YRC Public Data Repository - Protein Structure Prediction

Protein:	snRNP-U1-PA
Organism:	Drosophila melanogaster
Length:	145 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 snRNP-U1-PA.

Description	E-value	Query Range	Subject Range
gi\|67971420 - gi\|67971420\|dbj\|BAE02052.1\| unnamed protein product [Macaca fascicularis]	140.0	[0..1]	[62..1]
usp103 - U1 snRNP-associated protein Usp103 RU1C_SCHPO - U1 small nuclear ribonucleoprotein C OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=usp10...	139.0	[0..1]	[118..1]
gi\|125775241, gi... - gi\|54638613\|gb\|EAL28015.1\| GA18892 [Drosophila pseudoobscura pseudoobscura], gi\|125775241\|ref\|XP_001... gi\|194102311, gi... - gi\|195144768\|ref\|XP_002013368.1\| GL24104 [Drosophila persimilis], gi\|194102311\|gb\|EDW24354.1\| GL2410... RU1C_DROPS - U1 small nuclear ribonucleoprotein C OS=Drosophila pseudoobscura pseudoobscura GN=snRNP-U1-C PE=3 SV...	136.0	[0..1]	[145..1]
gi\|55670396 - gi\|55670396\|pdb\|1UW2\|A Chain A, The Structure Of The Zinc Finger From The Human Spliceosomal Protein...	135.0	[0..2]	[61..2]
gi\|48128367, gi\|... - ref\|XP_396626.1\| similar to CG5454-PA [Apis mellifera], gi\|110758091\|ref\|XP_001120253.1\| PREDICTED: ...	134.0	[0..1]	[72..1]
gi\|109070829 - gi\|109070829\|ref\|XP_001111611.1\| PREDICTED: similar to U1 small nuclear ribonucleoprotein C (U1 snRN...	133.0	[0..1]	[62..166]
gi\|109458031 - gi\|109458031\|ref\|XP_001076224.1\| PREDICTED: similar to Protein CXorf17 homolog [Rattus norvegicus]	129.0	[0..1]	[98..1]
gi\|73972600 - gi\|73972600\|ref\|XP_532115.2\| PREDICTED: similar to U1 small nuclear ribonucleoprotein C (U1 snRNP pr...	129.0	[0..1]	[62..90]
gi\|94397362, gi\|... - gi\|94398338\|ref\|XP_983686.1\| PREDICTED: similar to U1 small nuclear ribonucleoprotein C (U1 snRNP pr...	129.0	[0..1]	[62..1]

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Predicted Domain #1

Region A:
Residues: [1-63]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPKYYCDYCD TYLTHDSPSV RKTHCTGRKH RDNVKFYYQK WMEEQAQHLI DATTAAFKAG  60
   61 KIT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	33.30103
Match:	1uw2A
Description:	The structure of the zinc finger from the human spliceosomal protein U1C
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	4.58713908116892	bayes_pls_golite062009
transcription regulator activity	4.45227978528489	bayes_pls_golite062009
DNA binding	4.38016685175719	bayes_pls_golite062009
U1 snRNA binding	4.35911393951689	bayes_pls_golite062009
transcription factor activity	3.58239047728759	bayes_pls_golite062009
snRNA binding	3.38579636849163	bayes_pls_golite062009
RNA binding	3.1651307444578	bayes_pls_golite062009
binding	3.10743787485868	bayes_pls_golite062009
transcription activator activity	2.11897933474228	bayes_pls_golite062009
RNA polymerase II transcription factor activity	2.09399411278791	bayes_pls_golite062009
transcription repressor activity	1.60897793068008	bayes_pls_golite062009
chromatin binding	1.5138157530393	bayes_pls_golite062009
sequence-specific DNA binding	1.42975942698743	bayes_pls_golite062009
transcription factor binding	1.3759942192372	bayes_pls_golite062009
mRNA binding	1.30742677372942	bayes_pls_golite062009
protein binding	1.00484935878505	bayes_pls_golite062009
specific RNA polymerase II transcription factor activity	0.93573592336522	bayes_pls_golite062009
transcription cofactor activity	0.71612810774743	bayes_pls_golite062009
cytoskeletal protein binding	0.379360577438236	bayes_pls_golite062009
catalytic activity	0.245893663605433	bayes_pls_golite062009
structure-specific DNA binding	0.240825841910931	bayes_pls_golite062009
tubulin binding	0.194527341243124	bayes_pls_golite062009
microtubule binding	0.102991534426747	bayes_pls_golite062009
double-stranded DNA binding	0.0129353639725593	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [64-145]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NNPFAGGPGG APPKPAGVSI PPPNMGAPPR PGMPGMPYMP PLMNPMMGMR PPPIMNPMAM  60
   61 MGPPPPLGTI PGVRPGIMNG PK

[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.

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: