Ycf4 - PFAM28P - GREMLIN Contacts

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Ycf4 - Ycf4

PFAM:	PF02392	Sequences: DNILRQKILGSRRFSNYFWAFILFLGGLGFLLAGLSSYLGINLLPFSDPTQLVFIPQGIVMGFYGTAGLLLSLYLWLTILWDVGSGYNEFNKKEGIVRIFRWGFPGKNRRIELTYPLKDIQSIRVEIKEGLNPRRAIYLRLKGRRDIPLTRVGQPLTLSELEEQAAELARFLGVPLEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	178 (176)
Sequences:	907 (477)
Seq/√Len:	35.9
META:	0.614

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_G	68_G	5.725	1.00
91_N	94_E	5.192	1.00
77_L	81_W	4.918	1.00
97_V	120_I	4.895	1.00
24_F	72_S	4.120	1.00
81_W	105_P	3.551	1.00
34_G	62_G	3.145	1.00
55_I	59_I	3.028	1.00
20_A	76_W	2.954	1.00
97_V	117_L	2.879	1.00
48_D	51_Q	2.829	1.00
5_R	89_E	2.427	1.00
18_F	21_F	2.286	0.99
102_W	110_R	2.274	0.99
137_I	165_A	2.137	0.99
60_V	63_F	2.114	0.99
124_R	146_D	2.095	0.99
96_I	114_T	2.027	0.99
35_L	39_L	1.904	0.98
14_F	18_F	1.886	0.98
45_P	61_M	1.851	0.97
150_T	153_G	1.805	0.97
152_V	155_P	1.791	0.97
95_G	117_L	1.773	0.97
42_N	48_D	1.764	0.96
18_F	22_I	1.748	0.96
49_P	52_L	1.693	0.95
98_R	112_E	1.679	0.95
135_R	155_P	1.668	0.95
97_V	141_L	1.637	0.95
59_I	63_F	1.635	0.94
6_Q	87_Y	1.625	0.94
33_A	47_S	1.529	0.92
126_E	134_R	1.473	0.91
31_L	62_G	1.438	0.90
33_A	44_L	1.419	0.89
97_V	139_L	1.409	0.89
106_G	109_R	1.401	0.88
77_L	83_V	1.392	0.88
39_L	45_P	1.381	0.88
28_L	69_L	1.371	0.87
90_F	128_K	1.320	0.85
34_G	39_L	1.294	0.84
92_K	171_F	1.278	0.83
130_G	133_P	1.235	0.81
46_F	61_M	1.230	0.81
120_I	174_V	1.222	0.80
7_K	82_D	1.199	0.79
141_L	173_G	1.179	0.78
121_Q	140_R	1.161	0.77
143_G	146_D	1.160	0.77
115_Y	144_R	1.156	0.76
23_L	75_L	1.156	0.76
61_M	137_I	1.137	0.75
135_R	158_L	1.103	0.73
68_G	90_F	1.087	0.72
6_Q	165_A	1.083	0.72
72_S	76_W	1.078	0.71
10_G	16_N	1.078	0.71
140_R	146_D	1.073	0.71
24_F	76_W	1.072	0.71
16_N	19_W	1.071	0.71
26_G	91_N	1.047	0.69
96_I	137_I	1.036	0.68
96_I	116_P	1.029	0.68
92_K	111_I	1.025	0.67
33_A	52_L	1.024	0.67
162_E	169_A	1.010	0.66
48_D	127_I	1.009	0.66
73_L	159_S	1.005	0.66
67_A	137_I	0.985	0.64
2_N	93_K	0.980	0.64
13_R	85_S	0.979	0.64
87_Y	108_N	0.975	0.63
119_D	126_E	0.970	0.63
11_S	104_F	0.964	0.62
17_Y	171_F	0.949	0.61
122_S	141_L	0.941	0.61
105_P	109_R	0.936	0.60
71_L	78_T	0.936	0.60
125_V	143_G	0.934	0.60
87_Y	112_E	0.926	0.59
139_L	149_L	0.926	0.59
11_S	83_V	0.923	0.59
115_Y	145_R	0.923	0.59
130_G	135_R	0.916	0.58
14_F	28_L	0.914	0.58
147_I	150_T	0.913	0.58
22_I	28_L	0.912	0.58
29_G	33_A	0.905	0.58
135_R	150_T	0.903	0.57
156_L	161_L	0.897	0.57
69_L	142_K	0.896	0.57
87_Y	98_R	0.895	0.57
165_A	176_L	0.895	0.57
32_L	36_S	0.894	0.57
49_P	62_G	0.891	0.56
28_L	79_I	0.888	0.56
102_W	109_R	0.884	0.56
166_A	170_R	0.882	0.56
161_L	165_A	0.878	0.55
141_L	146_D	0.877	0.55
74_Y	157_T	0.873	0.55
61_M	125_V	0.867	0.54
11_S	15_S	0.866	0.54
45_P	143_G	0.864	0.54
23_L	71_L	0.863	0.54
114_T	117_L	0.859	0.54
161_L	170_R	0.857	0.53
26_G	29_G	0.852	0.53
4_L	7_K	0.848	0.53
53_V	61_M	0.843	0.52
66_T	167_E	0.824	0.51
122_S	140_R	0.823	0.50
20_A	75_L	0.817	0.50
44_L	77_L	0.815	0.50
44_L	49_P	0.804	0.49
19_W	104_F	0.803	0.49
79_I	82_D	0.799	0.48
55_I	82_D	0.796	0.48
81_W	106_G	0.792	0.48
21_F	63_F	0.792	0.48
19_W	81_W	0.790	0.48
59_I	125_V	0.790	0.48
87_Y	100_F	0.786	0.47
32_L	107_K	0.786	0.47
70_L	119_D	0.785	0.47
160_E	174_V	0.781	0.47
168_L	176_L	0.778	0.47
60_V	78_T	0.777	0.46
174_V	177_E	0.774	0.46
104_F	130_G	0.770	0.46
19_W	72_S	0.769	0.46
27_G	63_F	0.763	0.45
6_Q	168_L	0.763	0.45
13_R	16_N	0.755	0.45
76_W	79_I	0.753	0.44
34_G	43_L	0.752	0.44
70_L	153_G	0.747	0.44
69_L	149_L	0.742	0.43
48_D	110_R	0.742	0.43
47_S	176_L	0.737	0.43
62_G	66_T	0.737	0.43
17_Y	70_L	0.733	0.43
22_I	144_R	0.731	0.42
67_A	70_L	0.730	0.42
124_R	158_L	0.726	0.42
6_Q	164_Q	0.725	0.42
42_N	49_P	0.723	0.42
10_G	133_P	0.722	0.42
103_G	109_R	0.718	0.41
11_S	80_L	0.716	0.41
39_L	43_L	0.715	0.41
98_R	114_T	0.712	0.41
81_W	109_R	0.710	0.41
21_F	93_K	0.709	0.41
91_N	98_R	0.705	0.40
31_L	147_I	0.702	0.40
18_F	28_L	0.695	0.39
158_L	162_E	0.693	0.39
19_W	46_F	0.690	0.39
26_G	122_S	0.685	0.39
5_R	113_L	0.684	0.39
32_L	47_S	0.684	0.39
157_T	169_A	0.680	0.38
80_L	91_N	0.678	0.38
46_F	125_V	0.674	0.38
29_G	36_S	0.673	0.38
100_F	138_Y	0.673	0.38
11_S	78_T	0.672	0.38
114_T	146_D	0.669	0.37
12_R	32_L	0.669	0.37
30_F	162_E	0.659	0.37
160_E	167_E	0.657	0.36
74_Y	136_A	0.653	0.36
13_R	154_Q	0.652	0.36
89_E	106_G	0.652	0.36
41_I	47_S	0.651	0.36
52_L	173_G	0.650	0.36
83_V	167_E	0.648	0.36
55_I	87_Y	0.647	0.36
166_A	169_A	0.647	0.36
61_M	143_G	0.646	0.35
72_S	79_I	0.644	0.35
68_G	114_T	0.643	0.35
40_G	60_V	0.640	0.35
8_I	92_K	0.638	0.35
129_E	158_L	0.636	0.35
98_R	124_R	0.629	0.34
28_L	31_L	0.626	0.34
4_L	170_R	0.624	0.34
67_A	71_L	0.622	0.34
119_D	135_R	0.622	0.34
51_Q	83_V	0.621	0.34
5_R	114_T	0.619	0.33
138_Y	151_R	0.618	0.33
127_I	138_Y	0.609	0.33
25_L	28_L	0.609	0.33
23_L	49_P	0.609	0.33
88_N	158_L	0.608	0.33
33_A	55_I	0.608	0.33
52_L	55_I	0.607	0.32
41_I	154_Q	0.607	0.32
66_T	96_I	0.604	0.32
9_L	72_S	0.601	0.32
28_L	72_S	0.600	0.32
38_Y	163_E	0.599	0.32
123_I	169_A	0.599	0.32
2_N	5_R	0.597	0.32
107_K	121_Q	0.594	0.31
63_F	83_V	0.593	0.31
36_S	45_P	0.590	0.31
19_W	135_R	0.587	0.31
124_R	136_A	0.583	0.31
31_L	59_I	0.580	0.30
13_R	135_R	0.578	0.30
8_I	34_G	0.578	0.30
95_G	142_K	0.578	0.30
19_W	22_I	0.575	0.30
117_L	122_S	0.572	0.30
7_K	161_L	0.572	0.30
67_A	158_L	0.572	0.30
91_N	170_R	0.570	0.30
99_I	115_Y	0.567	0.29
42_N	128_K	0.567	0.29
97_V	145_R	0.563	0.29
166_A	175_P	0.554	0.29
23_L	68_G	0.548	0.28
39_L	114_T	0.546	0.28
33_A	176_L	0.546	0.28
90_F	171_F	0.545	0.28
135_R	152_V	0.545	0.28
141_L	145_R	0.544	0.28
37_S	54_F	0.542	0.28
87_Y	159_S	0.540	0.28
35_L	78_T	0.539	0.27
4_L	128_K	0.539	0.27
10_G	177_E	0.538	0.27
61_M	69_L	0.534	0.27
118_K	121_Q	0.533	0.27
83_V	106_G	0.533	0.27
26_G	68_G	0.533	0.27
115_Y	127_I	0.531	0.27
33_A	49_P	0.530	0.27
116_P	119_D	0.530	0.27
40_G	89_E	0.529	0.27
95_G	120_I	0.527	0.27
3_I	72_S	0.526	0.27
80_L	154_Q	0.525	0.27
74_Y	103_G	0.525	0.27
3_I	50_T	0.524	0.26
78_T	104_F	0.521	0.26
88_N	162_E	0.521	0.26
27_G	119_D	0.520	0.26
3_I	137_I	0.520	0.26
39_L	51_Q	0.513	0.26
99_I	158_L	0.509	0.25
120_I	136_A	0.508	0.25
141_L	144_R	0.507	0.25
102_W	118_K	0.507	0.25
16_N	75_L	0.506	0.25
123_I	144_R	0.502	0.25
74_Y	124_R	0.501	0.25
117_L	120_I	0.500	0.25

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
1ny4A	1	0.3933	16.1	0.963	Contact Map
4rb5J	1	0.1854	9.6	0.967	Contact Map
3w1yC	1	0.191	8.6	0.967	Contact Map
1p7bA	3	0.7865	8.3	0.968	Contact Map
3j20L	1	0.2022	7.4	0.968	Contact Map
4bpe1	1	0.3652	6.6	0.969	Contact Map
2jovA	1	0.264	6.3	0.969	Contact Map
4ujpV	1	0.2191	5.7	0.97	Contact Map
3j7aN	1	0.1742	5.6	0.97	Contact Map
2mewA	1	0.2191	5.5	0.97	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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