CLU - PFAM28P - GREMLIN Contacts

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CLU - Clustered mitochondria

PFAM:	PF13236	Sequences: DWNEEFQSARELPRETLQERLLRERALSKLASDFVEAATRGAKAIISENVLPLNPKEKPGGQKYIYNNIFFSFAVDSRGTYKSLGGDEAARKAAGHDLKGLKALNNLDIPGLHTPLTALVDYRGFRLVAQSILPGILKGEQESTLVYGSVDGGKTVHADEEFHELMKKAAKALNLKPHKVLDKEGKEVELYGSVDIKGHLGTDGRKYVLDLARLFPPDANF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	221 (219)
Sequences:	663 (519)
Seq/√Len:	35.1
META:	0.477

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
121_D	126_R	7.962	1.00
162_F	198_G	6.268	1.00
69_I	129_A	6.149	1.00
42_A	127_L	5.071	1.00
104_L	169_A	4.887	1.00
3_N	7_Q	3.823	1.00
104_L	214_L	2.978	1.00
177_P	189_E	2.820	1.00
42_A	46_I	2.772	1.00
96_H	99_K	2.719	1.00
134_P	201_G	2.252	0.99
63_K	72_S	2.207	0.99
201_G	205_R	2.202	0.99
42_A	71_F	2.189	0.99
71_F	129_A	2.080	0.99
14_R	23_R	2.060	0.99
104_L	192_G	2.051	0.99
197_K	210_D	2.016	0.98
41_G	71_F	2.016	0.98
193_S	196_I	1.992	0.98
73_F	127_L	1.894	0.97
74_A	128_V	1.879	0.97
169_A	214_L	1.871	0.97
6_F	10_R	1.866	0.97
167_K	177_P	1.853	0.97
158_A	163_H	1.825	0.97
146_V	162_F	1.820	0.97
46_I	127_L	1.807	0.97
179_K	189_E	1.793	0.96
201_G	207_Y	1.755	0.96
65_I	132_I	1.754	0.96
101_L	114_T	1.750	0.96
9_A	30_L	1.745	0.96
95_G	121_D	1.693	0.95
13_P	19_E	1.665	0.95
13_P	16_T	1.656	0.94
56_K	59_P	1.645	0.94
48_E	57_E	1.644	0.94
149_S	153_G	1.619	0.94
182_D	185_G	1.616	0.94
3_N	207_Y	1.612	0.94
72_S	197_K	1.605	0.94
96_H	212_A	1.590	0.93
203_D	207_Y	1.547	0.92
179_K	187_E	1.531	0.92
116_L	131_S	1.505	0.91
198_G	201_G	1.495	0.91
7_Q	201_G	1.494	0.91
151_D	155_T	1.489	0.91
95_G	126_R	1.488	0.91
74_A	94_A	1.475	0.90
198_G	208_V	1.468	0.90
47_S	123_R	1.453	0.90
159_D	206_K	1.415	0.88
76_D	87_D	1.409	0.88
38_A	120_V	1.402	0.88
48_E	56_K	1.332	0.85
15_E	19_E	1.329	0.85
112_L	165_L	1.314	0.84
134_P	207_Y	1.292	0.83
38_A	156_V	1.286	0.83
7_Q	205_R	1.283	0.83
13_P	23_R	1.278	0.82
120_V	129_A	1.275	0.82
200_L	214_L	1.261	0.82
4_E	205_R	1.255	0.81
83_S	86_G	1.254	0.81
76_D	93_A	1.251	0.81
63_K	197_K	1.251	0.81
104_L	208_V	1.222	0.79
8_S	11_E	1.190	0.78
156_V	190_L	1.168	0.76
60_G	199_H	1.149	0.75
101_L	190_L	1.143	0.75
104_L	121_D	1.133	0.74
6_F	116_L	1.123	0.73
144_T	199_H	1.120	0.73
100_G	169_A	1.109	0.72
182_D	188_V	1.104	0.72
195_D	213_R	1.099	0.72
129_A	172_A	1.092	0.71
167_K	191_Y	1.084	0.71
200_L	206_K	1.083	0.71
6_F	42_A	1.081	0.70
12_L	23_R	1.080	0.70
147_Y	156_V	1.072	0.70
60_G	197_K	1.068	0.69
34_F	216_P	1.064	0.69
3_N	11_E	1.057	0.69
64_Y	139_G	1.054	0.68
119_L	128_V	1.044	0.68
103_A	215_F	1.031	0.67
36_E	40_R	1.025	0.66
73_F	125_F	1.008	0.65
3_N	203_D	1.006	0.65
71_F	127_L	1.003	0.65
151_D	154_K	1.003	0.65
51_L	56_K	0.999	0.64
5_E	68_N	0.992	0.64
52_P	56_K	0.976	0.62
149_S	155_T	0.974	0.62
44_A	48_E	0.967	0.62
175_L	178_H	0.965	0.62
60_G	72_S	0.962	0.61
68_N	96_H	0.962	0.61
60_G	63_K	0.961	0.61
139_G	144_T	0.950	0.60
7_Q	113_H	0.948	0.60
4_E	16_T	0.926	0.58
161_E	206_K	0.914	0.57
63_K	116_L	0.914	0.57
90_A	133_L	0.912	0.57
177_P	191_Y	0.912	0.57
85_G	90_A	0.904	0.56
3_N	131_S	0.903	0.56
76_D	79_G	0.899	0.56
2_W	23_R	0.899	0.56
118_A	161_E	0.890	0.55
1_D	116_L	0.884	0.55
103_A	173_L	0.879	0.54
147_Y	190_L	0.879	0.54
70_F	210_D	0.877	0.54
49_N	73_F	0.876	0.54
16_T	19_E	0.868	0.53
30_L	35_V	0.862	0.53
173_L	208_V	0.852	0.52
162_F	208_V	0.851	0.52
103_A	169_A	0.850	0.52
78_R	110_P	0.845	0.51
54_N	130_Q	0.841	0.51
60_G	210_D	0.840	0.51
97_D	197_K	0.834	0.50
70_F	197_K	0.828	0.50
118_A	123_R	0.828	0.50
47_S	51_L	0.825	0.50
76_D	90_A	0.820	0.49
74_A	119_L	0.811	0.49
178_H	194_V	0.810	0.48
167_K	171_K	0.805	0.48
10_R	29_K	0.799	0.47
163_H	177_P	0.793	0.47
42_A	54_N	0.786	0.46
34_F	124_G	0.785	0.46
7_Q	11_E	0.785	0.46
101_L	105_N	0.784	0.46
48_E	125_F	0.784	0.46
162_F	200_L	0.783	0.46
101_L	166_M	0.781	0.46
40_R	160_E	0.778	0.46
72_S	137_L	0.775	0.45
175_L	192_G	0.773	0.45
118_A	168_K	0.766	0.45
30_L	68_N	0.763	0.44
51_L	58_K	0.761	0.44
33_D	41_G	0.761	0.44
10_R	14_R	0.748	0.43
182_D	186_K	0.747	0.43
145_L	157_H	0.745	0.43
85_G	93_A	0.740	0.42
166_M	172_A	0.737	0.42
109_I	112_L	0.737	0.42
61_G	144_T	0.730	0.42
159_D	200_L	0.724	0.41
119_L	202_T	0.718	0.41
38_A	186_K	0.716	0.40
21_L	59_P	0.716	0.40
61_G	72_S	0.716	0.40
98_L	180_V	0.715	0.40
11_E	113_H	0.715	0.40
40_R	170_A	0.715	0.40
75_V	215_F	0.713	0.40
12_L	17_L	0.711	0.40
199_H	210_D	0.710	0.40
72_S	210_D	0.708	0.40
52_P	59_P	0.707	0.40
127_L	153_G	0.704	0.39
75_V	188_V	0.702	0.39
77_S	97_D	0.700	0.39
64_Y	161_E	0.698	0.39
190_L	211_L	0.698	0.39
150_V	173_L	0.698	0.39
200_L	208_V	0.694	0.39
156_V	194_V	0.694	0.39
35_V	118_A	0.690	0.38
140_E	143_S	0.689	0.38
73_F	176_K	0.689	0.38
72_S	97_D	0.689	0.38
180_V	188_V	0.688	0.38
192_G	214_L	0.687	0.38
39_T	42_A	0.685	0.38
71_F	119_L	0.685	0.38
9_A	12_L	0.683	0.38
112_L	127_L	0.682	0.38
161_E	165_L	0.682	0.38
19_E	22_L	0.679	0.37
33_D	71_F	0.677	0.37
7_Q	207_Y	0.672	0.37
76_D	118_A	0.670	0.37
101_L	117_T	0.669	0.37
89_A	130_Q	0.664	0.36
140_E	144_T	0.664	0.36
198_G	214_L	0.661	0.36
30_L	181_L	0.661	0.36
90_A	94_A	0.655	0.36
146_V	200_L	0.655	0.36
5_E	29_K	0.654	0.35
1_D	4_E	0.654	0.35
100_G	104_L	0.654	0.35
61_G	197_K	0.653	0.35
63_K	199_H	0.650	0.35
9_A	65_I	0.649	0.35
97_D	159_D	0.649	0.35
149_S	193_S	0.649	0.35
89_A	192_G	0.648	0.35
32_S	47_S	0.647	0.35
45_I	88_E	0.646	0.35
47_S	177_P	0.643	0.35
144_T	152_G	0.641	0.34
174_N	196_I	0.641	0.34
60_G	152_G	0.640	0.34
45_I	127_L	0.639	0.34
120_V	126_R	0.638	0.34
92_K	217_P	0.635	0.34
52_P	119_L	0.633	0.34
160_E	164_E	0.629	0.34
67_N	126_R	0.628	0.33
41_G	44_A	0.627	0.33
1_D	7_Q	0.625	0.33
92_K	145_L	0.623	0.33
131_S	149_S	0.623	0.33
117_T	193_S	0.622	0.33
136_I	151_D	0.620	0.33
4_E	10_R	0.619	0.33
112_L	123_R	0.619	0.33
154_K	166_M	0.617	0.33
110_P	168_K	0.617	0.33
8_S	30_L	0.616	0.33
214_L	219_A	0.613	0.32
65_I	70_F	0.610	0.32
111_G	122_Y	0.609	0.32
2_W	10_R	0.608	0.32
118_A	145_L	0.608	0.32
79_G	82_K	0.607	0.32
33_D	38_A	0.604	0.32
102_K	169_A	0.604	0.32
2_W	213_R	0.603	0.32
72_S	199_H	0.602	0.31
72_S	135_G	0.601	0.31
92_K	101_L	0.600	0.31
104_L	173_L	0.600	0.31
180_V	208_V	0.598	0.31
109_I	168_K	0.598	0.31
146_V	159_D	0.596	0.31
39_T	43_K	0.593	0.31
100_G	103_A	0.593	0.31
33_D	211_L	0.590	0.31
74_A	122_Y	0.589	0.31
142_E	146_V	0.589	0.31
127_L	190_L	0.589	0.31
110_P	160_E	0.587	0.30
101_L	193_S	0.584	0.30
38_A	88_E	0.583	0.30
74_A	100_G	0.581	0.30
153_G	213_R	0.581	0.30
15_E	168_K	0.577	0.30
39_T	64_Y	0.570	0.29
28_S	31_A	0.569	0.29
162_F	182_D	0.566	0.29
180_V	204_G	0.565	0.29
181_L	185_G	0.561	0.29
196_I	211_L	0.561	0.29
29_K	33_D	0.559	0.28
192_G	196_I	0.557	0.28
39_T	90_A	0.553	0.28
27_L	30_L	0.553	0.28
44_A	131_S	0.552	0.28
24_E	79_G	0.551	0.28
63_K	149_S	0.551	0.28
164_E	167_K	0.550	0.28
17_L	25_R	0.546	0.27
76_D	147_Y	0.546	0.27
122_Y	130_Q	0.544	0.27
19_E	25_R	0.543	0.27
90_A	93_A	0.542	0.27
64_Y	154_K	0.541	0.27
46_I	69_I	0.541	0.27
5_E	21_L	0.539	0.27
51_L	164_E	0.539	0.27
34_F	129_A	0.536	0.27
150_V	195_D	0.536	0.27
147_Y	180_V	0.534	0.27
44_A	67_N	0.532	0.27
13_P	20_R	0.532	0.27
104_L	175_L	0.532	0.27
74_A	198_G	0.530	0.26
156_V	180_V	0.530	0.26
18_Q	27_L	0.527	0.26
72_S	149_S	0.526	0.26
46_I	125_F	0.524	0.26
104_L	114_T	0.523	0.26
85_G	89_A	0.523	0.26
102_K	112_L	0.523	0.26
3_N	201_G	0.520	0.26
129_A	151_D	0.520	0.26
55_P	97_D	0.516	0.25
92_K	213_R	0.516	0.25
88_E	160_E	0.515	0.25
60_G	115_P	0.515	0.25
33_D	65_I	0.514	0.25
48_E	217_P	0.514	0.25
20_R	24_E	0.514	0.25
147_Y	175_L	0.513	0.25
147_Y	198_G	0.513	0.25
38_A	41_G	0.512	0.25
5_E	25_R	0.511	0.25
88_E	123_R	0.510	0.25
51_L	54_N	0.508	0.25
91_R	117_T	0.508	0.25
36_E	47_S	0.507	0.25
215_F	218_D	0.507	0.25
111_G	130_Q	0.506	0.25
91_R	196_I	0.504	0.25
178_H	213_R	0.503	0.25
163_H	204_G	0.502	0.25
30_L	156_V	0.502	0.25
48_E	59_P	0.501	0.25
212_A	217_P	0.500	0.24
42_A	73_F	0.500	0.24

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
3epoA	2	0.086	9.6	0.96	Contact Map
2v8qA	1	0.3394	9.3	0.96	Contact Map
4g6tA	1	0.2896	8.2	0.961	Contact Map
2al6A	1	0.3891	7.6	0.962	Contact Map
2phcB	1	0.6063	7.4	0.962	Contact Map
2enjA	1	0.3077	7	0.962	Contact Map
1k3eA	2	0.2805	6.3	0.963	Contact Map
4ogqE	1	0.1403	6	0.964	Contact Map
4po6A	1	0.3665	5.7	0.964	Contact Map
4i7zE	1	0.1267	5.2	0.965	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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