YRC Public Data Repository - Protein Structure Prediction

Protein:	SMD3
Organism:	Saccharomyces cerevisiae
Length:	101 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 SMD3.

Description	E-value	Query Range	Subject Range
gi\|34902916, gi\|... - gi\|6016876\|dbj\|BAA85219.1\| unnamed protein product [Oryza sativa (japonica cultivar-group)], gi\|3490...	3.0E-23	[6..90]	[2..87]
LSM4_MOUSE - U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=1 SV=1	1.0E-22	[6..93]	[2..90]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	2.0E-22	[6..100]	[2..98]
gi\|13161882 - gi\|13161882\|emb\|CAC33027.1\| Lsm4 protein [Takifugu rubripes]	2.0E-22	[6..101]	[2..95]
SMD3A_ARATH - Small nuclear ribonucleoprotein SmD3a OS=Arabidopsis thaliana GN=SMD3A PE=2 SV=1	1.0E-21	[1..100]	[1..101]
SMD3_YEAST - Small nuclear ribonucleoprotein Sm D3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SM... gi\|151941309 - gi\|151941309\|gb\|EDN59687.1\| Sm D3 [Saccharomyces cerevisiae YJM789] SMD3 - Core Sm protein Sm D3; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Sme1p, Smx3p, and... gi\|190406176 - gi\|190406176\|gb\|EDV09443.1\| small nuclear ribonucleoprotein Sm D3 [Saccharomyces cerevisiae RM11-1a]	1.0E-21	[1..101]	[1..101]
ENSCJAT00000018661 - null SNRPD3 - small nuclear ribonucleoprotein D3 polypeptide 18kDa SMD3_XENLA - Small nuclear ribonucleoprotein Sm D3 OS=Xenopus laevis GN=snrpd3 PE=2 SV=1 gi\|50756613, gi\|... - gi\|56119060\|ref\|NP_001007839.1\| small nuclear ribonucleoprotein D3 polypeptide 18kDa [Gallus gallus]... gi\|55659962 - gi\|55659962\|ref\|XP_515037.1\| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide D3; s... gi\|149720126 - gi\|149720126\|ref\|XP_001489110.1\| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide D... gi\|149632566 - gi\|149632566\|ref\|XP_001509901.1\| PREDICTED: similar to Sm D3 [Ornithorhynchus anatinus] gi\|89266931, gi\|... - gi\|89266931\|emb\|CAJ81806.1\| small nuclear ribonucleoprotein D3 polypeptide 18kDa [Xenopus tropicalis... gi\|90085617 - gi\|90085617\|dbj\|BAE91549.1\| unnamed protein product [Macaca fascicularis] SMD3_MOUSE - Small nuclear ribonucleoprotein Sm D3 OS=Mus musculus GN=Snrpd3 PE=1 SV=1 gi\|73995845 - gi\|73995845\|ref\|XP_849660.1\| PREDICTED: similar to small nuclear ribonucleoprotein D3 [Canis familia... gi\|126344584 - gi\|126344584\|ref\|XP_001362481.1\| PREDICTED: similar to Sm D3 [Monodelphis domestica] CCDS13828.1_1 - null gi\|542170044\|ref... - PREDICTED: small nuclear ribonucleoprotein Sm D3 [Zonotrichia albicollis] gi\|149043764, gi... - gi\|149043764\|gb\|EDL97215.1\| rCG60635, isoform CRA_b [Rattus norvegicus], gi\|109509970\|ref\|XP_0010798... HGNC:11160\|MIM:6... - nuclear ribonucleoprotein D3 polypeptide 18kDa tr\|G1SMM7\|G1SMM7... - pep:novel scaffold:oryCun2:GL018810:639704:651617:1 gene:ENSOCUG00000004845 transcript:ENSOCUT000000... gi\|197129341, gi... - gi\|224072091\|ref\|XP_002199918.1\| PREDICTED: putative small nuclear ribonucleoprotein D3 polypeptide ... gi\|194043334, gi... - gi\|194043336\|ref\|XP_001929282.1\| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide D... tr\|F1MZ00\|F1MZ00... - Uncharacterized protein OS=Bos taurus GN=SNRPD3 PE=4 SV=2 gi\|109451504, gi... - gi\|208965532\|dbj\|BAG72780.1\| small nuclear ribonucleoprotein D3 polypeptide [synthetic construct], g... gi\|109093572, gi... - gi\|109093574\|ref\|XP_001096291.1\| PREDICTED: similar to small nuclear ribonucleoprotein D3 isoform 2 ...	5.0E-21	[1..100]	[1..99]

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Predicted Domain #1

Region A:
Residues: [1-101]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT EPQGAVTHMD  60
   61 QIFVRGSQIK FIVVPDLLKN APLFKKNSSR PMPPIRGPKR R

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	203.035458
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

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: