TraU - PFAM28P - GREMLIN Contacts

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TraU - TraU protein

PFAM:	PF06834	Sequences: KFVNPITDICWSCLFPIVIGGVTITANPSSICFCPVRTGIKVGFWEPARLVEVVRTPGCFPSLGGISLSPGLGGLLGGSSAGGGNTTNSGGDGSNLSFYQVHWYGYPLLYWLELLTDFPCPLETTPFDPAYLSELDPLWNDDELAEILNPEALLFGNPIAQAACAADCAAAGFPLDSLFWCAGCWGSVYPRTGFVTQHDGGQASALLAQRALAKLHRQGLVWDTLGADYALCGKYPGPIMEKSQYKWQMLYPVPSTSCHPFGRSTLLWGAGKNPPVKGRQASDEDFAYLLWRKRNCCA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	298 (288)
Sequences:	1735 (1221)
Seq/√Len:	71.9
META:	0.714

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
168_C	184_C	5.303	1.00
204_S	288_Y	4.876	1.00
176_D	243_S	4.811	1.00
10_C	13_C	4.602	1.00
13_C	258_C	4.009	1.00
142_D	194_F	3.276	1.00
101_V	211_A	2.950	1.00
182_A	206_L	2.910	1.00
51_V	103_W	2.872	1.00
161_Q	187_S	2.844	1.00
51_V	208_A	2.756	1.00
18_V	43_G	2.669	1.00
131_Y	136_D	2.636	1.00
164_C	181_C	2.631	1.00
102_H	134_E	2.631	1.00
101_V	207_L	2.527	1.00
173_F	246_K	2.317	1.00
260_P	263_R	2.301	1.00
212_L	261_F	2.294	1.00
182_A	188_V	2.289	1.00
32_C	297_C	2.277	1.00
98_F	193_G	2.255	1.00
247_W	261_F	2.253	1.00
223_D	237_G	2.244	1.00
62_S	287_A	2.142	1.00
169_A	175_L	2.080	1.00
214_K	218_Q	2.041	1.00
133_S	211_A	1.957	1.00
209_Q	261_F	1.946	1.00
191_R	213_A	1.937	1.00
179_F	189_Y	1.933	1.00
225_L	244_Q	1.913	1.00
185_W	205_A	1.906	1.00
138_L	148_L	1.900	1.00
188_V	213_A	1.881	1.00
278_G	284_E	1.873	1.00
255_S	259_H	1.865	1.00
103_W	212_L	1.847	1.00
48_A	292_R	1.825	1.00
133_S	218_Q	1.822	1.00
14_L	291_W	1.822	1.00
230_A	235_Y	1.808	1.00
131_Y	214_K	1.805	1.00
223_D	235_Y	1.765	1.00
105_G	130_A	1.741	1.00
172_G	263_R	1.737	1.00
100_Q	140_N	1.723	1.00
60_F	104_Y	1.706	1.00
138_L	218_Q	1.700	1.00
53_V	204_S	1.680	1.00
18_V	23_T	1.672	1.00
250_L	289_L	1.672	1.00
120_C	296_C	1.660	1.00
18_V	27_N	1.658	1.00
149_N	152_A	1.646	1.00
274_P	277_K	1.634	0.99
185_W	209_Q	1.634	0.99
151_E	217_R	1.629	0.99
206_L	210_R	1.626	0.99
52_E	60_F	1.611	0.99
176_D	241_E	1.604	0.99
104_Y	129_P	1.560	0.99
52_E	62_S	1.542	0.99
201_G	273_N	1.522	0.99
222_W	236_P	1.508	0.99
249_M	272_K	1.497	0.99
54_V	61_P	1.496	0.99
99_Y	200_G	1.483	0.99
74_G	77_G	1.481	0.99
20_G	41_K	1.474	0.99
212_L	247_W	1.471	0.99
101_V	133_S	1.468	0.99
49_R	105_G	1.442	0.99
98_F	140_N	1.441	0.99
4_N	7_T	1.439	0.99
222_W	234_K	1.433	0.99
151_E	179_F	1.397	0.98
169_A	174_P	1.394	0.98
155_F	179_F	1.390	0.98
145_A	192_T	1.389	0.98
33_F	38_T	1.383	0.98
195_V	203_A	1.371	0.98
265_T	269_G	1.338	0.98
27_N	295_N	1.335	0.98
195_V	206_L	1.317	0.98
139_W	193_G	1.313	0.98
182_A	209_Q	1.299	0.97
146_E	149_N	1.299	0.97
70_P	74_G	1.288	0.97
274_P	284_E	1.275	0.97
103_W	211_A	1.263	0.97
213_A	240_M	1.256	0.97
3_V	250_L	1.250	0.97
239_I	245_Y	1.250	0.97
148_L	218_Q	1.248	0.97
20_G	28_P	1.244	0.97
195_V	207_L	1.215	0.96
53_V	101_V	1.207	0.96
97_S	198_H	1.197	0.96
223_D	244_Q	1.197	0.96
60_F	129_P	1.189	0.96
52_E	61_P	1.188	0.96
19_I	24_I	1.185	0.95
189_Y	213_A	1.185	0.95
50_L	62_S	1.183	0.95
195_V	210_R	1.182	0.95
223_D	228_D	1.179	0.95
136_D	214_K	1.177	0.95
209_Q	213_A	1.140	0.94
58_G	132_L	1.137	0.94
211_A	214_K	1.128	0.94
133_S	214_K	1.124	0.94
252_P	297_C	1.119	0.94
152_A	156_G	1.118	0.94
105_G	125_T	1.115	0.94
138_L	145_A	1.098	0.93
50_L	250_L	1.086	0.93
25_T	30_S	1.076	0.92
54_V	102_H	1.067	0.92
60_F	132_L	1.065	0.92
76_L	79_S	1.064	0.92
51_V	247_W	1.058	0.92
248_Q	258_C	1.058	0.92
27_N	41_K	1.057	0.92
142_D	192_T	1.054	0.92
31_I	38_T	1.050	0.92
65_G	68_L	1.046	0.91
207_L	210_R	1.044	0.91
49_R	103_W	1.041	0.91
145_A	194_F	1.028	0.91
224_T	244_Q	1.014	0.90
53_V	288_Y	1.006	0.90
106_Y	289_L	0.999	0.89
27_N	30_S	0.999	0.89
14_L	17_I	0.998	0.89
139_W	210_R	0.993	0.89
62_S	104_Y	0.983	0.89
99_Y	204_S	0.981	0.88
277_K	284_E	0.978	0.88
200_G	204_S	0.973	0.88
57_P	134_E	0.973	0.88
223_D	226_G	0.973	0.88
48_A	224_T	0.968	0.88
192_T	196_T	0.962	0.88
215_L	220_L	0.952	0.87
216_H	245_Y	0.950	0.87
49_R	225_L	0.949	0.87
259_H	268_W	0.945	0.87
237_G	241_E	0.936	0.86
52_E	102_H	0.934	0.86
132_L	135_L	0.931	0.86
191_R	240_M	0.930	0.86
204_S	286_F	0.929	0.86
268_W	272_K	0.919	0.85
12_S	257_S	0.918	0.85
134_E	164_C	0.917	0.85
263_R	267_L	0.912	0.85
49_R	128_D	0.912	0.85
208_A	247_W	0.912	0.85
102_H	181_C	0.911	0.85
5_P	8_D	0.908	0.84
32_C	252_P	0.898	0.84
222_W	235_Y	0.889	0.83
10_C	258_C	0.886	0.83
50_L	106_Y	0.884	0.83
167_D	242_K	0.882	0.83
160_A	163_A	0.880	0.82
192_T	259_H	0.879	0.82
55_R	99_Y	0.878	0.82
195_V	202_Q	0.876	0.82
131_Y	215_L	0.875	0.82
46_E	294_R	0.874	0.82
242_K	245_Y	0.870	0.82
21_G	29_S	0.864	0.81
61_P	104_Y	0.862	0.81
208_A	211_A	0.857	0.81
205_A	288_Y	0.853	0.80
106_Y	151_E	0.849	0.80
223_D	230_A	0.849	0.80
55_R	285_D	0.842	0.80
208_A	290_L	0.838	0.79
198_H	273_N	0.834	0.79
97_S	203_A	0.831	0.79
255_S	272_K	0.830	0.79
2_F	148_L	0.830	0.79
219_G	238_P	0.828	0.78
188_V	240_M	0.828	0.78
114_L	118_F	0.827	0.78
43_G	295_N	0.827	0.78
50_L	287_A	0.825	0.78
185_W	261_F	0.825	0.78
52_E	104_Y	0.824	0.78
113_E	118_F	0.824	0.78
102_H	164_C	0.823	0.78
52_E	287_A	0.822	0.78
103_W	208_A	0.819	0.78
146_E	191_R	0.818	0.78
9_I	108_L	0.818	0.78
5_P	11_W	0.809	0.77
19_I	40_I	0.809	0.77
248_Q	291_W	0.807	0.77
18_V	295_N	0.802	0.76
151_E	167_D	0.797	0.76
53_V	99_Y	0.796	0.76
148_L	214_K	0.792	0.75
26_A	30_S	0.791	0.75
249_M	288_Y	0.788	0.75
98_F	194_F	0.786	0.75
216_H	221_V	0.786	0.75
166_A	169_A	0.784	0.74
59_C	285_D	0.782	0.74
101_V	214_K	0.778	0.74
179_F	248_Q	0.772	0.73
62_S	251_Y	0.768	0.73
135_L	269_G	0.766	0.73
3_V	106_Y	0.764	0.73
241_E	244_Q	0.761	0.72
259_H	263_R	0.761	0.72
8_D	11_W	0.761	0.72
211_A	218_Q	0.759	0.72
131_Y	218_Q	0.758	0.72
139_W	189_Y	0.757	0.72
273_N	286_F	0.754	0.72
188_V	210_R	0.752	0.71
163_A	180_W	0.751	0.71
4_N	11_W	0.747	0.71
177_S	236_P	0.745	0.71
66_I	69_S	0.745	0.71
23_T	30_S	0.744	0.71
212_L	290_L	0.741	0.70
113_E	123_E	0.741	0.70
138_L	144_L	0.739	0.70
134_E	181_C	0.738	0.70
3_V	50_L	0.736	0.70
275_P	278_G	0.736	0.70
59_C	246_K	0.734	0.70
212_L	245_Y	0.734	0.70
147_I	207_L	0.734	0.70
269_G	287_A	0.733	0.69
22_V	26_A	0.728	0.69
146_E	153_L	0.722	0.68
213_A	244_Q	0.721	0.68
104_Y	127_F	0.720	0.68
100_Q	133_S	0.719	0.68
223_D	241_E	0.716	0.68
16_P	19_I	0.714	0.67
255_S	258_C	0.713	0.67
186_G	206_L	0.713	0.67
30_S	177_S	0.712	0.67
164_C	167_D	0.711	0.67
131_Y	138_L	0.711	0.67
218_Q	222_W	0.709	0.67
142_D	145_A	0.709	0.67
46_E	292_R	0.708	0.67
202_Q	265_T	0.705	0.66
198_H	201_G	0.701	0.66
28_P	295_N	0.700	0.66
184_C	264_S	0.699	0.66
26_A	243_S	0.697	0.66
43_G	217_R	0.696	0.65
55_R	284_E	0.695	0.65
41_K	231_L	0.693	0.65
67_S	70_P	0.689	0.65
120_C	193_G	0.688	0.65
137_P	167_D	0.682	0.64
170_A	175_L	0.675	0.63
159_I	162_A	0.675	0.63
103_W	215_L	0.675	0.63
99_Y	207_L	0.671	0.63
19_I	43_G	0.671	0.63
143_E	152_A	0.670	0.62
198_H	203_A	0.670	0.62
244_Q	291_W	0.670	0.62
21_G	261_F	0.668	0.62
5_P	9_I	0.667	0.62
220_L	247_W	0.665	0.62
157_N	164_C	0.665	0.62
53_V	207_L	0.664	0.62
19_I	257_S	0.663	0.62
162_A	165_A	0.663	0.62
185_W	259_H	0.662	0.62
16_P	39_G	0.657	0.61
226_G	235_Y	0.657	0.61
13_C	291_W	0.654	0.61
205_A	209_Q	0.654	0.61
257_S	265_T	0.652	0.60
79_S	83_G	0.652	0.60
14_L	109_L	0.651	0.60
257_S	291_W	0.650	0.60
106_Y	221_V	0.646	0.60
178_L	181_C	0.646	0.60
24_I	28_P	0.645	0.60
65_G	71_G	0.643	0.59
96_L	194_F	0.641	0.59
146_E	161_Q	0.639	0.59
34_C	39_G	0.638	0.59
46_E	122_L	0.638	0.59
246_K	287_A	0.637	0.59
13_C	107_P	0.637	0.59
205_A	268_W	0.636	0.58
149_N	191_R	0.636	0.58
4_N	9_I	0.636	0.58
284_E	288_Y	0.635	0.58
273_N	284_E	0.634	0.58
278_G	285_D	0.632	0.58
47_P	291_W	0.627	0.57
110_Y	113_E	0.627	0.57
51_V	290_L	0.627	0.57
116_T	119_P	0.627	0.57
24_I	270_A	0.623	0.57
209_Q	247_W	0.622	0.57
4_N	8_D	0.621	0.57
274_P	285_D	0.620	0.57
151_E	189_Y	0.620	0.57
161_Q	178_L	0.616	0.56
258_C	296_C	0.616	0.56
105_G	126_P	0.616	0.56
20_G	27_N	0.612	0.56
54_V	98_F	0.612	0.56
251_Y	274_P	0.612	0.56
6_I	132_L	0.611	0.55
106_Y	122_L	0.611	0.55
154_L	164_C	0.607	0.55
221_V	244_Q	0.605	0.55
95_N	196_T	0.604	0.55
58_G	70_P	0.603	0.55
263_R	284_E	0.602	0.54
226_G	295_N	0.602	0.54
30_S	176_D	0.602	0.54
23_T	176_D	0.599	0.54
151_E	164_C	0.594	0.53
92_D	95_N	0.591	0.53
200_G	284_E	0.589	0.53
274_P	278_G	0.586	0.52
169_A	172_G	0.586	0.52
32_C	41_K	0.585	0.52
22_V	29_S	0.581	0.52
64_G	68_L	0.580	0.52
96_L	196_T	0.580	0.52
217_R	238_P	0.578	0.51
18_V	25_T	0.575	0.51
174_P	185_W	0.574	0.51
208_A	261_F	0.567	0.50
39_G	102_H	0.567	0.50
202_Q	206_L	0.565	0.50
188_V	209_Q	0.562	0.49
53_V	208_A	0.560	0.49
17_I	23_T	0.558	0.49
236_P	239_I	0.557	0.49
30_S	250_L	0.556	0.49
71_G	192_T	0.555	0.49
109_L	114_L	0.554	0.48
118_F	123_E	0.551	0.48
136_D	215_L	0.551	0.48
43_G	293_K	0.549	0.48
78_G	82_G	0.548	0.48
200_G	270_A	0.546	0.48
211_A	215_L	0.546	0.48
151_E	191_R	0.546	0.48
2_F	6_I	0.544	0.47
16_P	128_D	0.543	0.47
171_A	231_L	0.542	0.47
128_D	134_E	0.540	0.47
168_C	189_Y	0.539	0.47
134_E	137_P	0.538	0.47
49_R	113_E	0.538	0.47
23_T	174_P	0.537	0.46
293_K	296_C	0.537	0.46
58_G	197_Q	0.536	0.46
50_L	68_L	0.535	0.46
139_W	296_C	0.534	0.46
232_C	262_G	0.533	0.46
77_G	224_T	0.533	0.46
133_S	139_W	0.530	0.46
209_Q	233_G	0.529	0.45
68_L	80_S	0.528	0.45
20_G	295_N	0.526	0.45
190_P	296_C	0.525	0.45
131_Y	135_L	0.525	0.45
254_P	259_H	0.524	0.45
186_G	190_P	0.524	0.45
204_S	249_M	0.523	0.45
288_Y	293_K	0.523	0.45
258_C	291_W	0.523	0.45
18_V	28_P	0.522	0.45
237_G	244_Q	0.522	0.45
26_A	29_S	0.521	0.44
87_T	90_G	0.521	0.44
5_P	250_L	0.521	0.44
31_I	40_I	0.521	0.44
80_S	170_A	0.521	0.44
15_F	43_G	0.520	0.44
13_C	248_Q	0.520	0.44
216_H	237_G	0.519	0.44
30_S	173_F	0.518	0.44
212_L	239_I	0.517	0.44
30_S	41_K	0.517	0.44
153_L	156_G	0.517	0.44
143_E	278_G	0.516	0.44
73_G	77_G	0.516	0.44
39_G	245_Y	0.515	0.44
90_G	95_N	0.515	0.44
22_V	40_I	0.515	0.44
242_K	262_G	0.513	0.43
59_C	128_D	0.513	0.43
49_R	123_E	0.512	0.43
185_W	203_A	0.512	0.43
128_D	151_E	0.512	0.43
26_A	129_P	0.511	0.43
49_R	217_R	0.510	0.43
59_C	217_R	0.509	0.43
77_G	80_S	0.509	0.43
246_K	263_R	0.509	0.43
212_L	221_V	0.508	0.43
205_A	255_S	0.507	0.43
208_A	212_L	0.507	0.43
37_R	294_R	0.507	0.43
82_G	176_D	0.507	0.43
287_A	291_W	0.506	0.43
50_L	176_D	0.506	0.43
224_T	230_A	0.505	0.43
108_L	118_F	0.504	0.42
149_N	153_L	0.503	0.42
170_A	263_R	0.503	0.42
96_L	195_V	0.503	0.42
99_Y	201_G	0.502	0.42
43_G	46_E	0.502	0.42
21_G	30_S	0.501	0.42
61_P	100_Q	0.501	0.42
26_A	175_L	0.501	0.42
226_G	230_A	0.501	0.42
115_L	123_E	0.500	0.42

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
4wwxX	1	0.2819	3.1	0.975	Contact Map
1bzkA	1	0.0906	2	0.978	Contact Map
2jobA	1	0.3389	1.6	0.979	Contact Map
1pq1B	1	0.1107	1.5	0.979	Contact Map
2mi5A	1	0.1409	1.4	0.979	Contact Map
4aybN	1	0.1544	1.4	0.98	Contact Map
3a9bA	1	0.2081	1.3	0.98	Contact Map
4qiwN	1	0.1544	1.3	0.98	Contact Map
1pxqA	1	0.1107	1.3	0.98	Contact Map
4hicA	1	0.198	1.2	0.98	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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