OPA3 - PFAM28P - GREMLIN Contacts

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OPA3 - Optic atrophy 3 protein (OPA3)

PFAM:	PF07047	Sequences: AKLGSLAIRTLSKPIANRIKAQAKEHPRFRYFCIPLAQAYHRIEMRLRMRLLGLKPAKIRPLNEEKAIELGADLLGEAFIFSVAGGLIIYEYWRSSRKEAKKEEKVAEELEELEERIEELEEEVEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (123)
Sequences:	654 (474)
Seq/√Len:	42.7
META:	0.242

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
109_E	114_E	4.886	1.00
116_R	121_E	4.808	1.00
17_N	20_K	2.871	1.00
104_E	108_E	2.440	1.00
34_I	64_E	2.334	1.00
91_E	94_R	2.219	1.00
48_R	52_L	1.984	0.99
9_R	13_K	1.971	0.99
81_F	85_G	1.952	0.99
79_F	83_V	1.904	0.99
2_K	6_L	1.890	0.99
103_E	107_A	1.858	0.99
18_R	21_A	1.800	0.98
24_K	69_E	1.794	0.98
99_E	102_K	1.769	0.98
115_E	119_E	1.764	0.98
12_S	16_A	1.699	0.97
23_A	33_C	1.639	0.97
31_Y	35_P	1.634	0.97
38_Q	62_L	1.618	0.96
11_L	115_E	1.607	0.96
37_A	63_N	1.604	0.96
44_E	48_R	1.598	0.96
118_E	121_E	1.556	0.96
14_P	77_E	1.527	0.95
40_Y	74_L	1.512	0.95
6_L	20_K	1.489	0.94
53_G	75_L	1.480	0.94
38_Q	59_I	1.461	0.94
106_V	109_E	1.449	0.93
15_I	20_K	1.445	0.93
110_L	114_E	1.432	0.93
112_E	116_R	1.418	0.93
33_C	37_A	1.390	0.92
4_G	7_A	1.388	0.92
49_M	81_F	1.332	0.90
38_Q	41_H	1.310	0.89
46_R	50_R	1.295	0.89
62_L	67_A	1.295	0.89
37_A	84_A	1.282	0.88
43_I	47_L	1.274	0.88
98_K	101_K	1.271	0.88
40_Y	70_L	1.257	0.87
85_G	88_I	1.197	0.85
101_K	104_E	1.197	0.85
41_H	62_L	1.183	0.84
36_L	74_L	1.183	0.84
103_E	106_V	1.175	0.84
7_A	10_T	1.167	0.83
2_K	14_P	1.165	0.83
29_F	33_C	1.163	0.83
6_L	91_E	1.154	0.82
11_L	16_A	1.127	0.81
70_L	88_I	1.117	0.80
76_G	80_I	1.096	0.79
23_A	29_F	1.076	0.78
41_H	59_I	1.019	0.74
28_R	31_Y	1.018	0.74
64_E	120_L	1.014	0.73
4_G	81_F	1.007	0.73
65_E	68_I	1.007	0.73
38_Q	67_A	0.995	0.72
37_A	48_R	0.995	0.72
79_F	103_E	0.988	0.71
42_R	88_I	0.972	0.70
112_E	121_E	0.957	0.69
11_L	15_I	0.956	0.69
45_M	59_I	0.951	0.68
8_I	95_S	0.943	0.68
4_G	68_I	0.941	0.68
37_A	62_L	0.941	0.68
119_E	123_E	0.934	0.67
107_A	111_E	0.931	0.67
15_I	78_A	0.926	0.66
3_L	80_I	0.923	0.66
6_L	10_T	0.886	0.63
37_A	92_Y	0.886	0.63
12_S	76_G	0.868	0.61
7_A	87_L	0.865	0.61
102_K	107_A	0.864	0.61
10_T	81_F	0.863	0.61
116_R	119_E	0.861	0.61
62_L	70_L	0.852	0.60
114_E	121_E	0.835	0.58
44_E	76_G	0.835	0.58
115_E	122_E	0.828	0.58
27_P	86_G	0.825	0.57
9_R	84_A	0.825	0.57
114_E	118_E	0.823	0.57
31_Y	42_R	0.799	0.55
84_A	95_S	0.796	0.55
13_K	16_A	0.793	0.54
37_A	70_L	0.792	0.54
9_R	95_S	0.790	0.54
83_V	88_I	0.789	0.54
112_E	115_E	0.787	0.54
106_V	113_L	0.784	0.54
30_R	64_E	0.783	0.53
100_A	103_E	0.779	0.53
22_Q	26_H	0.775	0.53
10_T	13_K	0.773	0.53
86_G	97_R	0.771	0.52
64_E	76_G	0.767	0.52
23_A	75_L	0.764	0.52
33_C	71_G	0.762	0.51
49_M	63_N	0.755	0.51
117_I	121_E	0.755	0.51
76_G	92_Y	0.752	0.51
90_Y	94_R	0.748	0.50
59_I	77_E	0.737	0.49
81_F	88_I	0.734	0.49
116_R	120_L	0.733	0.49
16_A	19_I	0.733	0.49
9_R	15_I	0.720	0.47
117_I	123_E	0.718	0.47
13_K	81_F	0.710	0.47
31_Y	39_A	0.706	0.46
7_A	114_E	0.699	0.46
17_N	21_A	0.690	0.45
29_F	37_A	0.690	0.45
113_L	116_R	0.688	0.44
53_G	60_R	0.688	0.44
2_K	91_E	0.682	0.44
117_I	120_L	0.681	0.44
107_A	118_E	0.680	0.44
28_R	32_F	0.679	0.44
82_S	96_S	0.678	0.44
16_A	20_K	0.677	0.43
48_R	54_L	0.675	0.43
21_A	24_K	0.675	0.43
114_E	117_I	0.671	0.43
49_M	54_L	0.671	0.43
101_K	118_E	0.671	0.43
55_K	115_E	0.668	0.43
74_L	86_G	0.668	0.43
15_I	110_L	0.667	0.43
113_L	118_E	0.664	0.42
78_A	82_S	0.658	0.42
10_T	14_P	0.657	0.42
64_E	88_I	0.636	0.40
18_R	27_P	0.632	0.39
37_A	99_E	0.632	0.39
78_A	97_R	0.614	0.38
32_F	82_S	0.613	0.38
20_K	91_E	0.612	0.38
7_A	11_L	0.609	0.37
36_L	70_L	0.600	0.36
22_Q	25_E	0.600	0.36
7_A	28_R	0.598	0.36
1_A	76_G	0.595	0.36
60_R	66_K	0.589	0.36
69_E	79_F	0.584	0.35
9_R	14_P	0.580	0.35
24_K	73_D	0.580	0.35
19_I	24_K	0.579	0.35
37_A	42_R	0.572	0.34
19_I	65_E	0.556	0.33
53_G	56_P	0.552	0.32
50_R	54_L	0.550	0.32
87_L	100_A	0.549	0.32
49_M	53_G	0.546	0.32
12_S	63_N	0.546	0.32
89_I	114_E	0.543	0.32
23_A	30_R	0.538	0.31
54_L	90_Y	0.534	0.31
35_P	42_R	0.534	0.31
7_A	81_F	0.534	0.31
82_S	111_E	0.529	0.30
107_A	110_L	0.527	0.30
38_Q	72_A	0.527	0.30
38_Q	44_E	0.525	0.30
2_K	13_K	0.524	0.30
42_R	81_F	0.521	0.30
92_Y	120_L	0.521	0.30
102_K	106_V	0.518	0.30
80_I	107_A	0.517	0.30
37_A	68_I	0.516	0.29
27_P	31_Y	0.512	0.29
118_E	122_E	0.511	0.29
108_E	123_E	0.509	0.29
43_I	108_E	0.508	0.29
12_S	18_R	0.507	0.29
81_F	84_A	0.500	0.28
37_A	44_E	0.500	0.28

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
4rh7A	1	0.7937	27.4	0.905	Contact Map
3wuqA	1	0.7857	14.8	0.916	Contact Map
3rvyA	3	0.7063	11.1	0.921	Contact Map
1f5nA	1	0.881	9.8	0.923	Contact Map
1kd8A	1	0.1429	8.3	0.925	Contact Map
4cgkA	3	0.1825	6.2	0.929	Contact Map
2j5uA	4	0.2063	6.1	0.929	Contact Map
4etpA	1	0.3016	5.9	0.93	Contact Map
1fxkA	2	0.7063	5.9	0.93	Contact Map
2l5gA	1	0.2619	5.6	0.931	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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