YRC Public Data Repository - Protein Structure Prediction

Protein:	SNRPA
Organism:	Homo sapiens
Length:	282 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 SNRPA.

Description	E-value	Query Range	Subject Range
gi\|187607541, gi... - gi\|187607541\|ref\|NP_001119825.1\| small nuclear ribonucleoprotein polypeptide A [Ovis aries], gi\|1841... SNRPA_BOVIN - U1 small nuclear ribonucleoprotein A OS=Bos taurus GN=SNRPA PE=2 SV=1	1.0E-41	[1..282]	[1..282]
gi\|109124828 - gi\|109124828\|ref\|XP_001098504.1\| PREDICTED: small nuclear ribonucleoprotein polypeptide A isoform 7 ... gi\|114677331 - gi\|114677331\|ref\|XP_512674.2\| PREDICTED: hypothetical protein [Pan troglodytes]	1.0E-41	[1..282]	[1..282]
gi\|149722301 - gi\|149722301\|ref\|XP_001499386.1\| PREDICTED: similar to U1 small nuclear ribonucleoprotein A (U1 snRN... gi\|73948310 - gi\|73948310\|ref\|XP_533663.2\| PREDICTED: similar to U1 small nuclear ribonucleoprotein A (U1 snRNP pr...	1.0E-41	[1..282]	[1..282]
SNRPA_PIG - U1 small nuclear ribonucleoprotein A OS=Sus scrofa GN=SNRPA PE=1 SV=1	1.0E-41	[1..282]	[1..282]
gi\|38641409, gi\|... - gi\|38641409\|gb\|AAR26269.1\| nuclear ribonucleoprotein A [Oryctolagus cuniculus], gi\|126723082\|ref\|NP_...	2.0E-41	[1..282]	[1..282]
gi\|62857647, gi\|... - gi\|89273875\|emb\|CAJ82017.1\| small nuclear ribonucleoprotein polypeptide A [Xenopus tropicalis], gi\|6...	1.0E-40	[1..282]	[1..282]
gi\|34855379, gi\|... - gi\|56605690\|ref\|NP_001008304.1\| small nuclear ribonucleoprotein polypeptide A [Rattus norvegicus], g...	2.0E-40	[1..282]	[1..281]
gi\|12851426, gi\|... - gi\|31980689\|ref\|NP_056597.2\| small nuclear ribonucleoprotein polypeptide A [Mus musculus], gi\|128514...	1.0E-39	[1..282]	[7..287]

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Predicted Domain #1

Region A:
Residues: [1-104]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAVPETRPNH TIYINNLNEK IKKDELKKSL YAIFSQFGQI LDILVSRSLK MRGQAFVIFK  60
   61 EVSSATNALR SMQGFPFYDK PMRIQYAKTD SDIIAKMKGT FVER

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	19.39794
Match:	1fhtA
Description:	RNA-BINDING DOMAIN OF THE U1A SPLICEOSOMAL PROTEIN U1A117, NMR, 43 STRUCTURES
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	3.81920018903278	bayes_pls_golite062009
snRNA binding	3.28448936696877	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
binding	3.05116833253954	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
U1 snRNA binding	2.26303528058407	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
transcription regulator activity	1.07788694919471	bayes_pls_golite062009
DNA binding	0.978604858165557	bayes_pls_golite062009
mRNA 3'-UTR binding	0.591700155096213	bayes_pls_golite062009
protein binding	0.42571879933058	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [105-192]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DRKREKRKPK SQETPATKKA VQGGGATPVV GAVQGPVPGM PPMTQAPRIM HHMPGQPPYM  60
   61 PPPGMIPPPG LAPGQIPPGA MPPQQLMP

[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.

Found no structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [193-282]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GQMPPAQPLS ENPPNHILFL TNLPEETNEL MLSMLFNQFP GFKEVRLVPG RHDIAFVEFD  60
   61 NEVQAGAARD ALQGFKITQN NAMKISFAKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.522879
Match:	2u1aA
Description:	RNA BINDING DOMAIN 2 OF HUMAN U1A PROTEIN, NMR, 20 STRUCTURES
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	3.81920018903278	bayes_pls_golite062009
snRNA binding	3.28448936696877	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
binding	3.05116833253954	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
U1 snRNA binding	2.26303528058407	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
transcription regulator activity	1.07788694919471	bayes_pls_golite062009
DNA binding	0.978604858165557	bayes_pls_golite062009
mRNA 3'-UTR binding	0.591700155096213	bayes_pls_golite062009
protein binding	0.42571879933058	bayes_pls_golite062009
transcription factor activity	0.234742017105535	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:

Predicted functions: