YRC Public Data Repository - Protein Structure Prediction

Protein:	SMB1
Organism:	Saccharomyces cerevisiae
Length:	196 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 SMB1.

Description	E-value	Query Range	Subject Range
gi\|190247 - gi\|190247\|gb\|AAA60151.1\| snRNP polypeptide B [Homo sapiens]	134.0	[0..4]	[111..1]
gi\|114656016 - gi\|114656016\|ref\|XP_523182.2\| PREDICTED: hypothetical protein [Pan troglodytes]	133.0	[0..4]	[111..38]
RSMB_MACEU - Small nuclear ribonucleoprotein-associated protein B' OS=Macropus eugenii GN=SNRPB PE=2 SV=1	132.0	[0..4]	[116..1]
gi\|86438323 - gi\|86438323\|gb\|AAI12635.1\| SNRPB protein [Bos taurus]	131.0	[0..4]	[111..1]
gi\|112305, gi\|206694 - gi\|206694\|gb\|AAA42059.1\| snRNP-associated polypeptide N, pir\|\|A35448 small nuclear ribonucleoprotein...	131.0	[0..4]	[116..1]
gi\|57045593, gi\|... - gi\|73950980\|ref\|XP_848476.1\| PREDICTED: similar to small nuclear ribonucleoparticle-associated prote... gi\|149691049 - gi\|149691049\|ref\|XP_001492752.1\| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide N...	131.0	[0..4]	[111..1]
gi\|114680545 - gi\|114680545\|ref\|XP_001155793.1\| PREDICTED: hypothetical protein LOC470014 isoform 1 [Pan troglodyte... gi\|119631003, gi... - gi\|45708426\|gb\|AAH03530.1\| SNRPB protein [Homo sapiens], gi\|194375339\|dbj\|BAG62782.1\| unnamed protei... gi\|109092660 - gi\|109092660\|ref\|XP_001113926.1\| PREDICTED: small nuclear ribonucleoprotein polypeptides B and B1 is...	130.0	[0..4]	[111..1]
gi\|3142634 - gi\|3142634\|gb\|AAC78612.1\| small nuclear ribonucleoprotein N [Mus musculus]	130.0	[0..4]	[111..1]

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Predicted Domain #1

Region A:
Residues: [1-131]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKIQVAHSS RLANLIDYKL RVLTQDGRVY IGQLMAFDKH MNLVLNECIE ERVPKTQLDK  60
   61 LRPRKDSKDG TTLNIKVEKR VLGLTILRGE QILSTVVEDK PLLSKKERLV RDKKEKKQAQ 120
  121 KQTKLRKEKE K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	172.626727
Match:	1d3bB
Description:	B core SNRNP protein
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [132-196]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPGKIAKPNT ANAKHTSSNS REIAQPSSSR YNGGNDNIGA NRSRFNNEAP PQTRKFQPPP  60
   61 GFKRK

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.265	a.7.13	Description not found.
View	Download	0.246	b.84.2	Rudiment single hybrid motif
View	Download	0.231	a.10.2	Description not found.
View	Download	0.215	d.28.1	Ribosomal protein S19
View	Download	0.213	g.28.1	Thyroglobulin type-1 domain

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