YRC Public Data Repository - Protein Structure Prediction

Protein:	SMD3_XENLA
Organism:	Xenopus laevis
Length:	126 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 SMD3_XENLA.

Description	E-value	Query Range	Subject Range
gi\|66362186 - gi\|66362186\|ref\|XP_628057.1\| small nucealr riboprotein SMD3, SM domain [Cryptosporidium parvum Iowa ... gi\|46227630 - gi\|46227630\|gb\|EAK88565.1\| small nucealr riboprotein SMD3, SM domain [Cryptosporidium parvum Iowa II...	9.0E-27	[1..120]	[23..140]
gi\|148227688, gi... - gi\|27371312\|gb\|AAH40973.1\| MGC52856 protein [Xenopus laevis], gi\|148227688\|ref\|NP_001079359.1\| hypot...	1.0E-26	[1..126]	[1..126]
gi\|74007795 - gi\|74007795\|ref\|XP_534749.2\| PREDICTED: similar to small nuclear ribonucleoprotein D3 [Canis familia...	2.0E-26	[1..126]	[1..126]
gi\|15079335 - gi\|15079335\|gb\|AAH11510.1\| Small nuclear ribonucleoprotein D3 [Mus musculus]	7.0E-26	[1..126]	[1..126]
gi\|54657392 - gi\|54657392\|gb\|EAL36172.1\| aspartyl protease-like [Cryptosporidium hominis] gi\|67601489 - gi\|67601489\|ref\|XP_666403.1\| aspartyl protease-like [Cryptosporidium hominis TU502]	1.0E-25	[1..120]	[1..118]
gi\|86437979, gi\|... - gi\|86437979\|gb\|AAI12525.1\| Small nuclear ribonucleoprotein D3 polypeptide 18kDa [Bos taurus], gi\|115...	2.0E-25	[1..126]	[1..125]
gi\|54635267, gi\|... - gi\|54635267\|gb\|EAL24670.1\| GA21375-PA [Drosophila pseudoobscura], gi\|125806629\|ref\|XP_001360096.1\| G...	2.0E-25	[1..108]	[1..108]
gi\|47211785 - gi\|47211785\|emb\|CAF93753.1\| unnamed protein product [Tetraodon nigroviridis]	2.0E-25	[1..126]	[1..127]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	6.0E-24	[5..119]	[2..118]
gi\|92899281 - gi\|92899281\|gb\|ABE94617.1\| Like-Sm ribonucleoprotein-related, core [Medicago truncatula]	1.0E-23	[2..119]	[4..127]

Back

Predicted Domain #1

Region A:
Residues: [1-126]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ  60
   61 VYIRGSKIRF LILPDMLKNA PMLKSMKNKN QGSGAGRGKA AILKAQVAAR GRGRGMGRGN 120
  121 IFQKRR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	18.154902
Match:	1d3bA
Description:	D3 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	2.04681172391952	bayes_pls_golite062009
protein binding	0.187097443004706	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: