TRAM_LAG1_CLN8 - PFAM28P - GREMLIN Contacts

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TRAM_LAG1_CLN8 - TLC domain

PFAM:	PF03798	Sequences: KFNERGVSLVHYLVSGILGLYVLYDEPELWEGYPDRPLGYTSPLLKFYYLLQLGYFLYDLLVLLFYEKKRKDFWEMLLHHIVTLLLISLSYLFNFTRIGLLVLLLHELSDPFLNLRKLLKYLGGKSKKSCLYLFNGVLFAVSFFVTRLVLFPYLILWSTLDESRLILPTGPFPLYYIFLVLLLVLQVLNIYWFYLILR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	198 (194)
Sequences:	4117 (3064)
Seq/√Len:	220.0
META:	0.298

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
144_F	193_F	4.609	1.00
191_Y	195_L	4.390	1.00
113_L	139_F	3.884	1.00
145_V	149_V	3.226	1.00
52_Q	56_F	2.860	1.00
139_F	196_I	2.701	1.00
49_Y	90_S	2.560	1.00
19_G	48_Y	2.515	1.00
53_L	84_L	2.475	1.00
28_E	31_E	2.329	1.00
144_F	149_V	2.325	1.00
140_A	196_I	2.301	1.00
158_S	162_E	2.268	1.00
136_G	139_F	2.185	1.00
21_Y	25_D	2.101	1.00
157_W	161_D	2.052	1.00
156_L	160_L	2.038	1.00
55_Y	59_D	1.966	1.00
11_H	52_Q	1.942	1.00
144_F	148_L	1.912	1.00
152_P	190_I	1.909	1.00
130_C	134_F	1.860	1.00
187_V	191_Y	1.806	1.00
29_L	32_G	1.781	1.00
36_R	39_G	1.771	1.00
117_K	121_Y	1.769	1.00
148_L	193_F	1.733	1.00
158_S	161_D	1.708	1.00
49_Y	99_G	1.677	1.00
11_H	15_S	1.670	1.00
17_I	21_Y	1.669	1.00
159_T	179_L	1.661	1.00
109_S	143_F	1.642	1.00
107_E	110_D	1.614	1.00
53_L	87_I	1.604	1.00
167_L	170_G	1.592	1.00
8_S	114_N	1.582	1.00
106_H	151_F	1.578	1.00
185_L	189_N	1.572	1.00
157_W	162_E	1.545	1.00
29_L	33_Y	1.531	1.00
106_H	110_D	1.528	1.00
1_K	5_R	1.487	1.00
63_L	66_Y	1.475	1.00
124_G	127_K	1.456	1.00
56_F	59_D	1.448	1.00
120_K	136_G	1.445	1.00
56_F	107_E	1.426	1.00
112_F	138_L	1.423	1.00
34_P	37_P	1.400	1.00
193_F	197_L	1.383	1.00
8_S	12_Y	1.380	1.00
32_G	35_D	1.368	1.00
75_E	188_L	1.359	1.00
78_L	184_V	1.355	1.00
64_L	77_L	1.307	1.00
37_P	40_Y	1.303	1.00
52_Q	59_D	1.293	1.00
8_S	11_H	1.287	1.00
154_L	157_W	1.287	1.00
149_V	152_P	1.262	1.00
109_S	146_T	1.256	1.00
186_Q	190_I	1.251	1.00
188_L	192_W	1.244	1.00
35_D	38_L	1.243	1.00
172_F	175_Y	1.229	1.00
14_V	18_L	1.226	1.00
52_Q	107_E	1.225	1.00
106_H	189_N	1.197	1.00
90_S	99_G	1.192	1.00
5_R	114_N	1.189	1.00
140_A	143_F	1.185	1.00
128_K	132_Y	1.184	1.00
156_L	159_T	1.184	1.00
191_Y	194_Y	1.177	1.00
13_L	111_P	1.160	1.00
178_F	183_L	1.152	1.00
76_M	80_H	1.151	1.00
53_L	88_S	1.146	1.00
155_I	163_S	1.133	1.00
127_K	131_L	1.121	1.00
109_S	142_S	1.112	1.00
50_L	54_G	1.108	1.00
148_L	186_Q	1.099	1.00
20_L	24_Y	1.099	1.00
142_S	146_T	1.089	1.00
183_L	187_V	1.088	1.00
182_L	185_L	1.088	1.00
62_V	66_Y	1.064	1.00
125_K	129_S	1.061	1.00
140_A	197_L	1.060	1.00
20_L	104_L	1.038	1.00
42_S	45_L	1.035	1.00
12_Y	107_E	1.034	1.00
129_S	132_Y	1.032	1.00
9_L	114_N	1.025	1.00
12_Y	110_D	1.017	1.00
110_D	117_K	1.015	1.00
190_I	194_Y	1.008	1.00
13_L	17_I	1.008	1.00
114_N	117_K	1.004	1.00
61_L	65_F	1.001	1.00
14_V	17_I	0.990	1.00
83_T	185_L	0.990	1.00
159_T	162_E	0.981	1.00
6_G	118_L	0.980	1.00
143_F	148_L	0.979	1.00
112_F	139_F	0.959	1.00
5_R	8_S	0.957	1.00
116_R	132_Y	0.950	1.00
138_L	142_S	0.949	1.00
175_Y	178_F	0.945	1.00
75_E	191_Y	0.941	1.00
63_L	80_H	0.937	1.00
137_V	141_V	0.935	1.00
148_L	152_P	0.932	1.00
117_K	120_K	0.928	0.99
60_L	80_H	0.928	0.99
12_Y	56_F	0.922	0.99
74_W	77_L	0.921	0.99
83_T	86_L	0.909	0.99
161_D	165_L	0.906	0.99
113_L	116_R	0.906	0.99
139_F	143_F	0.904	0.99
116_R	120_K	0.904	0.99
60_L	77_L	0.899	0.99
174_L	177_I	0.892	0.99
173_P	177_I	0.880	0.99
127_K	132_Y	0.874	0.99
36_R	40_Y	0.871	0.99
56_F	83_T	0.871	0.99
159_T	163_S	0.866	0.99
186_Q	189_N	0.866	0.99
145_V	150_L	0.861	0.99
139_F	192_W	0.860	0.99
146_T	150_L	0.858	0.99
59_D	114_N	0.856	0.99
108_L	146_T	0.851	0.99
74_W	78_L	0.848	0.99
12_Y	55_Y	0.840	0.99
161_D	164_R	0.832	0.99
30_W	33_Y	0.826	0.99
116_R	136_G	0.823	0.99
87_I	103_L	0.820	0.99
79_H	192_W	0.817	0.99
18_L	48_Y	0.817	0.99
172_F	176_Y	0.808	0.99
168_P	171_P	0.798	0.98
143_F	193_F	0.797	0.98
67_E	70_R	0.795	0.98
76_M	79_H	0.795	0.98
130_C	133_L	0.792	0.98
119_L	129_S	0.792	0.98
58_Y	62_V	0.785	0.98
156_L	183_L	0.780	0.98
192_W	196_I	0.769	0.98
109_S	114_N	0.766	0.98
83_T	87_I	0.765	0.98
80_H	84_L	0.763	0.98
129_S	133_L	0.757	0.98
153_Y	156_L	0.741	0.98
96_T	111_P	0.737	0.97
118_L	122_L	0.737	0.97
110_D	113_L	0.733	0.97
148_L	190_I	0.727	0.97
75_E	78_L	0.724	0.97
114_N	118_L	0.722	0.97
80_H	83_T	0.721	0.97
8_S	59_D	0.717	0.97
115_L	133_L	0.714	0.97
112_F	142_S	0.710	0.97
166_I	169_T	0.706	0.97
62_V	65_F	0.706	0.97
43_P	47_F	0.706	0.97
175_Y	179_L	0.703	0.97
155_I	182_L	0.701	0.97
102_V	110_D	0.690	0.96
38_L	43_P	0.689	0.96
22_V	25_D	0.687	0.96
60_L	84_L	0.684	0.96
174_L	179_L	0.682	0.96
7_V	11_H	0.678	0.96
57_L	84_L	0.676	0.96
35_D	39_G	0.675	0.96
153_Y	157_W	0.674	0.96
79_H	83_T	0.672	0.96
80_H	106_H	0.664	0.95
157_W	164_R	0.663	0.95
5_R	11_H	0.660	0.95
88_S	92_L	0.660	0.95
167_L	171_P	0.659	0.95
173_P	179_L	0.659	0.95
181_L	184_V	0.659	0.95
34_P	38_L	0.659	0.95
166_I	170_G	0.657	0.95
18_L	44_L	0.656	0.95
144_F	197_L	0.654	0.95
56_F	110_D	0.652	0.95
50_L	91_Y	0.652	0.95
162_E	165_L	0.651	0.95
19_G	22_V	0.650	0.95
116_R	133_L	0.649	0.95
86_L	90_S	0.647	0.95
111_P	114_N	0.638	0.94
21_Y	44_L	0.635	0.94
160_L	163_S	0.633	0.94
28_E	32_G	0.633	0.94
73_F	143_F	0.633	0.94
176_Y	180_V	0.632	0.94
63_L	77_L	0.625	0.94
140_A	193_F	0.624	0.94
41_T	44_L	0.623	0.93
114_N	143_F	0.622	0.93
172_F	197_L	0.620	0.93
87_I	185_L	0.620	0.93
23_L	26_E	0.619	0.93
117_K	136_G	0.619	0.93
179_L	183_L	0.617	0.93
99_G	102_V	0.612	0.93
19_G	104_L	0.612	0.93
23_L	27_P	0.611	0.93
18_L	22_V	0.608	0.93
85_L	89_L	0.606	0.93
10_V	13_L	0.605	0.92
113_L	136_G	0.604	0.92
2_F	118_L	0.601	0.92
119_L	133_L	0.597	0.92
119_L	125_K	0.595	0.92
33_Y	37_P	0.594	0.92
76_M	143_F	0.590	0.92
16_G	108_L	0.589	0.91
160_L	164_R	0.588	0.91
103_L	151_F	0.584	0.91
15_S	18_L	0.580	0.91
76_M	110_D	0.580	0.91
115_L	164_R	0.575	0.90
26_E	44_L	0.575	0.90
129_S	134_F	0.575	0.90
6_G	9_L	0.572	0.90
57_L	194_Y	0.572	0.90
9_L	115_L	0.569	0.90
99_G	103_L	0.567	0.90
49_Y	91_Y	0.566	0.90
4_E	7_V	0.562	0.89
7_V	58_Y	0.560	0.89
152_P	192_W	0.558	0.89
77_L	84_L	0.558	0.89
164_R	167_L	0.553	0.89
113_L	196_I	0.553	0.89
79_H	113_L	0.551	0.89
16_G	19_G	0.548	0.88
108_L	142_S	0.548	0.88
3_N	115_L	0.548	0.88
9_L	13_L	0.546	0.88
24_Y	27_P	0.546	0.88
106_H	117_K	0.541	0.88
16_G	20_L	0.541	0.88
58_Y	80_H	0.540	0.88
5_R	12_Y	0.538	0.87
151_F	186_Q	0.534	0.87
8_S	55_Y	0.533	0.87
168_P	173_P	0.531	0.87
49_Y	100_L	0.531	0.87
110_D	114_N	0.529	0.86
152_P	186_Q	0.526	0.86
12_Y	16_G	0.525	0.86
9_L	118_L	0.524	0.86
73_F	77_L	0.524	0.86
53_L	91_Y	0.524	0.86
130_C	137_V	0.524	0.86
151_F	155_I	0.522	0.86
67_E	71_K	0.522	0.86
60_L	81_I	0.522	0.86
20_L	25_D	0.520	0.86
59_D	64_L	0.517	0.85
33_Y	36_R	0.517	0.85
52_Q	103_L	0.515	0.85
150_L	153_Y	0.514	0.85
183_L	186_Q	0.514	0.85
159_T	165_L	0.513	0.85
132_Y	136_G	0.513	0.85
143_F	151_F	0.513	0.85
111_P	142_S	0.512	0.85
106_H	188_L	0.511	0.85
165_L	171_P	0.510	0.84
166_I	171_P	0.508	0.84
170_G	177_I	0.506	0.84
159_T	164_R	0.504	0.84
119_L	132_Y	0.504	0.84
106_H	148_L	0.504	0.84
104_L	108_L	0.500	0.83

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
5a63D	1	0.1919	1.7	0.944	Contact Map
4izzA	2	0.298	0.6	0.957	Contact Map
2irfG	1	0.1919	0.6	0.958	Contact Map
4d2gD	1	0.0606	0.6	0.959	Contact Map
4pgrA	1	0.4495	0.6	0.959	Contact Map
3qu6A	1	0.1818	0.6	0.959	Contact Map
2nr9A	2	0.3788	0.5	0.961	Contact Map
2k2wA	1	0.202	0.5	0.961	Contact Map
3ap1A	2	0.2576	0.5	0.961	Contact Map
2xovA	1	0.3687	0.5	0.962	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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