Thermopsin - PFAM28P - GREMLIN Contacts

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Thermopsin - Thermopsin

PFAM:	PF05317	Sequences: SVNVYPLYSSEPAPMGIADYGLGNNSGSLVPYSYNTSSVLGTVNINSLSAYNSSPPGPYGASLQLNAVLVVVTGGGSYYYWVQNVAFFNTSTNTLSFVDNIWNFSSPSANLSNSTISGNGTVYNSGGGGYYYAYGPTYFTLSLPFTLYLYINVSVTSNGVPEVYFGYSVDGGSGWYDNVTFNSPGGVSAYFLVSGYNYTPSGLPYDAELVLGGPGGGSTTTFNSLNATLALYYWNGGNYQPVPSAYNFGSDTAETASNV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	259 (253)
Sequences:	513 (417)
Seq/√Len:	26.2
META:	0.805

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_S	239_Y	4.074	1.00
82_V	191_F	3.801	1.00
65_L	231_L	3.389	1.00
166_G	175_W	3.265	1.00
34_Y	39_V	3.128	1.00
67_A	151_I	3.096	1.00
165_F	179_V	2.986	1.00
101_I	179_V	2.885	1.00
34_Y	193_V	2.787	1.00
242_V	245_A	2.750	1.00
41_G	209_L	2.651	0.99
20_Y	250_S	2.607	0.99
67_A	207_A	2.606	0.99
38_S	152_N	2.558	0.99
66_N	83_Q	2.537	0.99
48_L	61_A	2.530	0.99
151_I	191_F	2.426	0.99
82_V	151_I	2.350	0.98
39_V	207_A	2.252	0.98
68_V	104_F	2.175	0.97
204_P	251_D	2.166	0.97
105_S	200_P	2.163	0.97
39_V	193_V	2.119	0.97
79_Y	205_Y	2.112	0.97
45_I	227_A	2.106	0.97
84_N	176_Y	2.023	0.96
86_A	147_L	2.000	0.96
162_E	180_T	1.997	0.96
66_N	252_T	1.958	0.95
8_Y	13_A	1.938	0.95
199_T	203_L	1.905	0.94
193_V	207_A	1.886	0.94
99_D	220_T	1.875	0.94
52_N	220_T	1.869	0.94
209_L	229_L	1.857	0.93
19_D	32_Y	1.855	0.93
219_T	255_T	1.822	0.93
35_N	192_L	1.820	0.93
33_S	194_S	1.819	0.93
116_I	122_V	1.798	0.92
97_F	247_N	1.783	0.92
45_I	48_L	1.773	0.92
215_G	218_S	1.767	0.92
99_D	177_D	1.741	0.91
199_T	205_Y	1.735	0.91
123_Y	133_A	1.720	0.90
222_F	225_L	1.708	0.90
84_N	116_I	1.615	0.87
43_V	147_L	1.588	0.86
64_Q	83_Q	1.567	0.86
68_V	79_Y	1.554	0.85
16_G	21_G	1.554	0.85
83_Q	254_E	1.543	0.85
48_L	211_L	1.528	0.84
22_L	31_P	1.504	0.83
214_P	218_S	1.467	0.82
42_T	148_Y	1.462	0.81
61_A	211_L	1.454	0.81
18_A	250_S	1.431	0.80
222_F	256_A	1.423	0.80
191_F	195_G	1.410	0.79
167_Y	247_N	1.393	0.78
112_S	115_T	1.374	0.77
48_L	227_A	1.360	0.76
24_N	246_Y	1.346	0.76
97_F	167_Y	1.342	0.75
79_Y	200_P	1.331	0.75
85_V	214_P	1.324	0.74
192_L	205_Y	1.322	0.74
71_V	181_F	1.306	0.73
213_G	254_E	1.298	0.73
85_V	215_G	1.298	0.73
17_I	48_L	1.293	0.73
149_L	209_L	1.292	0.72
234_W	238_N	1.285	0.72
61_A	88_F	1.283	0.72
42_T	232_Y	1.281	0.72
198_Y	204_P	1.273	0.71
24_N	29_L	1.271	0.71
164_Y	178_N	1.271	0.71
235_N	240_Q	1.254	0.70
19_D	242_V	1.246	0.70
203_L	251_D	1.243	0.69
211_L	227_A	1.243	0.69
60_G	214_P	1.240	0.69
14_P	249_G	1.235	0.69
100_N	132_Y	1.235	0.69
70_V	192_L	1.230	0.69
100_N	165_F	1.222	0.68
83_Q	252_T	1.214	0.68
23_G	31_P	1.210	0.67
21_G	32_Y	1.205	0.67
150_Y	166_G	1.193	0.66
84_N	151_I	1.160	0.64
101_I	165_F	1.149	0.63
119_N	123_Y	1.146	0.63
54_S	220_T	1.142	0.63
154_S	164_Y	1.139	0.63
123_Y	132_Y	1.129	0.62
19_D	34_Y	1.123	0.61
168_S	172_G	1.122	0.61
202_G	208_E	1.120	0.61
255_T	258_N	1.117	0.61
33_S	196_Y	1.109	0.60
26_S	29_L	1.107	0.60
83_Q	213_G	1.095	0.59
64_Q	254_E	1.091	0.59
82_V	101_I	1.084	0.59
66_N	254_E	1.076	0.58
45_I	63_L	1.071	0.58
163_V	179_V	1.069	0.58
194_S	197_N	1.058	0.57
17_I	220_T	1.051	0.56
88_F	211_L	1.049	0.56
85_V	98_V	1.045	0.56
20_Y	204_P	1.045	0.56
249_G	254_E	1.044	0.56
64_Q	213_G	1.044	0.56
175_W	178_N	1.039	0.55
44_N	146_T	1.032	0.55
48_L	225_L	1.032	0.55
66_N	213_G	1.030	0.55
168_S	173_S	1.018	0.54
56_P	109_A	1.015	0.54
50_A	61_A	1.014	0.54
87_F	98_V	1.014	0.54
109_A	112_S	0.997	0.52
101_I	116_I	0.996	0.52
39_V	242_V	0.995	0.52
234_W	247_N	0.989	0.52
68_V	251_D	0.989	0.52
17_I	231_L	0.989	0.52
230_A	241_P	0.987	0.52
61_A	222_F	0.983	0.51
43_V	63_L	0.968	0.50
125_S	128_G	0.967	0.50
43_V	47_S	0.963	0.50
87_F	96_S	0.963	0.50
94_T	189_A	0.962	0.50
63_L	211_L	0.960	0.50
249_G	252_T	0.958	0.49
95_L	151_I	0.954	0.49
166_G	173_S	0.953	0.49
35_N	190_Y	0.948	0.49
123_Y	127_G	0.937	0.48
84_N	224_S	0.931	0.47
62_S	116_I	0.931	0.47
105_S	189_A	0.928	0.47
6_P	204_P	0.915	0.46
62_S	98_V	0.906	0.46
230_A	245_A	0.905	0.45
63_L	143_L	0.902	0.45
68_V	199_T	0.900	0.45
62_S	130_Y	0.898	0.45
84_N	99_D	0.892	0.44
96_S	137_T	0.889	0.44
8_Y	14_P	0.886	0.44
65_L	242_V	0.882	0.44
24_N	27_G	0.871	0.43
69_L	250_S	0.869	0.43
13_A	250_S	0.868	0.43
62_S	212_G	0.867	0.43
209_L	212_G	0.865	0.43
231_L	247_N	0.860	0.42
71_V	80_Y	0.855	0.42
88_F	166_G	0.854	0.42
63_L	141_L	0.854	0.42
130_Y	134_Y	0.853	0.42
81_W	208_E	0.851	0.42
231_L	242_V	0.849	0.41
88_F	93_N	0.845	0.41
100_N	131_Y	0.843	0.41
50_A	220_T	0.840	0.41
240_Q	256_A	0.836	0.40
81_W	206_D	0.835	0.40
234_W	237_G	0.830	0.40
90_T	169_V	0.827	0.40
136_P	218_S	0.826	0.40
14_P	18_A	0.825	0.40
35_N	67_A	0.825	0.40
231_L	243_P	0.819	0.39
81_W	202_G	0.815	0.39
18_A	229_L	0.814	0.39
105_S	181_F	0.810	0.39
220_T	255_T	0.809	0.39
17_I	69_L	0.799	0.38
118_G	179_V	0.798	0.38
116_I	209_L	0.798	0.38
171_G	244_S	0.797	0.38
80_Y	181_F	0.796	0.38
45_I	141_L	0.792	0.37
42_T	230_A	0.787	0.37
47_S	211_L	0.784	0.37
95_L	138_Y	0.783	0.37
10_S	24_N	0.778	0.36
14_P	20_Y	0.769	0.36
131_Y	195_G	0.763	0.35
42_T	210_V	0.759	0.35
65_L	149_L	0.757	0.35
31_P	196_Y	0.757	0.35
34_Y	222_F	0.754	0.35
20_Y	212_G	0.749	0.34
19_D	118_G	0.748	0.34
82_V	163_V	0.748	0.34
8_Y	255_T	0.747	0.34
18_A	21_G	0.744	0.34
130_Y	133_A	0.743	0.34
12_P	19_D	0.743	0.34
64_Q	100_N	0.739	0.34
64_Q	85_V	0.739	0.34
61_A	112_S	0.738	0.34
22_L	29_L	0.735	0.33
19_D	63_L	0.732	0.33
51_Y	115_T	0.727	0.33
121_T	131_Y	0.720	0.32
19_D	244_S	0.719	0.32
42_T	255_T	0.718	0.32
141_L	145_F	0.716	0.32
92_T	107_P	0.712	0.32
206_D	216_G	0.708	0.32
108_S	230_A	0.708	0.32
82_V	165_F	0.706	0.32
154_S	218_S	0.705	0.31
81_W	213_G	0.705	0.31
20_Y	117_S	0.703	0.31
15_M	19_D	0.702	0.31
52_N	61_A	0.699	0.31
70_V	194_S	0.697	0.31
105_S	207_A	0.695	0.31
50_A	90_T	0.695	0.31
31_P	195_G	0.693	0.31
105_S	153_V	0.691	0.31
18_A	208_E	0.690	0.31
105_S	247_N	0.689	0.30
92_T	128_G	0.688	0.30
86_A	210_V	0.685	0.30
156_T	162_E	0.684	0.30
20_Y	248_F	0.683	0.30
26_S	222_F	0.673	0.29
222_F	227_A	0.671	0.29
63_L	186_G	0.665	0.29
126_G	129_G	0.660	0.29
51_Y	59_Y	0.660	0.29
80_Y	143_L	0.660	0.29
222_F	231_L	0.659	0.29
61_A	193_V	0.659	0.29
165_F	214_P	0.659	0.29
156_T	161_P	0.655	0.28
25_N	29_L	0.653	0.28
25_N	28_S	0.652	0.28
110_N	198_Y	0.651	0.28
63_L	88_F	0.649	0.28
85_V	216_G	0.649	0.28
71_V	183_S	0.648	0.28
62_S	224_S	0.648	0.28
97_F	111_L	0.645	0.28
53_S	211_L	0.641	0.28
82_V	161_P	0.640	0.27
18_A	87_F	0.639	0.27
63_L	227_A	0.638	0.27
145_F	227_A	0.637	0.27
118_G	165_F	0.636	0.27
44_N	211_L	0.636	0.27
81_W	104_F	0.636	0.27
26_S	41_G	0.632	0.27
115_T	118_G	0.632	0.27
45_I	145_F	0.632	0.27
204_P	248_F	0.631	0.27
113_N	246_Y	0.631	0.27
69_L	163_V	0.629	0.27
7_L	10_S	0.629	0.27
63_L	222_F	0.629	0.27
87_F	214_P	0.629	0.27
92_T	141_L	0.625	0.27
28_S	238_N	0.625	0.27
58_P	93_N	0.625	0.27
96_S	123_Y	0.624	0.27
34_Y	242_V	0.623	0.26
106_S	109_A	0.621	0.26
75_G	187_V	0.621	0.26
185_G	188_S	0.618	0.26
223_N	229_L	0.618	0.26
194_S	205_Y	0.617	0.26
41_G	65_L	0.617	0.26
37_S	42_T	0.617	0.26
80_Y	145_F	0.616	0.26
172_G	235_N	0.613	0.26
99_D	193_V	0.612	0.26
194_S	198_Y	0.612	0.26
55_P	214_P	0.611	0.26
54_S	62_S	0.610	0.26
221_T	257_S	0.609	0.26
53_S	93_N	0.599	0.25
67_A	82_V	0.593	0.25
210_V	229_L	0.591	0.25
66_N	84_N	0.590	0.25
64_Q	252_T	0.587	0.24
153_V	189_A	0.587	0.24
39_V	191_F	0.585	0.24
105_S	120_G	0.584	0.24
192_L	224_S	0.583	0.24
118_G	123_Y	0.583	0.24
43_V	48_L	0.582	0.24
66_N	81_W	0.582	0.24
74_G	181_F	0.582	0.24
237_G	240_Q	0.581	0.24
111_L	210_V	0.578	0.24
126_G	226_N	0.577	0.24
7_L	20_Y	0.575	0.24
18_A	209_L	0.575	0.24
209_L	223_N	0.573	0.24
43_V	86_A	0.572	0.24
79_Y	231_L	0.572	0.24
23_G	26_S	0.571	0.24
19_D	197_N	0.570	0.24
36_T	39_V	0.569	0.23
75_G	150_Y	0.567	0.23
111_L	134_Y	0.565	0.23
166_G	174_G	0.563	0.23
150_Y	173_S	0.563	0.23
98_V	212_G	0.563	0.23
166_G	239_Y	0.562	0.23
109_A	212_G	0.559	0.23
166_G	178_N	0.559	0.23
110_N	113_N	0.557	0.23
38_S	150_Y	0.555	0.23
57_G	211_L	0.554	0.23
33_S	192_L	0.554	0.23
84_N	242_V	0.553	0.23
225_L	240_Q	0.549	0.22
87_F	210_V	0.549	0.22
51_Y	216_G	0.548	0.22
214_P	217_G	0.548	0.22
38_S	154_S	0.547	0.22
164_Y	175_W	0.547	0.22
62_S	196_Y	0.547	0.22
39_V	202_G	0.547	0.22
19_D	194_S	0.546	0.22
144_P	243_P	0.545	0.22
149_L	212_G	0.544	0.22
231_L	245_A	0.544	0.22
99_D	132_Y	0.543	0.22
67_A	96_S	0.541	0.22
144_P	208_E	0.541	0.22
43_V	69_L	0.541	0.22
90_T	93_N	0.540	0.22
117_S	123_Y	0.540	0.22
105_S	157_S	0.537	0.22
86_A	92_T	0.536	0.22
97_F	136_P	0.533	0.22
126_G	132_Y	0.532	0.22
108_S	111_L	0.531	0.22
90_T	246_Y	0.530	0.21
21_G	193_V	0.526	0.21
213_G	252_T	0.525	0.21
80_Y	163_V	0.524	0.21
50_A	143_L	0.523	0.21
45_I	241_P	0.522	0.21
137_T	188_S	0.521	0.21
93_N	140_T	0.521	0.21
186_G	189_A	0.520	0.21
70_V	193_V	0.520	0.21
172_G	227_A	0.517	0.21
106_S	247_N	0.517	0.21
101_I	224_S	0.516	0.21
49_S	228_T	0.515	0.21
59_Y	90_T	0.511	0.21
146_T	167_Y	0.510	0.20
49_S	223_N	0.508	0.20
97_F	170_D	0.508	0.20
142_S	180_T	0.507	0.20
234_W	240_Q	0.507	0.20
21_G	177_D	0.506	0.20
116_I	150_Y	0.506	0.20
144_P	227_A	0.504	0.20
48_L	151_I	0.503	0.20
115_T	183_S	0.503	0.20
181_F	216_G	0.502	0.20
68_V	102_W	0.502	0.20
114_S	126_G	0.500	0.20

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
1m3yA	4	0.3089	2.9	0.973	Contact Map
2d9sA	2	0.166	1.8	0.975	Contact Map
2ag4A	1	0.3205	1.6	0.976	Contact Map
4nuuC	1	0.0463	1.5	0.977	Contact Map
1ac5A	1	0.3822	1.2	0.978	Contact Map
4ci9A	2	0.3745	1.1	0.978	Contact Map
3gmtA	1	0.2008	1	0.979	Contact Map
2ccvA	3	0.1313	0.9	0.98	Contact Map
1novD	1	0.0386	0.9	0.98	Contact Map
1p6xA	3	0.2278	0.9	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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