YRC Public Data Repository - Protein Structure Prediction

Protein:	SMD2
Organism:	Saccharomyces cerevisiae
Length:	110 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 SMD2.

Description	E-value	Query Range	Subject Range
snr-4 - small nuclear ribonucleoprotein D2 like status:Confirmed UniProt:Q18786 protein_id:CAB01413.1	3.0E-23	[1..109]	[1..114]
smd2 - Sm snRNP core protein Smd2 SMD2_SCHPO - Small nuclear ribonucleoprotein Sm D2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd2...	4.0E-23	[3..108]	[2..113]
gi\|190405334 - gi\|190405334\|gb\|EDV08601.1\| small nuclear ribonucleoprotein Sm D2 [Saccharomyces cerevisiae RM11-1a] gi\|151940982 - gi\|151940982\|gb\|EDN59363.1\| Sm D2 [Saccharomyces cerevisiae YJM789] SMD2_YEAST - Small nuclear ribonucleoprotein Sm D2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SM... SMD2 - Core Sm protein Sm D2; part of heteroheptameric complex (with Smb1p, Smd1p, Smd3p, Sme1p, Smx3p, and...	3.0E-21	[1..110]	[1..110]
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	2.0E-20	[5..109]	[3..114]
gi\|20197310, gi\|... - gi\|20197310\|gb\|AAC63620.2\| putative small nuclear ribonucleoprotein D2 [Arabidopsis thaliana], gi\|20...	2.0E-20	[6..109]	[1..109]
gi\|85101285 - gi\|85101285\|ref\|XP_961124.1\| hypothetical protein [Neurospora crassa OR74A] gi\|28922663, gi\|... - gi\|32404932\|ref\|XP_323079.1\| hypothetical protein [Neurospora crassa], gi\|28922663\|gb\|EAA31888.1\| hy...	3.0E-20	[4..96]	[10..108]

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Predicted Domain #1

Region A:
Residues: [1-110]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSQIIDRPK HELSRAELEE LEEFEFKHGP MSLINDAMVT RTPVIISLRN NHKIIARVKA  60
   61 FDRHCNMVLE NVKELWTEKK GKNVINRERF ISKLFLRGDS VIVVLKTPVE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	246.450636
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: