YRC Public Data Repository - Protein Structure Prediction

Protein:	pdl-1
Organism:	Caenorhabditis elegans
Length:	159 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 pdl-1.

Description	E-value	Query Range	Subject Range
gi\|187028916, gi... - gi\|39582310\|emb\|CAE67559.1\| Hypothetical protein CBG13085 [Caenorhabditis briggsae], gi\|187028916\|em...	257.0	[0..1]	[159..1]
gi\|50752331 - gi\|50752331\|ref\|XP_422739.1\| PREDICTED: similar to rod phosphodiesterase delta subunit [Gallus gallu...	243.0	[0..11]	[158..103]
gi\|21465907 - gi\|21465907\|pdb\|1KSG\|B Chain B, Complex Of Arl2 And Pde Delta, Crystal Form 1	238.0	[0..11]	[158..4]
PDE6D_CANLF - Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta OS=Canis lupus fam...	238.0	[0..11]	[158..2]
tr\|M3VY49\|M3VY49... - Phosphodiesterase 6D OS=Felis catus GN=PDE6D PE=4 SV=1 PDE6D_BOVIN - Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta OS=Bos taurus GN=P...	237.0	[0..11]	[158..2]
PDE6D_MOUSE - Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta OS=Mus musculus GN...	236.0	[0..11]	[158..2]
gi\|109101433 - gi\|109101433\|ref\|XP_001113642.1\| PREDICTED: similar to phosphodiesterase 6D, cGMP-specific, rod, del...	236.0	[0..11]	[158..2]
gi\|149016351, gi... - gi\|34877551\|ref\|XP_343614.1\| PREDICTED: similar to Retinal rod rhodopsin-sensitive cGMP 3,5-cyclic p...	235.0	[0..11]	[158..2]

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Predicted Domain #1

Region A:
Residues: [1-159]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MATTATRHQD SKLSEKAESI LAGFKLNWMN LRDAETGKVL WQSTEDMADP KREHKAHVPK  60
   61 NLLKCRTVSR EINFTSSVKI EKFRLEQRVY LKGTIIEEWY FDFGFVIPDS TNTWQNMIEA 120
  121 APESQMFPPS VLSGNVVVET LFYDGDLLVS TSRVRLYYD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	63.39794
Match:	1ksgB
Description:	GMP-PDE delta
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.21867595762264	bayes_pls_golite062009
ligand-gated ion channel activity	1.5302582659987	bayes_pls_golite062009
ligand-gated channel activity	1.5302582659987	bayes_pls_golite062009
protein binding	1.52579295917981	bayes_pls_golite062009
gated channel activity	1.42896395862304	bayes_pls_golite062009
cation channel activity	1.4256218398774	bayes_pls_golite062009
ion channel activity	1.40005559320777	bayes_pls_golite062009
substrate-specific channel activity	1.36653752383074	bayes_pls_golite062009
channel activity	1.35767020846709	bayes_pls_golite062009
passive transmembrane transporter activity	1.35767020846709	bayes_pls_golite062009
voltage-gated cation channel activity	0.855931938850398	bayes_pls_golite062009
voltage-gated ion channel activity	0.789955030733139	bayes_pls_golite062009
voltage-gated channel activity	0.780717736949525	bayes_pls_golite062009
potassium channel activity	0.559325988586613	bayes_pls_golite062009
metal ion transmembrane transporter activity	0.521778252711535	bayes_pls_golite062009
voltage-gated potassium channel activity	0.512152861387956	bayes_pls_golite062009
inward rectifier potassium channel activity	0.0912506266585198	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: