YRC Public Data Repository - Protein Structure Prediction

Protein:	lsm4
Organism:	Schizosaccharomyces pombe
Length:	121 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 lsm4.

Description	E-value	Query Range	Subject Range
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	125.0	[0..1]	[121..1]
gi\|82623401, gi\|... - gi\|82623401\|gb\|ABB87115.1\| glycine rich protein-like [Solanum tuberosum], gi\|77745469\|gb\|ABB02633.1\|...	115.0	[0..1]	[121..1]
gi\|92899039 - gi\|92899039\|gb\|ABE94505.1\| Like-Sm ribonucleoprotein, eukaryotic and archaea-type, core [Medicago tr...	114.0	[0..1]	[120..1]
FBpp0293054, CG1... - This gene is referred to in FlyBase by the symbol Dmel\CG17768 (CG17768, FBgn0032240). It is a prote...	112.0	[0..1]	[104..1]
LSM4_ORYSJ - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Oryza sativa subsp. japonica GN=Os01g0256900 PE... LSM4_ORYSA - Probable U6 snRNA-associated Sm-like protein LSm4 - Oryza sativa (Rice)	111.0	[0..1]	[118..1]
gi\|13161882 - gi\|13161882\|emb\|CAC33027.1\| Lsm4 protein [Takifugu rubripes]	111.0	[0..1]	[118..1]
gi\|47217413 - gi\|47217413\|emb\|CAG00773.1\| unnamed protein product [Tetraodon nigroviridis]	111.0	[0..2]	[99..2]
gi\|91084013 - gi\|91084013\|ref\|XP_975325.1\| PREDICTED: similar to LSM4 homolog, U6 small nuclear RNA associated [Tr...	111.0	[0..2]	[115..14]
LSM4_MOUSE - U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=1 SV=1	110.0	[0..1]	[98..1]

Back

Predicted Domain #1

Region A:
Residues: [1-121]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLPLTLLNAT QGRPILVELK NGETFNGHLE NCDNYMNLTL REVIRTMPDG DKFFRLPECY  60
   61 IRGNNIKYLR IQDEVLSQVA KQQAQQRENR GSRFRGRGQR GRGNYGHTAP NRRGRGRGGH 120
  121 M

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	20.0
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	2.04681172391952	bayes_pls_golite062009
protein binding	0.187097443004706	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: