YRC Public Data Repository - Protein Structure Prediction

Protein:	smd1
Organism:	Schizosaccharomyces pombe
Length:	117 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 smd1.

Description	E-value	Query Range	Subject Range
gi\|71018117, gi\|... - gi\|71018117\|ref\|XP_759289.1\| hypothetical protein UM03142.1 [Ustilago maydis 521], ref\|XP_400757.1\| ...	113.0	[0..1]	[102..68]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	112.0	[0..1]	[112..1]
gi\|50732862 - gi\|50732862\|ref\|XP_418799.1\| PREDICTED: similar to KIAA0851 protein [Gallus gallus]	112.0	[0..5]	[96..652]
gi\|42546775, gi\|... - gi\|46105460\|ref\|XP_380534.1\| hypothetical protein FG00358.1 [Gibberella zeae PH-1], gi\|42546775\|gb\|E...	112.0	[0..1]	[96..1]
gi\|88181855, gi\|... - gi\|88181855\|gb\|EAQ89323.1\| hypothetical protein CHGG_05942 [Chaetomium globosum CBS 148.51], gi\|1161...	110.0	[0..1]	[96..1]
gi\|49250837, gi\|... - gi\|52345462\|ref\|NP_001004780.1\| small nuclear ribonucleoprotein D1 polypeptide 16kDa [Xenopus (Silur... gi\|148227202, gi... - gi\|76779906\|gb\|AAI06262.1\| MGC78968 protein [Xenopus laevis], gi\|49255946\|gb\|AAH71069.1\| MGC78968 pr...	110.0	[0..1]	[96..1]
gi\|113564620, gi... - gi\|115458898\|ref\|NP_001053049.1\| Os04g0470200 [Oryza sativa (japonica cultivar-group)], gi\|113564620...	110.0	[0..1]	[95..1]
gi\|60832252 - gi\|60832252\|gb\|AAX37003.1\| small nuclear ribonucleoprotein D1 polypeptide [synthetic construct]	109.0	[0..1]	[96..1]
CCDS32801.1_1 - null ENSCJAT00000040295 - null gi\|208967432 - gi\|208967432\|dbj\|BAG73730.1\| small nuclear ribonucleoprotein D1 polypeptide [synthetic construct] gi\|109121754 - gi\|109121754\|ref\|XP_001091972.1\| PREDICTED: similar to Small nuclear ribonucleoprotein Sm D1 (snRNP ... gi\|197127450, gi... - gi\|197129948\|gb\|ACH46446.1\| putative small nuclear ribonucleoprotein D1 [Taeniopygia guttata], gi\|19... gi\|126321779 - gi\|126321779\|ref\|XP_001363297.1\| PREDICTED: similar to small nuclear riboprotein Sm-D [Monodelphis d... gi\|114672526 - gi\|114672526\|ref\|XP_512054.2\| PREDICTED: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Pan t... SMD1_MACFA - Small nuclear ribonucleoprotein Sm D1 OS=Macaca fascicularis GN=SNRPD1 PE=3 SV=1 gi\|57089749 - gi\|57089749\|ref\|XP_537302.1\| PREDICTED: similar to Small nuclear ribonucleoprotein Sm D1 (snRNP core... SNRPD1 - small nuclear ribonucleoprotein D1 polypeptide 16kDa SMD1_MOUSE - Small nuclear ribonucleoprotein Sm D1 OS=Mus musculus GN=Snrpd1 PE=1 SV=1 tr\|G3HGH4\|G3HGH4... - Small nuclear ribonucleoprotein Sm D1 OS=Cricetulus griseus GN=I79_009701 PE=4 SV=1 gi\|542154109\|ref... - PREDICTED: small nuclear ribonucleoprotein Sm D1-like [Zonotrichia albicollis] gi\|149031722, gi... - gi\|34877889\|ref\|XP_214621.2\| PREDICTED: similar to Small nuclear ribonucleoprotein Sm D1 (snRNP core... SMD1_BOVIN - Small nuclear ribonucleoprotein Sm D1 OS=Bos taurus GN=SNRPD1 PE=3 SV=1	108.0	[0..1]	[96..1]
gi\|114192048, gi... - gi\|115399152\|ref\|XP_001215165.1\| small nuclear ribonucleoprotein Sm D1 [Aspergillus terreus NIH2624]...	108.0	[0..1]	[96..1]

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Predicted Domain #1

Region A:
Residues: [1-117]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKLVRFLMKL TNETVSIELK NGTIVHGTIT SVDMQMNTHL KAVKMTVKGR EPVPVETLSI  60
   61 RGNNIRYYIL PDSLPLDTLL IDDSTKPKQK KKEVVRGRGR GRGRGTRGRG RGASRGF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	24.522879
Match:	1b34A
Description:	D1 core SNRNP protein
Matching Structure (courtesy of the PDB):

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