Mpv17_PMP22 - PFAM28P - GREMLIN Contacts

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Mpv17_PMP22 - Mpv17 / PMP22 family

PFAM:	PF04117	Sequences: GLLEGKSLEEIKEKLKRDFWPTLKANWKVWPPVQLINFRFVPLQLRVLFVNVVSLFWNTYLSYLNH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (64)
Sequences:	4652 (3460)
Seq/√Len:	432.5
META:	0.56

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_K	18_D	2.565	1.00
29_V	53_V	2.519	1.00
23_L	27_W	2.454	1.00
33_V	49_F	2.391	1.00
33_V	53_V	2.328	1.00
7_S	10_E	2.223	1.00
37_N	49_F	2.164	1.00
20_W	24_K	2.146	1.00
12_K	16_K	1.973	1.00
24_K	28_K	1.956	1.00
25_A	28_K	1.662	1.00
13_E	17_R	1.582	1.00
52_V	56_F	1.508	1.00
16_K	20_W	1.455	1.00
22_T	64_L	1.428	1.00
8_L	11_I	1.421	1.00
8_L	12_K	1.415	1.00
55_L	59_T	1.379	1.00
41_V	49_F	1.365	1.00
48_L	51_N	1.352	1.00
60_Y	64_L	1.335	1.00
15_L	19_F	1.296	1.00
19_F	23_L	1.285	1.00
47_V	51_N	1.252	1.00
57_W	60_Y	1.179	1.00
36_I	49_F	1.132	1.00
29_V	56_F	1.120	1.00
28_K	32_P	1.109	1.00
6_K	10_E	1.108	1.00
27_W	31_P	1.104	1.00
11_I	15_L	1.079	1.00
24_K	27_W	1.053	1.00
9_E	13_E	1.043	1.00
35_L	39_R	1.033	1.00
25_A	60_Y	1.031	1.00
14_K	65_N	0.990	1.00
23_L	26_N	0.988	1.00
59_T	63_Y	0.966	1.00
12_K	15_L	0.956	1.00
37_N	46_R	0.930	1.00
37_N	41_V	0.883	1.00
34_Q	38_F	0.878	1.00
9_E	12_K	0.867	1.00
6_K	14_K	0.852	1.00
18_D	22_T	0.836	1.00
45_L	48_L	0.821	1.00
35_L	40_F	0.807	1.00
26_N	58_N	0.801	1.00
54_S	58_N	0.781	1.00
34_Q	37_N	0.777	1.00
36_I	40_F	0.767	1.00
33_V	37_N	0.761	1.00
2_L	8_L	0.757	1.00
21_P	64_L	0.739	1.00
10_E	13_E	0.728	1.00
51_N	54_S	0.727	1.00
34_Q	50_V	0.715	1.00
43_L	46_R	0.715	1.00
50_V	54_S	0.701	1.00
26_N	54_S	0.694	1.00
13_E	16_K	0.693	1.00
7_S	11_I	0.683	1.00
2_L	11_I	0.673	1.00
29_V	33_V	0.669	1.00
37_N	40_F	0.668	1.00
60_Y	63_Y	0.656	0.99
32_P	35_L	0.655	0.99
18_D	65_N	0.641	0.99
29_V	60_Y	0.629	0.99
34_Q	51_N	0.627	0.99
26_N	57_W	0.625	0.99
29_V	32_P	0.617	0.99
38_F	46_R	0.617	0.99
25_A	29_V	0.599	0.99
6_K	11_I	0.598	0.99
17_R	21_P	0.590	0.99
57_W	61_L	0.589	0.99
34_Q	58_N	0.581	0.99
20_W	23_L	0.580	0.99
59_T	62_S	0.576	0.99
21_P	25_A	0.569	0.99
46_R	50_V	0.562	0.98
2_L	6_K	0.560	0.98
9_E	16_K	0.559	0.98
56_F	60_Y	0.551	0.98
4_E	65_N	0.550	0.98
7_S	12_K	0.542	0.98
26_N	30_W	0.541	0.98
22_T	25_A	0.534	0.98
2_L	7_S	0.532	0.98
22_T	61_L	0.531	0.98
34_Q	47_V	0.510	0.97
42_P	45_L	0.506	0.97
20_W	27_W	0.504	0.97
53_V	56_F	0.502	0.97
37_N	50_V	0.500	0.97

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
3qufA	1	0.3485	6.1	0.867	Contact Map
3g3dA	2	0.4242	5.2	0.872	Contact Map
3oo8A	1	0.3636	4.7	0.874	Contact Map
4c1uA	1	0.3333	4.5	0.875	Contact Map
4rjzA	1	0.3636	4.4	0.875	Contact Map
3tr2A	2	0.3333	4.2	0.877	Contact Map
4rk2A	1	0.3485	4	0.878	Contact Map
3f3fC	2	0.9091	4	0.878	Contact Map
4g68A	1	0.303	3.9	0.879	Contact Map
1rpxA	4	0.3333	3.9	0.879	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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