YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|220951570
Organism:	synthetic construct
Length:	95 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 gi|220951570.

Description	E-value	Query Range	Subject Range
gi\|114606503 - gi\|114606503\|ref\|XP_518362.2\| PREDICTED: similar to snRNP core Sm protein homolog Sm-X5 [Pan troglod...	123.0	[0..1]	[95..82]
gi\|11138539 - gi\|11138539\|gb\|AAG31434.1\|AF204157_1 snRNP core protein SMX5d [Mus musculus]	120.0	[0..2]	[95..26]
gi\|110760170 - gi\|110760170\|ref\|XP_001120188.1\| PREDICTED: similar to CG10418-PA [Apis mellifera]	117.0	[0..1]	[95..1]
gi\|125818555, gi... - gi\|61097894\|ref\|NP_571571.1\| smx5 [Danio rerio], gi\|55715812\|gb\|AAH85441.1\| Smx5 [Danio rerio], gi\|1...	117.0	[0..1]	[95..1]
gi\|109509738, gi... - gi\|149028025\|gb\|EDL83476.1\| rCG38360, isoform CRA_b [Rattus norvegicus], gi\|109509738\|ref\|XP_0010608... LSM2 - LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) gi\|178056596, gi... - gi\|178056596\|ref\|NP_001116608.1\| LSM2 homolog, U6 small nuclear RNA associated [Sus scrofa], gi\|1472... gi\|109070461 - gi\|109070461\|ref\|XP_001105870.1\| PREDICTED: LSM2 homolog, U6 small nuclear RNA associated (S. cerevi... CCDS4722.1_1 - null ENSCJAT00000004970 - null ENSPTRT00000033228 - null tr\|G1SHV1\|G1SHV1... - pep:novel chromosome:oryCun2:12:20606176:20612202:-1 gene:ENSOCUG00000002583 transcript:ENSOCUT00000... LSM2_MOUSE - U6 snRNA-associated Sm-like protein LSm2 OS=Mus musculus GN=Lsm2 PE=1 SV=1 gi\|226443174, gi... - gi\|226443174\|ref\|NP_001140070.1\| U6 snRNA-associated Sm-like protein LSm2 [Salmo salar], gi\|22122167... gi\|151557081, gi... - gi\|76650929\|ref\|XP_581859.2\| PREDICTED: similar to snRNP core Sm protein homolog Sm-X5 [Bos taurus],... gi\|73972304 - gi\|73972304\|ref\|XP_532081.2\| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm2 (SnRNP c... gi\|124000059, gi... - gi\|208968015\|dbj\|BAG73846.1\| U6 snRNA-associated Sm-like protein LSm2 [synthetic construct], gi\|1240...	117.0	[0..1]	[95..1]
gi\|92899039 - gi\|92899039\|gb\|ABE94505.1\| Like-Sm ribonucleoprotein, eukaryotic and archaea-type, core [Medicago tr...	117.0	[0..1]	[94..1]
gi\|109509736, gi... - gi\|46237602\|emb\|CAE83980.1\| LSM2 homolog, U6 small nuclear RNA associated [S. cerevisiae] [Rattus no...	116.0	[0..2]	[95..38]
gi\|90306422, gi\|... - gi\|90306422\|gb\|EAS36053.1\| hypothetical protein CIMG_01407 [Coccidioides immitis RS], gi\|119194065\|r...	116.0	[0..1]	[93..81]
gi\|194118277, gi... - gi\|195160603\|ref\|XP_002021164.1\| GL25187 [Drosophila persimilis], gi\|194118277\|gb\|EDW40320.1\| GL2518... gi\|54642144, gi\|... - gi\|54642144\|gb\|EAL30893.1\| GA10305 [Drosophila pseudoobscura pseudoobscura], gi\|125978707\|ref\|XP_001... gi\|54642144\|gb\|E... - GA10305-PA [Drosophila pseudoobscura], GA10305 [Drosophila pseudoobscura pseudoobscura]	115.0	[0..1]	[95..1]

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Predicted Domain #1

Region A:
Residues: [1-95]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLFYSFFKSL VGKEVVVELK NDLSICGTLH SVDQYLNIKL TDISVTDPDK YPHMLSVKNC  60
   61 FIRGSVVRYV QLPGDEVDTQ LLQDAARKEA VVSTR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	20.69897
Match:	1b34A
Description:	D1 core SNRNP protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
	9.36615441177233	bayes_pls_golite062009
RNA binding	5.81718051012035	bayes_pls_golite062009
nucleic acid binding	3.79237851568526	bayes_pls_golite062009
binding	2.63965180938967	bayes_pls_golite062009
mRNA binding	2.57166143288861	bayes_pls_golite062009
protein binding	0.418315253537627	bayes_pls_golite062009

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: