YRC Public Data Repository - Protein Structure Prediction

Protein:	snr-4
Organism:	Caenorhabditis elegans
Length:	118 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 snr-4.

Description	E-value	Query Range	Subject Range
gi\|66500455 - gi\|66500455\|ref\|XP_397475.2\| PREDICTED: similar to CG1249-PA isoform 1 [Apis mellifera]	133.0	[0..1]	[117..1]
gi\|115928632, gi... - gi\|115928632\|ref\|XP_001177104.1\| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus], gi...	130.0	[0..1]	[117..1]
gi\|157762608 - gi\|157762608\|ref\|XP_001673646.1\| Hypothetical protein CBG23345 [Caenorhabditis briggsae AF16] gi\|39592141, gi\|... - gi\|39592141\|emb\|CAE75361.1\| Hypothetical protein CBG23345 [Caenorhabditis briggsae], gi\|187021090\|em...	124.0	[0..1]	[118..1]
gi\|82889713 - gi\|82889713\|ref\|XP_910243.1\| PREDICTED: similar to Sm D2 [Mus musculus]	124.0	[0..1]	[116..1]
gi\|60834798 - gi\|60834798\|gb\|AAX37111.1\| small nuclear ribonucleoprotein D2 polypeptide [synthetic construct]	123.0	[0..1]	[116..1]
SMD2_MOUSE - Small nuclear ribonucleoprotein Sm D2 OS=Mus musculus GN=Snrpd2 PE=1 SV=1 tr\|G1TI40\|G1TI40... - Uncharacterized protein OS=Oryctolagus cuniculus GN=SNRPD2 PE=4 SV=2 tr\|M3X0Z8\|M3X0Z8... - Uncharacterized protein OS=Felis catus GN=SNRPD2 PE=4 SV=1 SNRPD2 - small nuclear ribonucleoprotein D2 polypeptide 16.5kDa gi\|114677908, gi... - gi\|55649427\|ref\|XP_512755.1\| PREDICTED: small nuclear ribonucleoprotein polypeptide D2 isoform 5 [Pa... gi\|123980686, gi... - gi\|208967434\|dbj\|BAG73731.1\| small nuclear ribonucleoprotein D2 polypeptide [synthetic construct], g... gi\|157820925, gi... - gi\|27676406\|ref\|XP_214847.1\| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide D2 [R... gi\|109125202, gi... - gi\|109125204\|ref\|XP_001111101.1\| PREDICTED: similar to small nuclear ribonucleoprotein D2 isoform 2 ... gi\|149722210 - gi\|149722210\|ref\|XP_001502799.1\| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide D... SMD2_BOVIN - Small nuclear ribonucleoprotein Sm D2 OS=Bos taurus GN=SNRPD2 PE=3 SV=1	122.0	[0..1]	[116..1]
gi\|94733476, gi\|... - gi\|94733476\|emb\|CAK04394.1\| novel protein [Danio rerio], gi\|68439655\|ref\|XP_699983.1\| PREDICTED: sim... gi\|225706716 - gi\|225706716\|gb\|ACO09204.1\| Small nuclear ribonucleoprotein Sm D2 [Osmerus mordax]	122.0	[0..1]	[116..1]
gi\|89272067, gi\|... - gi\|89272067\|emb\|CAJ81304.1\| small nuclear ribonucleoprotein D2 polypeptide 16.5kDa [Xenopus tropical...	121.0	[0..1]	[116..1]
gi\|62717927, gi\|... - gi\|62717927\|ref\|XP_576676.1\| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide D2 [R...	121.0	[0..1]	[116..1]

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Predicted Domain #1

Region A:
Residues: [1-118]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSAQAKPRSE MTAEELAAKE DEEFNVGPLS ILTNSVKNNH QVLINCRNNK KLLGRVKAFD  60
   61 RHCNMVLENV KEMWTEVPKT GKGKKKAKSV AKDRFISKMF LRGDSVILVV KNPLAQAE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.69897
Match:	1b34B
Description:	D2 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	2.69031444148163	bayes_pls_golite062009
mRNA binding	2.57166143288861	bayes_pls_golite062009
binding	2.44117021254507	bayes_pls_golite062009
protein binding	0.318488892917007	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: