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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 are all of our structure predictions for this domain.
Click here to view only most confident match.

    MCM
Score		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.201 N/A N/A d.58.41 SEA 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