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View Structure Prediction Details

Protein: NAM8
Organism: Saccharomyces cerevisiae
Length: 523 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 NAM8.

Description E-value Query
Range		 Subject
Range
NAM8_YEAST - Protein NAM8 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NAM8 PE=1 SV=2
NAM8 - RNA binding protein, component of the U1 snRNP protein; mutants are defective in meiotic recombinati...
gi|190405867 - gi|190405867|gb|EDV09134.1| RNA-binding protein [Saccharomyces cerevisiae RM11-1a]
gi|207344656 - gi|207344656|gb|EDZ71726.1| YHR086Wp-like protein [Saccharomyces cerevisiae AWRI1631]
 0.0 [1..523] [1..523]
PABP1_BOVIN - Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1
gi|109087089 - gi|109087089|ref|XP_001098239.1| PREDICTED: poly(A) binding protein, cytoplasmic 1 isoform 2 [Macaca...
gi|123993665, gi... - gi|168278070|dbj|BAG11013.1| polyadenylate-binding protein 1 [synthetic construct], gi|123999981|gb|...
gi|194036975 - gi|194036975|ref|XP_001927782.1| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-bind...
PABPC1 - poly(A) binding protein, cytoplasmic 1
gi|73974130, gi|... - gi|73974178|ref|XP_857695.1| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-binding ...
 0.0 [44..507] [1..487]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1
 0.0 [44..507] [1..487]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2
 0.0 [44..507] [1..487]
PAB1_XENLA, PABP... - (P20965) Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1), (P20965) Polyadenylat...
 0.0 [44..507] [1..486]
gi|19526272 - gi|19526272|gb|AAL89666.1|AF411956_7 polyA-binding protein [Takifugu rubripes]
 9.0E-95 [51..511] [8..493]

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Predicted Domain #1
Region A:
Residues: [1-164] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSYKQTTYYP SRGNLVRNDS SPYTNTISSE TNNSSTSVLS LQGASNVSLG TTGNQLYMGD  60
   61 LDPTWDKNTV RQIWASLGEA NINVRMMWNN TLNNGSRSSM GPKNNQGYCF VDFPSSTHAA 120
  121 NALLKNGMLI PNFPNKKLKL NWATSSYSNS NNSLNNVKSG NNCS

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 126.67837
Match: 1cvjA_
Description: Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 6.73097473547076 bayes_pls_golite062009
6.62953239642182 bayes_pls_golite062009
mRNA binding 5.29759606920196 bayes_pls_golite062009
nucleic acid binding 4.92126426323641 bayes_pls_golite062009
U1 snRNA binding 4.22094068431436 bayes_pls_golite062009
snRNA binding 4.06596327298973 bayes_pls_golite062009
binding 3.64400841800969 bayes_pls_golite062009
poly-pyrimidine tract binding 3.11990160533699 bayes_pls_golite062009
single-stranded RNA binding 2.93798024346416 bayes_pls_golite062009
structural molecule activity 2.78501986457503 bayes_pls_golite062009
protein binding 2.17260848225967 bayes_pls_golite062009
transcription regulator activity 1.92450390013691 bayes_pls_golite062009
DNA binding 1.8021593476478 bayes_pls_golite062009
transcription factor activity 1.15127506309683 bayes_pls_golite062009
transcription activator activity 1.12833244388568 bayes_pls_golite062009
transcription repressor activity 0.998305828880243 bayes_pls_golite062009
mRNA 3'-UTR binding 0.824614388276642 bayes_pls_golite062009
mRNA 5'-UTR binding 0.625848256054783 bayes_pls_golite062009
translation repressor activity, nucleic acid binding 0.461000905454505 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.425042944899091 bayes_pls_golite062009
hydrolase activity 0.389390547875764 bayes_pls_golite062009
sequence-specific DNA binding 0.383589644462932 bayes_pls_golite062009
translation regulator activity 0.38120065819101 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.128616879457381 bayes_pls_golite062009
snoRNA binding 0.0568636182001701 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [165-303] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IFVGDLAPNV TESQLFELFI NRYASTSHAK IVHDQVTGMS KGYGFVKFTN SDEQQLALSE  60
   61 MQGVFLNGRA IKVGPTSGQQ QHVSGNNDYN RSSSSLNNEN VDSRFLSKGQ SFLSNGNNNM 120
  121 GFKRNHMSQF IYPVQQQPS

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 14.522879
Match: 1qm9A_
Description: Polypyrimidine tract-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 6.73097473547076 bayes_pls_golite062009
6.62953239642182 bayes_pls_golite062009
mRNA binding 5.29759606920196 bayes_pls_golite062009
nucleic acid binding 4.92126426323641 bayes_pls_golite062009
U1 snRNA binding 4.22094068431436 bayes_pls_golite062009
snRNA binding 4.06596327298973 bayes_pls_golite062009
binding 3.64400841800969 bayes_pls_golite062009
poly-pyrimidine tract binding 3.11990160533699 bayes_pls_golite062009
single-stranded RNA binding 2.93798024346416 bayes_pls_golite062009
structural molecule activity 2.78501986457503 bayes_pls_golite062009
protein binding 2.17260848225967 bayes_pls_golite062009
transcription regulator activity 1.92450390013691 bayes_pls_golite062009
DNA binding 1.8021593476478 bayes_pls_golite062009
transcription factor activity 1.15127506309683 bayes_pls_golite062009
transcription activator activity 1.12833244388568 bayes_pls_golite062009
transcription repressor activity 0.998305828880243 bayes_pls_golite062009
mRNA 3'-UTR binding 0.824614388276642 bayes_pls_golite062009
mRNA 5'-UTR binding 0.625848256054783 bayes_pls_golite062009
translation repressor activity, nucleic acid binding 0.461000905454505 bayes_pls_golite062009
general RNA polymerase II transcription factor activity 0.425042944899091 bayes_pls_golite062009
hydrolase activity 0.389390547875764 bayes_pls_golite062009
sequence-specific DNA binding 0.383589644462932 bayes_pls_golite062009
translation regulator activity 0.38120065819101 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.128616879457381 bayes_pls_golite062009
snoRNA binding 0.0568636182001701 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [304-396] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LNHFTDPNNT TVFIGGLSSL VTEDELRAYF QPFGTIVYVK IPVGKCCGFV QYVDRLSAEA  60
   61 AIAGMQGFPI ANSRVRLSWG RSAKQTALLQ QAM

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 14.522879
Match: 1qm9A_
Description: Polypyrimidine tract-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [397-523] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LSNSLQVQQQ QPGLQQPNYG YIPSSTCEAP VLPDNNVSST MLPGCQILNY SNPYANANGL  60
   61 GSNNFSFYSN NNATNTQATS LLADTSSMDL SGTGGQQVIM QGSEAVVNST NAMLNRLEQG 120
  121 SNGFMFA

[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 0.400 0.268 commitment complex d.14.1 Ribosomal protein S5 domain 2-like
View Download 0.383 0.068 commitment complex a.40.1 Calponin-homology domain, CH-domain
View Download 0.465 0.027 commitment complex a.80.1 DNA polymerase III clamp loader subunits, C-terminal domain
View Download 0.424 N/A N/A d.224.1 SufE-like
View Download 0.359 N/A N/A a.19.1 Fertilization protein
View Download 0.345 N/A N/A c.2.1 NAD(P)-binding Rossmann-fold domains
View Download 0.306 N/A N/A a.1.1 Globin-like
View Download 0.289 N/A N/A c.53.1 Resolvase-like
View Download 0.289 N/A N/A a.24.16 Nucleotidyltransferase substrate binding subunit/domain
View Download 0.275 N/A N/A a.1.1 Globin-like
View Download 0.210 N/A N/A a.71.2 Helical domain of Sec23/24
View Download 0.204 N/A N/A a.3.1 Cytochrome c
View Download 0.204 N/A N/A a.2.3 Chaperone J-domain

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