bayes_pls_golite062009
DNA binding 0.978604858165557 bayes_pls_golite062009
snoRNA binding 0.87536768969411 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.764716918216811 bayes_pls_golite062009
snRNA binding 0.45487108214667 bayes_pls_golite062009
transcription factor activity 0.234742017105535 bayes_pls_golite062009

Predicted Domain #6
Region A:
Residues: [628-754] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PVEVKPSSND LMEANKDVTE GSSNAHDEDV IDGPTVSIFI KNLNFSTTNQ NLTDRFKVFT  60
   61 GFVVAQVKTK PDPKHQGKTL SMGFGFVEFR TKEQANAVIA AMDGTVIDGH KIQLKLSHRQ 120
  121 ASQSGNT

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 97.40824
Match: 1l3kA_
Description: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted Domain #7
Region A:
Residues: [755-887] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KTKSNKKSGK IIVKNLPFEA TRKDVFELFN SFGQLKSVRV PKKFDKSARG FAFVEFLLPK  60
   61 EAENAMDQLH GVHLLGRRLV MQYAEEDAVD AEEEIARMTK KVRKQVATNE MAALRNGGGR 120
  121 KKLDVDDEEN EGF

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 97.40824
Match: 1l3kA_
Description: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle