Intg_mem_TP0381 - PFAM28P - GREMLIN Contacts

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Intg_mem_TP0381 - Integral membrane protein (intg_mem_TP0381)

PFAM:	PF09529	Sequences: LFGPSHLIALALIILLIVLLVLLGRRLRRKPERKRRRIRRILAILLLLNEIAWQIWLLLTGGWSLQESLPLHLCDIAALLAAIALLTKNRRLFEFLYFWGLAGALQALLTPDLLGYGFPHFRFFQFFISHGLIVLAALYLVFVLGYRPTWKSLLRVFLILNIYAVIVGLVNLLLGTNYMFLNEKPEGASLLDPIADLLGPWPWYILVLELLALVLFLLLYLLYY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	224 (214)
Sequences:	6546 (5310)
Seq/√Len:	363.0
META:	0.863

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
161_N	209_E	4.487	1.00
93_F	141_V	4.064	1.00
94_E	152_S	2.956	1.00
170_V	174_L	2.917	1.00
13_I	131_G	2.857	1.00
7_L	11_A	2.651	1.00
171_N	176_T	2.401	1.00
188_A	192_D	2.337	1.00
36_R	40_R	2.286	1.00
41_I	45_L	2.268	1.00
99_W	160_L	2.256	1.00
138_L	142_F	2.209	1.00
167_V	170_V	2.185	1.00
10_L	108_L	2.183	1.00
102_A	215_L	2.144	1.00
9_A	123_F	2.091	1.00
168_G	182_N	2.062	1.00
74_C	103_G	2.061	1.00
168_G	172_L	2.018	1.00
95_F	99_W	1.999	1.00
199_G	207_V	1.981	1.00
165_V	169_L	1.968	1.00
37_R	41_I	1.926	1.00
5_S	117_G	1.922	1.00
154_L	158_L	1.921	1.00
79_L	83_I	1.899	1.00
47_L	82_A	1.893	1.00
94_E	155_R	1.891	1.00
171_N	182_N	1.883	1.00
151_K	155_R	1.866	1.00
139_Y	143_V	1.852	1.00
163_Y	179_M	1.824	1.00
83_I	92_L	1.818	1.00
50_E	53_W	1.808	1.00
151_K	154_L	1.782	1.00
40_R	86_L	1.764	1.00
169_L	173_L	1.752	1.00
90_R	94_E	1.745	1.00
40_R	44_I	1.664	1.00
44_I	48_L	1.648	1.00
4_P	8_I	1.619	1.00
189_S	192_D	1.598	1.00
201_W	204_Y	1.588	1.00
24_G	27_L	1.587	1.00
116_Y	120_H	1.574	1.00
160_L	164_A	1.552	1.00
83_I	87_T	1.542	1.00
106_Q	110_T	1.520	1.00
32_E	35_R	1.514	1.00
21_V	24_G	1.506	1.00
81_A	136_A	1.504	1.00
80_L	92_L	1.503	1.00
119_P	124_F	1.495	1.00
13_I	17_I	1.492	1.00
150_W	154_L	1.486	1.00
84_A	140_L	1.480	1.00
54_Q	63_W	1.480	1.00
169_L	172_L	1.480	1.00
18_V	22_L	1.479	1.00
149_T	152_S	1.470	1.00
17_I	135_L	1.453	1.00
33_R	37_R	1.451	1.00
17_I	21_V	1.423	1.00
31_P	34_K	1.409	1.00
90_R	152_S	1.408	1.00
53_W	57_L	1.402	1.00
89_N	92_L	1.389	1.00
172_L	182_N	1.372	1.00
3_G	7_L	1.356	1.00
16_L	135_L	1.319	1.00
43_A	82_A	1.310	1.00
107_A	126_F	1.300	1.00
168_G	181_L	1.245	1.00
156_V	160_L	1.240	1.00
93_F	146_Y	1.237	1.00
198_L	207_V	1.235	1.00
66_Q	176_T	1.224	1.00
166_I	169_L	1.222	1.00
163_Y	167_V	1.221	1.00
93_F	140_L	1.213	1.00
97_Y	219_L	1.182	1.00
168_G	171_N	1.182	1.00
63_W	68_S	1.168	1.00
77_A	104_A	1.166	1.00
81_A	96_L	1.156	1.00
210_L	214_V	1.142	1.00
207_V	210_L	1.126	1.00
64_S	67_E	1.122	1.00
91_R	159_I	1.121	1.00
157_F	161_N	1.086	1.00
206_L	210_L	1.085	1.00
49_N	52_A	1.081	1.00
50_E	54_Q	1.080	1.00
121_F	125_Q	1.074	1.00
49_N	53_W	1.074	1.00
22_L	26_R	1.071	1.00
183_E	186_E	1.068	1.00
102_A	105_L	1.067	1.00
90_R	149_T	1.065	1.00
184_K	192_D	1.058	1.00
212_A	216_F	1.053	1.00
35_R	39_R	1.053	1.00
51_I	55_I	1.052	1.00
164_A	179_M	1.035	1.00
43_A	85_L	1.033	1.00
34_K	38_I	1.012	1.00
164_A	181_L	1.009	1.00
52_A	121_F	1.006	1.00
84_A	96_L	1.000	1.00
14_I	17_I	0.998	1.00
30_K	34_K	0.996	1.00
150_W	217_L	0.976	1.00
52_A	55_I	0.970	1.00
49_N	129_S	0.969	1.00
84_A	92_L	0.965	1.00
77_A	80_L	0.964	1.00
74_C	133_I	0.961	1.00
8_I	12_L	0.956	1.00
98_F	152_S	0.955	1.00
171_N	181_L	0.940	1.00
25_R	28_R	0.939	1.00
95_F	159_I	0.938	1.00
158_L	162_I	0.932	1.00
175_G	182_N	0.931	1.00
50_E	78_A	0.931	1.00
158_L	161_N	0.920	1.00
162_I	166_I	0.906	1.00
55_I	59_L	0.903	1.00
16_L	20_L	0.902	1.00
84_A	93_F	0.901	1.00
203_W	206_L	0.899	1.00
68_S	178_Y	0.897	1.00
159_I	162_I	0.894	1.00
215_L	219_L	0.893	1.00
100_G	133_I	0.893	1.00
101_L	134_V	0.889	1.00
74_C	130_H	0.884	1.00
91_R	155_R	0.881	1.00
104_A	134_V	0.877	1.00
72_H	107_A	0.864	1.00
49_N	125_Q	0.851	1.00
39_R	42_L	0.847	1.00
42_L	49_N	0.845	1.00
73_L	103_G	0.842	1.00
108_L	131_G	0.829	1.00
9_A	127_F	0.827	1.00
72_H	179_M	0.826	1.00
58_L	63_W	0.826	1.00
56_W	116_Y	0.822	1.00
118_F	123_F	0.816	1.00
112_D	180_F	0.814	1.00
107_A	111_P	0.813	1.00
57_L	68_S	0.813	1.00
53_W	125_Q	0.808	1.00
69_L	178_Y	0.807	1.00
14_I	18_V	0.806	1.00
50_E	79_L	0.806	1.00
26_R	29_R	0.805	1.00
154_L	157_F	0.804	1.00
50_E	125_Q	0.798	1.00
164_A	168_G	0.796	1.00
40_R	43_A	0.793	1.00
72_H	75_D	0.792	1.00
77_A	99_W	0.787	1.00
30_K	33_R	0.783	1.00
75_D	125_Q	0.780	1.00
203_W	207_V	0.776	1.00
41_I	44_I	0.772	1.00
38_I	41_I	0.771	1.00
47_L	50_E	0.766	1.00
104_A	133_I	0.759	1.00
9_A	12_L	0.757	1.00
36_R	39_R	0.756	1.00
81_A	137_A	0.753	1.00
39_R	139_Y	0.753	1.00
217_L	220_Y	0.741	1.00
157_F	209_E	0.740	1.00
39_R	88_K	0.738	1.00
34_K	37_R	0.731	1.00
98_F	148_P	0.724	1.00
205_I	209_E	0.724	1.00
90_R	146_Y	0.722	1.00
211_L	214_V	0.722	1.00
71_L	167_V	0.719	0.99
122_R	125_Q	0.717	0.99
33_R	40_R	0.715	0.99
85_L	136_A	0.713	0.99
33_R	36_R	0.709	0.99
82_A	86_L	0.709	0.99
153_L	217_L	0.706	0.99
106_Q	189_S	0.704	0.99
106_Q	190_L	0.701	0.99
45_L	49_N	0.699	0.99
198_L	202_P	0.699	0.99
71_L	178_Y	0.697	0.99
108_L	134_V	0.695	0.99
105_L	109_L	0.695	0.99
153_L	157_F	0.695	0.99
23_L	27_L	0.694	0.99
9_A	13_I	0.694	0.99
15_L	19_L	0.692	0.99
71_L	76_I	0.691	0.99
2_F	9_A	0.689	0.99
140_L	144_L	0.685	0.99
209_E	213_L	0.683	0.99
118_F	124_F	0.681	0.99
155_R	158_L	0.679	0.99
18_V	21_V	0.679	0.99
83_I	89_N	0.678	0.99
54_Q	57_L	0.678	0.99
112_D	115_G	0.678	0.99
22_L	25_R	0.673	0.99
112_D	187_G	0.673	0.99
28_R	31_P	0.672	0.99
136_A	140_L	0.668	0.99
182_N	204_Y	0.666	0.99
141_V	145_G	0.664	0.99
171_N	178_Y	0.662	0.99
88_K	144_L	0.662	0.99
39_R	144_L	0.659	0.99
44_I	86_L	0.658	0.99
73_L	99_W	0.656	0.99
206_L	209_E	0.656	0.99
71_L	170_V	0.655	0.99
13_I	24_G	0.648	0.99
97_Y	141_V	0.646	0.99
100_G	137_A	0.645	0.99
43_A	46_L	0.641	0.99
12_L	16_L	0.637	0.99
190_L	197_L	0.636	0.99
198_L	209_E	0.636	0.99
200_P	207_V	0.635	0.99
161_N	165_V	0.630	0.99
50_E	57_L	0.630	0.99
20_L	24_G	0.628	0.99
22_L	27_L	0.628	0.99
5_S	9_A	0.625	0.99
67_E	176_T	0.620	0.99
9_A	131_G	0.615	0.98
152_S	156_V	0.613	0.98
97_Y	148_P	0.611	0.98
21_V	142_F	0.607	0.98
184_K	191_L	0.606	0.98
39_R	43_A	0.604	0.98
49_N	128_I	0.601	0.98
54_Q	125_Q	0.601	0.98
110_T	123_F	0.597	0.98
124_F	128_I	0.592	0.98
163_Y	166_I	0.590	0.98
187_G	190_L	0.589	0.98
6_H	10_L	0.586	0.98
157_F	213_L	0.584	0.98
146_Y	152_S	0.581	0.98
42_L	132_L	0.580	0.98
150_W	220_Y	0.580	0.98
58_L	61_G	0.579	0.98
37_R	40_R	0.576	0.98
31_P	35_R	0.576	0.98
170_V	178_Y	0.575	0.98
139_Y	144_L	0.574	0.98
58_L	62_G	0.574	0.98
103_G	133_I	0.574	0.98
102_A	106_Q	0.571	0.97
48_L	52_A	0.570	0.97
94_E	98_F	0.570	0.97
211_L	215_L	0.568	0.97
117_G	123_F	0.568	0.97
13_I	16_L	0.567	0.97
76_I	167_V	0.566	0.97
207_V	211_L	0.566	0.97
11_A	15_L	0.566	0.97
177_N	183_E	0.565	0.97
102_A	219_L	0.564	0.97
170_V	176_T	0.564	0.97
70_P	180_F	0.563	0.97
100_G	104_A	0.562	0.97
200_P	203_W	0.562	0.97
78_A	129_S	0.561	0.97
167_V	179_M	0.560	0.97
119_P	123_F	0.560	0.97
84_A	136_A	0.558	0.97
73_L	160_L	0.558	0.97
93_F	137_A	0.558	0.97
53_W	122_R	0.556	0.97
207_V	212_A	0.551	0.97
44_I	51_I	0.545	0.97
11_A	14_I	0.543	0.97
152_S	155_R	0.542	0.97
35_R	139_Y	0.537	0.96
68_S	176_T	0.536	0.96
166_I	170_V	0.536	0.96
77_A	133_I	0.535	0.96
61_G	64_S	0.535	0.96
20_L	135_L	0.535	0.96
201_W	205_I	0.534	0.96
214_V	218_L	0.534	0.96
22_L	30_K	0.532	0.96
53_W	56_W	0.530	0.96
19_L	22_L	0.529	0.96
89_N	93_F	0.528	0.96
56_W	120_H	0.527	0.96
156_V	159_I	0.527	0.96
97_Y	146_Y	0.526	0.96
74_C	107_A	0.526	0.96
52_A	57_L	0.520	0.96
8_I	11_A	0.519	0.96
55_I	58_L	0.518	0.96
18_V	24_G	0.516	0.95
165_V	168_G	0.515	0.95
77_A	126_F	0.511	0.95
57_L	121_F	0.511	0.95
4_P	10_L	0.507	0.95
105_L	187_G	0.505	0.95
184_K	200_P	0.504	0.95
77_A	100_G	0.504	0.95
44_I	47_L	0.503	0.95
78_A	125_Q	0.501	0.95
101_L	137_A	0.501	0.95
75_D	180_F	0.501	0.95
72_H	112_D	0.500	0.95
97_Y	153_L	0.500	0.95

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
5a2fA	1	0	3.3	0.947	Contact Map
2ks1B	1	0.1473	3	0.948	Contact Map
2l2tA	2	0.1518	2.8	0.949	Contact Map
2kv5A	1	0.1473	2.8	0.949	Contact Map
4oh3A	2	0.1875	2.4	0.951	Contact Map
3mk7C	2	0.317	2.1	0.952	Contact Map
2jwaA	2	0.1429	2	0.953	Contact Map
2rddB	1	0.1607	1.8	0.954	Contact Map
4u0qB	1	0	1.5	0.956	Contact Map
1fftA	1	0	1.4	0.957	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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