PSD5 - PFAM28P - GREMLIN Contacts

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PSD5 - Protein of unknown function (DUF1595)

PFAM:	PF07637	Sequences: CARRILSTFARRAYRRPVTDAEVDRLLAFYRAGRAEGGSFEAGIRLALEAVLVSPEFLFRVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (62)
Sequences:	75101 (40565)
Seq/√Len:	5151.7
META:	0.992

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_S	23_V	2.456	1.00
10_A	51_V	2.383	1.00
6_L	47_A	2.305	1.00
10_A	18_V	2.181	1.00
46_L	49_E	2.049	1.00
3_R	27_L	1.957	1.00
10_A	26_L	1.559	1.00
3_R	7_S	1.550	1.00
30_Y	47_A	1.521	1.00
19_T	22_E	1.518	1.00
39_S	42_A	1.477	1.00
20_D	24_D	1.412	1.00
2_A	30_Y	1.390	1.00
27_L	31_R	1.335	1.00
25_R	28_A	1.323	1.00
16_R	56_E	1.305	1.00
5_I	48_L	1.290	1.00
11_R	18_V	1.286	1.00
45_R	49_E	1.244	1.00
29_F	50_A	1.228	1.00
31_R	35_A	1.201	1.00
50_A	54_S	1.198	1.00
30_Y	34_R	1.183	1.00
33_G	46_L	1.177	1.00
28_A	32_A	1.169	1.00
5_I	44_I	1.165	1.00
9_F	13_A	1.162	1.00
4_R	8_T	1.127	1.00
42_A	45_R	1.122	1.00
3_R	23_V	1.093	1.00
18_V	23_V	1.085	1.00
26_L	50_A	1.079	1.00
13_A	51_V	1.076	1.00
32_A	35_A	1.061	1.00
14_Y	26_L	1.051	1.00
7_S	20_D	1.039	1.00
32_A	36_E	1.037	1.00
3_R	20_D	1.036	1.00
28_A	31_R	1.034	1.00
7_S	11_R	1.027	1.00
40_F	44_I	1.025	1.00
20_D	23_V	1.015	1.00
24_D	28_A	0.988	1.00
8_T	12_R	0.986	1.00
26_L	51_V	0.974	1.00
16_R	22_E	0.949	1.00
46_L	50_A	0.938	1.00
8_T	11_R	0.934	1.00
2_A	40_F	0.925	1.00
9_F	51_V	0.906	1.00
42_A	46_L	0.904	1.00
21_A	24_D	0.891	1.00
38_G	42_A	0.876	1.00
3_R	24_D	0.845	1.00
33_G	36_E	0.841	1.00
23_V	27_L	0.840	1.00
56_E	61_V	0.840	1.00
50_A	53_V	0.795	1.00
34_R	43_G	0.792	1.00
30_Y	43_G	0.792	1.00
49_E	53_V	0.789	1.00
14_Y	54_S	0.771	1.00
33_G	38_G	0.744	1.00
4_R	7_S	0.711	1.00
37_G	42_A	0.707	1.00
34_R	38_G	0.682	1.00
24_D	27_L	0.657	1.00
29_F	46_L	0.653	1.00
33_G	37_G	0.651	1.00
26_L	47_A	0.641	1.00
46_L	53_V	0.637	1.00
5_I	9_F	0.634	1.00
30_Y	40_F	0.616	1.00
31_R	34_R	0.610	1.00
34_R	37_G	0.609	1.00
22_E	56_E	0.601	1.00
43_G	47_A	0.598	1.00
6_L	51_V	0.592	1.00
41_E	45_R	0.591	1.00
5_I	40_F	0.586	1.00
5_I	8_T	0.569	1.00
27_L	30_Y	0.564	1.00
58_L	62_E	0.555	1.00
9_F	48_L	0.553	1.00
22_E	25_R	0.549	1.00
44_I	48_L	0.545	1.00
29_F	33_G	0.543	1.00
38_G	43_G	0.542	1.00
33_G	43_G	0.522	1.00
14_Y	22_E	0.516	1.00
21_A	25_R	0.507	1.00
14_Y	56_E	0.507	1.00
36_E	46_L	0.500	1.00

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1kblA	2	1	13.5	0.836	Contact Map
1vbgA	2	1	13.3	0.837	Contact Map
3gjxA	1	0.9839	10.9	0.843	Contact Map
2gq0A	1	0.8548	10.9	0.843	Contact Map
2qiaA	3	1	10.5	0.844	Contact Map
2x0sA	2	1	9.7	0.847	Contact Map
2xolA	2	0.9194	9.3	0.848	Contact Map
3hsqA	3	1	9.1	0.849	Contact Map
4eqyA	3	1	8.3	0.851	Contact Map
4fgvA	1	0.9839	8.3	0.851	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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