YRC Public Data Repository - Protein Structure Prediction

Protein:	YTH1
Organism:	Saccharomyces cerevisiae
Length:	208 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 YTH1.

Description	E-value	Query Range	Subject Range
YTH1 - Essential RNA-binding component of cleavage and polyadenylation factor, contains five zinc fingers; ... YTH1_YEAST - mRNA 3'-end-processing protein YTH1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=YTH1...	3.0E-39	[1..208]	[1..208]
CPSF4 - cleavage and polyadenylation specific factor 4, 30kDa gi\|109065990 - gi\|109065990\|ref\|XP_001094527.1\| PREDICTED: cleavage and polyadenylation specific factor 4, 30kD sub...	7.0E-33	[1..173]	[1..172]
gi\|1575709, gi\|1... - gi\|28277462\|gb\|AAH45289.1\| No arches [Danio rerio], gi\|18859059\|ref\|NP_571084.1\| no arches [Danio re...	9.0E-33	[1..173]	[1..172]
CPSF4_BOVIN - Cleavage and polyadenylation specificity factor subunit 4 OS=Bos taurus GN=CPSF4 PE=1 SV=1	1.0E-32	[1..173]	[1..172]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	5.0E-32	[1..181]	[15..194]
YTH1_NEUCR - mRNA 3'-end-processing protein yth-1 OS=Neurospora crassa GN=yth-1 PE=3 SV=1 YTH1_NEUCR - mRNA 3'-end-processing protein yth-1 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708....	6.0E-31	[2..186]	[25..218]
gi\|5931741 - gi\|5931741\|emb\|CAB56623.1\| zinc finger protein [Rattus norvegicus]	8.0E-29	[6..189]	[5..190]

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Predicted Domain #1

Region A:
Residues: [1-120]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLIHPDTAK YPFKFEPFLR QEYSFSLDPD RPICEFYNSR EGPKSCPRGP LCPKKHVLPI  60
   61 FQNKIVCRHW LRGLCKKNDQ CEYLHEYNLR KMPECVFFSK NGYCTQSPDC QYLHIDPASK 120
  121

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.0
Match:	1m9oA_
Description:	Tristetraproline (ttp, tis11, nup475)
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [121-208]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IPKCENYEMG FCPLGSSCPR RHIKKVFCQR YMTGFCPLGK DECDMEHPQF IIPDEGSKLR  60
   61 IKRDDEINTR KMDEEKERRL NAIINGEV

[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	0.256	0.342	mRNA cleavage	a.3.1	Cytochrome c
View	Download	0.273	0.054	mRNA cleavage	a.74.1	Cyclin-like
View	Download	0.272	0.016	mRNA cleavage	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.368	0.015	mRNA cleavage	d.64.1	eIF1-like
View	Download	0.316	N/A	N/A	i.1.1	Ribosome and ribosomal fragments
View	Download	0.252	N/A	N/A	d.198.1	Type III secretory system chaperone
View	Download	0.251	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.236	N/A	N/A	a.4.1	Homeodomain-like
View	Download	0.211	N/A	N/A	a.71.1	Endoplasmic reticulum protein ERP29, C-domain

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