YRC Public Data Repository - Protein Structure Prediction

Protein:	TIF3
Organism:	Saccharomyces cerevisiae
Length:	436 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 TIF3.

Description	E-value	Query Range	Subject Range
IF4B_YEAST - Eukaryotic translation initiation factor 4B OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c)... TIF3 - Translation initiation factor eIF-4B, has RNA annealing activity; contains an RNA recognition motif ... gi\|190408087 - gi\|190408087\|gb\|EDV11352.1\| eukaryotic translation initiation factor 4B [Saccharomyces cerevisiae RM...	3.0E-78	[1..436]	[1..436]
gi\|47086453, gi\|... - gi\|47086453\|ref\|NP_997961.1\| musashi homolog 2a [Danio rerio], gi\|28374420\|gb\|AAH45335.1\| Musashi ho...	3.0E-60	[1..358]	[1..369]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	5.0E-57	[1..353]	[1..352]
MSI2H_MOUSE - RNA-binding protein Musashi homolog 2 OS=Mus musculus GN=Msi2 PE=1 SV=1	2.0E-54	[1..358]	[1..327]
ENSPTRT00000017310 - null gi\|21752839, gi\|... - gi\|25121993\|ref\|NP_733839.1\| musashi 2 isoform b [Homo sapiens], gi\|21752839\|dbj\|BAC04244.1\| unnamed...	3.0E-51	[32..244]	[25..240]
gi\|32307763 - gi\|32307763\|gb\|AAP79278.1\| musashi nrp-1 [Saccoglossus kowalevskii]	3.0E-50	[1..356]	[1..371]

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Predicted Domain #1

Region A:
Residues: [1-92]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAPPKKTVKK MDLTSFLNDD TFGSSWAEED VDLNKITIPI ETANANTIPL SELAHAKNNS  60
   61 NNTRSGGFGG SFGGRSRLDP ALGGGSSDRR EE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	46.522879
Match:	2up1A_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	4.50438526063124	bayes_pls_golite062009
structural molecule activity	4.28696884073791	bayes_pls_golite062009
translation initiation factor activity	3.27900316559423	bayes_pls_golite062009
nucleic acid binding	3.2381342715237	bayes_pls_golite062009
mRNA binding	2.92795844574986	bayes_pls_golite062009
binding	2.62183511329394	bayes_pls_golite062009
	1.49431666307335	bayes_pls_golite062009
single-stranded RNA binding	0.90573796517364	bayes_pls_golite062009
RNA cap binding	0.65495719965273	bayes_pls_golite062009
protein binding	0.42571879933058	bayes_pls_golite062009
translation regulator activity	0.38120065819101	bayes_pls_golite062009
poly-pyrimidine tract binding	0.32812362201346	bayes_pls_golite062009
DNA binding	0.139020718026377	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.128616879457381	bayes_pls_golite062009
transcription regulator activity	0.0995666109361987	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [93-217]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YPVPDAPPYR AVINNIPWDI TPEGVQAWVE DGLVKPEAVE EVVLPKNLRD PTRLKGNAFV  60
   61 TLKERADLVA VLKFNGTKLN ERTVYVSVAA PRRGGGADVD WSSARGSNFQ GDGREDAPDL 120
  121 DWGAA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.045757
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	4.50438526063124	bayes_pls_golite062009
structural molecule activity	4.28696884073791	bayes_pls_golite062009
translation initiation factor activity	3.27900316559423	bayes_pls_golite062009
nucleic acid binding	3.2381342715237	bayes_pls_golite062009
mRNA binding	2.92795844574986	bayes_pls_golite062009
binding	2.62183511329394	bayes_pls_golite062009
	1.49431666307335	bayes_pls_golite062009
single-stranded RNA binding	0.90573796517364	bayes_pls_golite062009
RNA cap binding	0.65495719965273	bayes_pls_golite062009
protein binding	0.42571879933058	bayes_pls_golite062009
translation regulator activity	0.38120065819101	bayes_pls_golite062009
poly-pyrimidine tract binding	0.32812362201346	bayes_pls_golite062009
DNA binding	0.139020718026377	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.128616879457381	bayes_pls_golite062009
transcription regulator activity	0.0995666109361987	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [218-336]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RGSNFRGPRR EREEVDIDWT AARGSNFQGS SRPPRREREE VDIDWSAARG SNFQGSSRPP  60
   61 RREREEPDID WSAARGSNFQ SSSRPPRRER EEPDIDWSAA RGSNFQSSSR PPRREREKE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.045757
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [337-436]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPALDWGAAR GAQFGKPQQT KNTYKDRSLT NKKTTDEQPK IQKSVYDVLR TEDDDEDEEA  60
   61 EKQNGDAKEN KVDAAVEKLQ DKTAQLTVED GDNWEVVGKK

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.209	a.118.14	FliG

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: