YRC Public Data Repository - Protein Structure Prediction

Protein:	SMD1
Organism:	Saccharomyces cerevisiae
Length:	146 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 SMD1.

Description	E-value	Query Range	Subject Range
gi\|151943351 - gi\|151943351\|gb\|EDN61664.1\| Sm D1 [Saccharomyces cerevisiae YJM789] SMD1_YEAST - Small nuclear ribonucleoprotein Sm D1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SM... SMD1 - Core Sm protein Sm D1; part of heteroheptameric complex (with Smb1p, Smd2p, Smd3p, Sme1p, Smx3p, and... gi\|190406906 - gi\|190406906\|gb\|EDV10173.1\| small nuclear ribonucleoprotein Sm D1 [Saccharomyces cerevisiae RM11-1a]	2.0E-42	[1..146]	[1..146]
gi\|8778615 - gi\|8778615\|gb\|AAF79623.1\|AC027665_24 F5M15.9 [Arabidopsis thaliana]	2.0E-34	[3..133]	[8..143]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	2.0E-28	[1..132]	[1..100]
gi\|34902916, gi\|... - gi\|6016876\|dbj\|BAA85219.1\| unnamed protein product [Oryza sativa (japonica cultivar-group)], gi\|3490...	4.0E-28	[1..116]	[1..88]
LSM4_MOUSE - U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=1 SV=1	9.0E-28	[1..124]	[1..96]
gi\|13161882 - gi\|13161882\|emb\|CAC33027.1\| Lsm4 protein [Takifugu rubripes]	3.0E-27	[1..124]	[1..96]
tr\|M3W8L3\|M3W8L3... - LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated OS=Felis catus GN=LSM4 PE=4 SV=1 LSM4 - LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) gi\|208966682, gi... - gi\|208966682\|dbj\|BAG73355.1\| LSM4 homolog, U6 small nuclear RNA associated [synthetic construct], gi... gi\|73986139, gi\|... - gi\|73986139\|ref\|XP_852362.1\| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm4 (Glycine... LSM4_BOVIN - U6 snRNA-associated Sm-like protein LSm4 OS=Bos taurus GN=LSM4 PE=2 SV=1	2.0E-26	[1..116]	[1..88]

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Predicted Domain #1

Region A:
Residues: [1-146]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP RLNKLNSNGI  60
   61 AMASLYLTGG QQPTASDNIA SLQYINIRGN TIRQIILPDS LNLDSLLVDQ KQLNSLRRSG 120
  121 QIANDPSKKR RRDFGAPANK RPRRGL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	144.025158
Match:	1b34A_
Description:	D1 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: