Trp_oprn_chp - PFAM28P - GREMLIN Contacts

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Trp_oprn_chp - Tryptophan-associated transmembrane protein (Trp_oprn_chp)

PFAM:	PF09534	Sequences: VLLLAAGAALALLASRQTWATVTVADGLGPPVTVTVTGADAAPALTALALVALAAAVAVLATRGVGRRVVGVLLALAGAGAAAAAVAGLADPAAAARAAAAAATGVAGGVAAVSVTAWPWLALAGGVLLLAAGVLALRRGRRWPAMSSRYERPAARRAAAAAADDPRDLWDALDRGEDPT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	180 (179)
Sequences:	2462 (1876)
Seq/√Len:	140.2
META:	0.657

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_A	129_L	4.436	1.00
7_G	125_G	3.990	1.00
51_V	77_A	3.901	1.00
68_R	141_R	3.718	1.00
11_A	81_A	3.504	1.00
71_G	133_G	3.370	1.00
7_G	132_A	3.335	1.00
78_G	126_G	3.015	1.00
78_G	133_G	2.675	1.00
78_G	130_L	2.642	1.00
17_Q	118_W	2.433	1.00
82_A	126_G	2.346	1.00
168_D	171_D	2.265	1.00
55_A	74_L	2.238	1.00
59_V	136_A	2.234	1.00
120_W	124_A	2.175	1.00
71_G	136_A	2.168	1.00
85_A	126_G	2.087	1.00
9_A	13_L	2.046	1.00
74_L	133_G	1.999	1.00
64_G	68_R	1.977	1.00
81_A	126_G	1.941	1.00
76_L	80_G	1.927	1.00
10_L	125_G	1.914	1.00
26_D	29_G	1.839	1.00
4_L	56_A	1.820	1.00
14_A	122_A	1.816	1.00
140_G	143_W	1.816	1.00
58_A	61_A	1.783	1.00
65_V	69_V	1.753	1.00
10_L	13_L	1.748	1.00
8_A	52_A	1.748	1.00
61_A	146_M	1.706	1.00
171_D	174_D	1.701	1.00
71_G	137_L	1.542	1.00
3_L	132_A	1.540	1.00
42_A	84_A	1.451	1.00
72_V	76_L	1.411	1.00
86_V	123_L	1.409	1.00
172_A	177_E	1.408	1.00
18_T	21_T	1.403	1.00
127_V	131_A	1.400	1.00
48_L	80_G	1.386	1.00
11_A	125_G	1.379	1.00
19_W	38_G	1.332	1.00
8_A	53_L	1.329	1.00
42_A	45_L	1.314	1.00
165_D	168_D	1.313	1.00
68_R	140_G	1.311	1.00
18_T	37_T	1.293	1.00
66_G	70_V	1.282	1.00
37_T	40_D	1.275	1.00
167_R	171_D	1.258	1.00
5_A	9_A	1.246	1.00
75_A	130_L	1.228	1.00
50_L	54_A	1.211	1.00
86_V	89_L	1.204	1.00
176_G	179_P	1.201	1.00
52_A	78_G	1.198	1.00
176_G	180_T	1.175	1.00
54_A	58_A	1.163	0.99
75_A	133_G	1.161	0.99
45_L	55_A	1.160	0.99
89_L	92_P	1.155	0.99
85_A	122_A	1.136	0.99
45_L	77_A	1.108	0.99
62_T	70_V	1.101	0.99
78_G	129_L	1.099	0.99
118_W	143_W	1.088	0.99
65_V	68_R	1.086	0.99
165_D	169_L	1.069	0.99
120_W	123_L	1.068	0.99
6_A	10_L	1.068	0.99
78_G	85_A	1.067	0.99
101_A	104_T	1.065	0.99
4_L	132_A	1.065	0.99
63_R	145_A	1.063	0.99
96_A	100_A	1.058	0.99
15_S	45_L	1.054	0.99
36_V	100_A	1.052	0.99
83_A	87_A	1.049	0.99
101_A	105_G	1.047	0.99
7_G	128_L	1.044	0.99
14_A	125_G	1.044	0.99
129_L	132_A	1.029	0.99
21_T	35_T	1.028	0.99
109_G	112_A	1.019	0.99
88_G	92_P	1.015	0.99
164_D	168_D	0.995	0.98
47_A	58_A	0.992	0.98
80_G	84_A	0.988	0.98
156_R	161_A	0.975	0.98
131_A	134_V	0.973	0.98
96_A	99_A	0.960	0.98
7_G	129_L	0.946	0.98
157_R	163_A	0.930	0.97
85_A	123_L	0.922	0.97
62_T	66_G	0.909	0.97
12_L	46_T	0.905	0.97
111_A	114_S	0.892	0.97
58_A	98_A	0.887	0.97
44_A	84_A	0.883	0.97
92_P	95_A	0.880	0.96
23_T	27_G	0.880	0.96
49_A	59_V	0.876	0.96
24_V	27_G	0.873	0.96
84_A	87_A	0.864	0.96
82_A	86_V	0.864	0.96
125_G	132_A	0.860	0.96
169_L	173_L	0.859	0.96
43_P	118_W	0.853	0.96
54_A	57_V	0.852	0.96
71_G	78_G	0.850	0.96
109_G	113_V	0.849	0.96
50_L	119_P	0.848	0.96
158_A	161_A	0.835	0.95
47_A	51_V	0.835	0.95
13_L	17_Q	0.828	0.95
75_A	137_L	0.825	0.95
27_G	30_P	0.820	0.95
60_L	68_R	0.815	0.95
2_L	161_A	0.815	0.95
126_G	130_L	0.811	0.94
8_A	56_A	0.802	0.94
158_A	164_D	0.801	0.94
45_L	56_A	0.800	0.94
18_T	35_T	0.800	0.94
166_P	175_R	0.791	0.94
51_V	55_A	0.789	0.94
105_G	108_G	0.789	0.94
166_P	171_D	0.788	0.94
135_L	139_R	0.785	0.93
110_V	114_S	0.779	0.93
62_T	146_M	0.772	0.93
50_L	60_L	0.768	0.93
67_R	143_W	0.766	0.93
53_L	57_V	0.764	0.93
81_A	129_L	0.761	0.92
36_V	41_A	0.761	0.92
55_A	77_A	0.761	0.92
166_P	169_L	0.759	0.92
6_A	156_R	0.755	0.92
72_V	137_L	0.747	0.92
99_A	102_A	0.746	0.92
60_L	177_E	0.742	0.91
74_L	129_L	0.739	0.91
24_V	32_V	0.730	0.91
5_A	56_A	0.728	0.91
130_L	133_G	0.725	0.90
146_M	150_Y	0.718	0.90
98_A	131_A	0.717	0.90
70_V	113_V	0.716	0.90
7_G	52_A	0.713	0.90
114_S	148_S	0.705	0.89
46_T	50_L	0.703	0.89
60_L	80_G	0.700	0.89
159_A	163_A	0.700	0.89
157_R	161_A	0.695	0.89
85_A	89_L	0.693	0.88
170_W	178_D	0.691	0.88
12_L	17_Q	0.691	0.88
51_V	57_V	0.690	0.88
2_L	173_L	0.685	0.88
92_P	96_A	0.684	0.88
8_A	12_L	0.682	0.88
93_A	97_R	0.681	0.88
11_A	49_A	0.680	0.87
45_L	119_P	0.680	0.87
52_A	74_L	0.677	0.87
91_D	94_A	0.673	0.87
153_P	156_R	0.671	0.87
61_A	149_R	0.667	0.86
160_A	163_A	0.667	0.86
22_V	28_L	0.665	0.86
82_A	123_L	0.665	0.86
138_R	142_R	0.663	0.86
47_A	54_A	0.655	0.85
17_Q	143_W	0.654	0.85
153_P	157_R	0.651	0.85
101_A	106_V	0.650	0.85
120_W	127_V	0.644	0.84
105_G	113_V	0.643	0.84
167_R	174_D	0.642	0.84
73_L	76_L	0.636	0.84
136_A	143_W	0.629	0.83
11_A	126_G	0.625	0.83
170_W	176_G	0.622	0.82
60_L	64_G	0.618	0.82
52_A	81_A	0.616	0.82
59_V	143_W	0.613	0.81
93_A	138_R	0.612	0.81
53_L	67_R	0.611	0.81
16_R	49_A	0.611	0.81
144_P	147_S	0.611	0.81
8_A	129_L	0.609	0.81
15_S	55_A	0.605	0.81
154_A	159_A	0.604	0.80
163_A	168_D	0.604	0.80
69_V	72_V	0.599	0.80
3_L	131_A	0.598	0.80
156_R	160_A	0.596	0.80
49_A	53_L	0.596	0.80
63_R	66_G	0.589	0.79
55_A	80_G	0.584	0.78
132_A	147_S	0.584	0.78
161_A	164_D	0.583	0.78
55_A	62_T	0.580	0.78
3_L	72_V	0.578	0.78
133_G	137_L	0.578	0.78
22_V	96_A	0.576	0.77
94_A	98_A	0.576	0.77
5_A	152_R	0.574	0.77
82_A	127_V	0.574	0.77
156_R	169_L	0.570	0.77
104_T	109_G	0.564	0.76
171_D	175_R	0.564	0.76
4_L	149_R	0.561	0.75
173_L	179_P	0.561	0.75
18_T	157_R	0.560	0.75
18_T	99_A	0.558	0.75
64_G	140_G	0.557	0.75
60_L	153_P	0.556	0.75
147_S	152_R	0.555	0.75
3_L	128_L	0.554	0.75
38_G	69_V	0.551	0.74
22_V	36_V	0.551	0.74
57_V	145_A	0.549	0.74
16_R	39_A	0.549	0.74
164_D	171_D	0.548	0.74
50_L	156_R	0.547	0.74
90_A	123_L	0.545	0.73
26_D	30_P	0.544	0.73
14_A	144_P	0.543	0.73
104_T	108_G	0.541	0.73
63_R	67_R	0.541	0.73
2_L	9_A	0.540	0.73
106_V	109_G	0.540	0.73
56_A	62_T	0.539	0.73
158_A	163_A	0.535	0.72
45_L	84_A	0.533	0.72
146_M	151_E	0.531	0.71
3_L	18_T	0.529	0.71
25_A	29_G	0.529	0.71
170_W	180_T	0.525	0.71
21_T	33_T	0.525	0.71
21_T	107_A	0.522	0.70
52_A	80_G	0.520	0.70
23_T	28_L	0.520	0.70
12_L	140_G	0.520	0.70
7_G	14_A	0.520	0.70
51_V	118_W	0.519	0.70
61_A	70_V	0.518	0.70
131_A	135_L	0.516	0.69
137_L	141_R	0.514	0.69
13_L	121_L	0.513	0.69
103_A	106_V	0.513	0.69
108_G	113_V	0.512	0.69
80_G	83_A	0.512	0.69
37_T	41_A	0.512	0.69
43_P	59_V	0.511	0.69
6_A	83_A	0.511	0.69
20_A	39_A	0.510	0.68
123_L	126_G	0.508	0.68
38_G	41_A	0.504	0.67
12_L	16_R	0.504	0.67
110_V	113_V	0.504	0.67
170_W	179_P	0.500	0.67
86_V	94_A	0.500	0.67

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
2m20A	2	0.3167	16.2	0.919	Contact Map
2kncB	1	0.3444	5.6	0.934	Contact Map
2l2tA	2	0.2389	4.6	0.937	Contact Map
2kncA	1	0.2944	3.5	0.94	Contact Map
3wdoA	1	0.9556	3.4	0.941	Contact Map
2ks1B	1	0.2333	2.7	0.944	Contact Map
3iozB	1	0.0444	1.8	0.949	Contact Map
2kluA	1	0.3889	1.8	0.949	Contact Map
1iijA	1	0.1889	1.3	0.953	Contact Map
4a01A	2	0.2333	1.2	0.954	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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