DUF2270 - PFAM28P - GREMLIN Contacts

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DUF2270 - Predicted integral membrane protein (DUF2270)

PFAM:	PF10028	Sequences: AHLYRGEVYRSTVWRTRLDTTTNWAVVTTGAALSFAFSSPEAPHLVLLLVMLLVTLFLLIEARRYRYYDVWRARVRLLETNFFAPMLRPEGFHPDPDWAELLAEDLRRPRFKISFWEALGRRLRRNYLWIFLILLLAWLLKITIHPTPATSLAEFVERAAIGPIPGWLVLAAGVLFYAALIALA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	184 (183)
Sequences:	2060 (1202)
Seq/√Len:	88.8
META:	0.872

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_T	131_F	4.823	1.00
39_S	42_A	3.098	1.00
105_D	112_K	2.843	1.00
59_L	115_F	2.798	1.00
16_T	20_T	2.743	1.00
141_K	145_H	2.696	1.00
146_P	158_R	2.584	1.00
177_Y	180_L	2.501	1.00
13_V	16_T	2.449	1.00
159_A	166_G	2.395	1.00
2_H	5_R	2.223	1.00
173_G	177_Y	2.166	1.00
73_A	112_K	2.152	1.00
156_V	170_L	2.110	1.00
151_S	154_E	2.080	1.00
85_P	89_P	2.072	1.00
69_D	112_K	2.068	1.00
154_E	157_E	2.054	1.00
149_A	155_F	1.887	1.00
7_E	10_R	1.873	1.00
150_T	154_E	1.843	1.00
49_L	57_F	1.810	1.00
142_I	159_A	1.788	1.00
29_T	54_V	1.758	1.00
51_M	134_L	1.753	1.00
65_Y	121_R	1.732	1.00
44_H	138_W	1.729	1.00
165_P	168_L	1.728	1.00
32_A	50_V	1.723	1.00
9_Y	13_V	1.712	1.00
174_V	178_A	1.646	1.00
70_V	73_A	1.639	1.00
56_L	133_I	1.625	1.00
77_L	81_N	1.621	1.00
157_E	160_A	1.609	1.00
179_A	182_A	1.597	1.00
58_L	119_L	1.570	1.00
114_S	117_E	1.565	1.00
161_I	169_V	1.528	1.00
69_D	117_E	1.517	1.00
10_R	15_R	1.458	0.99
51_M	173_G	1.458	0.99
177_Y	181_I	1.451	0.99
104_E	108_R	1.426	0.99
69_D	72_R	1.421	0.99
55_T	180_L	1.408	0.99
59_L	119_L	1.403	0.99
43_P	141_K	1.393	0.99
87_L	99_A	1.388	0.99
100_E	104_E	1.385	0.99
88_R	107_R	1.374	0.99
146_P	149_A	1.367	0.99
95_D	105_D	1.354	0.99
54_V	134_L	1.352	0.99
3_L	83_F	1.344	0.99
178_A	182_A	1.339	0.99
48_L	173_G	1.335	0.99
171_A	178_A	1.318	0.99
156_V	166_G	1.314	0.99
173_G	176_F	1.310	0.99
3_L	106_L	1.306	0.99
135_L	173_G	1.305	0.99
174_V	177_Y	1.296	0.99
14_W	71_W	1.293	0.99
3_L	6_G	1.215	0.98
65_Y	133_I	1.213	0.98
66_R	109_P	1.208	0.98
152_L	170_L	1.206	0.98
9_Y	12_T	1.206	0.98
37_F	45_L	1.204	0.98
67_Y	111_F	1.196	0.98
135_L	177_Y	1.192	0.98
139_L	170_L	1.180	0.98
153_A	157_E	1.179	0.98
156_V	167_W	1.177	0.98
79_E	121_R	1.175	0.97
72_R	121_R	1.159	0.97
10_R	14_W	1.152	0.97
168_L	172_A	1.137	0.97
97_D	100_E	1.127	0.97
156_V	159_A	1.108	0.96
53_L	71_W	1.095	0.96
150_T	153_A	1.066	0.96
40_P	131_F	1.059	0.95
168_L	178_A	1.058	0.95
69_D	77_L	1.058	0.95
25_A	29_T	1.044	0.95
86_M	90_E	1.043	0.95
79_E	106_L	1.033	0.95
35_F	42_A	1.024	0.94
123_L	128_L	1.018	0.94
1_A	106_L	1.017	0.94
147_T	165_P	1.007	0.94
142_I	155_F	1.006	0.94
167_W	171_A	1.003	0.94
73_A	110_R	1.001	0.94
133_I	159_A	1.000	0.94
53_L	129_W	0.998	0.94
97_D	101_L	0.997	0.94
10_R	60_I	0.992	0.93
46_V	138_W	0.951	0.92
67_Y	121_R	0.950	0.92
149_A	153_A	0.943	0.92
50_V	130_I	0.927	0.91
152_L	156_V	0.926	0.91
34_S	38_S	0.923	0.91
155_F	170_L	0.921	0.91
45_L	134_L	0.918	0.90
4_Y	12_T	0.915	0.90
128_L	177_Y	0.909	0.90
30_G	53_L	0.897	0.89
60_I	81_N	0.896	0.89
31_A	35_F	0.892	0.89
105_D	110_R	0.892	0.89
78_L	83_F	0.890	0.89
22_T	28_T	0.888	0.89
52_L	136_L	0.885	0.89
11_S	71_W	0.883	0.89
90_E	124_R	0.879	0.88
142_I	177_Y	0.872	0.88
30_G	50_V	0.869	0.88
159_A	170_L	0.867	0.88
179_A	183_L	0.866	0.88
80_T	112_K	0.865	0.88
135_L	181_I	0.859	0.87
89_P	107_R	0.855	0.87
8_V	75_V	0.853	0.87
168_L	171_A	0.852	0.87
26_V	57_F	0.845	0.86
169_V	172_A	0.837	0.86
51_M	135_L	0.836	0.86
123_L	177_Y	0.823	0.85
84_A	103_A	0.819	0.85
56_L	60_I	0.811	0.84
129_W	132_L	0.809	0.84
12_T	75_V	0.806	0.84
136_L	139_L	0.804	0.84
90_E	99_A	0.802	0.83
123_L	181_I	0.801	0.83
70_V	105_D	0.795	0.83
85_P	107_R	0.794	0.83
43_P	131_F	0.789	0.82
81_N	98_W	0.780	0.82
65_Y	113_I	0.775	0.81
119_L	183_L	0.764	0.80
116_W	183_L	0.761	0.80
78_L	86_M	0.758	0.80
103_A	146_P	0.757	0.80
116_W	143_T	0.757	0.80
76_R	109_P	0.755	0.80
113_I	121_R	0.749	0.79
154_E	158_R	0.743	0.78
13_V	20_T	0.735	0.78
26_V	37_F	0.733	0.78
58_L	133_I	0.733	0.78
55_T	119_L	0.733	0.78
160_A	171_A	0.730	0.77
51_M	131_F	0.728	0.77
172_A	175_L	0.717	0.76
157_E	170_L	0.713	0.76
160_A	167_W	0.711	0.75
83_F	117_E	0.710	0.75
167_W	177_Y	0.710	0.75
150_T	160_A	0.707	0.75
7_E	12_T	0.706	0.75
40_P	141_K	0.706	0.75
55_T	59_L	0.703	0.75
133_I	137_A	0.696	0.74
31_A	138_W	0.695	0.74
29_T	123_L	0.694	0.74
18_L	21_T	0.693	0.74
88_R	103_A	0.689	0.73
29_T	106_L	0.687	0.73
34_S	43_P	0.683	0.72
55_T	179_A	0.681	0.72
90_E	94_P	0.679	0.72
132_L	164_I	0.679	0.72
70_V	76_R	0.677	0.72
33_L	37_F	0.676	0.72
35_F	68_Y	0.674	0.71
132_L	171_A	0.672	0.71
117_E	181_I	0.669	0.71
135_L	139_L	0.667	0.71
93_H	96_P	0.665	0.70
90_E	102_L	0.658	0.70
3_L	43_P	0.657	0.69
3_L	28_T	0.655	0.69
32_A	79_E	0.655	0.69
76_R	114_S	0.654	0.69
152_L	164_I	0.653	0.69
4_Y	13_V	0.649	0.69
171_A	175_L	0.649	0.69
18_L	41_E	0.647	0.68
25_A	176_F	0.644	0.68
11_S	16_T	0.644	0.68
55_T	176_F	0.641	0.68
29_T	35_F	0.636	0.67
143_T	155_F	0.634	0.67
120_G	158_R	0.631	0.66
6_G	112_K	0.628	0.66
66_R	137_A	0.628	0.66
38_S	141_K	0.627	0.66
20_T	32_A	0.625	0.66
85_P	105_D	0.623	0.65
13_V	26_V	0.621	0.65
42_A	46_V	0.621	0.65
170_L	178_A	0.620	0.65
15_R	61_E	0.619	0.65
102_L	123_L	0.616	0.65
39_S	130_I	0.613	0.64
109_P	137_A	0.613	0.64
12_T	71_W	0.609	0.64
36_A	47_L	0.609	0.64
175_L	179_A	0.605	0.63
81_N	94_P	0.605	0.63
27_V	31_A	0.603	0.63
4_Y	93_H	0.597	0.62
69_D	73_A	0.594	0.62
51_M	177_Y	0.594	0.62
102_L	129_W	0.594	0.62
172_A	178_A	0.590	0.61
143_T	159_A	0.590	0.61
84_A	89_P	0.590	0.61
89_P	124_R	0.588	0.61
119_L	180_L	0.588	0.61
58_L	62_A	0.587	0.61
113_I	117_E	0.586	0.61
147_T	155_F	0.585	0.61
45_L	142_I	0.585	0.61
44_H	141_K	0.583	0.60
69_D	105_D	0.579	0.60
2_H	6_G	0.579	0.60
149_A	167_W	0.578	0.60
71_W	121_R	0.575	0.59
145_H	158_R	0.572	0.59
7_E	74_R	0.572	0.59
36_A	46_V	0.565	0.58
73_A	76_R	0.564	0.58
29_T	37_F	0.564	0.58
163_P	170_L	0.564	0.58
35_F	38_S	0.560	0.57
123_L	180_L	0.560	0.57
46_V	158_R	0.559	0.57
106_L	138_W	0.558	0.57
73_A	77_L	0.555	0.57
117_E	120_G	0.550	0.56
29_T	77_L	0.548	0.56
159_A	173_G	0.548	0.56
103_A	107_R	0.546	0.55
32_A	67_Y	0.545	0.55
166_G	169_V	0.545	0.55
33_L	137_A	0.543	0.55
21_T	74_R	0.539	0.54
68_Y	118_A	0.538	0.54
76_R	137_A	0.538	0.54
94_P	99_A	0.533	0.54
159_A	167_W	0.529	0.53
55_T	128_L	0.527	0.53
81_N	101_L	0.526	0.53
81_N	105_D	0.526	0.53
131_F	176_F	0.523	0.52
82_F	86_M	0.522	0.52
68_Y	83_F	0.520	0.52
153_A	182_A	0.519	0.52
94_P	119_L	0.515	0.51
139_L	143_T	0.513	0.51
50_V	134_L	0.511	0.51
3_L	7_E	0.509	0.50
136_L	157_E	0.508	0.50
78_L	89_P	0.508	0.50
99_A	112_K	0.503	0.50
1_A	131_F	0.502	0.49
43_P	51_M	0.500	0.49
59_L	105_D	0.500	0.49

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
1zoyC	1	0.4728	18.7	0.959	Contact Map
4k0jA	3	0.3696	16.6	0.96	Contact Map
2h88C	2	0.4783	15.4	0.961	Contact Map
2l8sA	1	0.1467	7.1	0.966	Contact Map
4b03D	5	0.3207	3.5	0.971	Contact Map
2wdqC	1	0.3967	3.2	0.971	Contact Map
4ysxC	1	0.462	3.2	0.972	Contact Map
2k1aA	1	0.1522	2.8	0.972	Contact Map
2m20A	2	0.1196	2.8	0.972	Contact Map
4ytpC	1	0.4783	2.4	0.973	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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