YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|208967436
Organism:	synthetic construct
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 gi|208967436.

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 is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident 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: