DUF3786 - PFAM28P - GREMLIN Contacts

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DUF3786 - Domain of unknown function (DUF3786)

PFAM:	PF12654	Sequences: DPEEVARRLGAEYDGDGGLTLPFLGRDYRVDPPGGEISDGDGGEEVPPWEQILLLHYLLNAKGTPLSGKWISFRELPGGAFYFPAFHKRAEKPLAKRFGGDPELLLEAAEKLGGEPLDLGDASVVFPALPRVPLLLILWEGDEEFPASANILFDASAEDYLPTEDLAVLGELLVRM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (173)
Sequences:	6339 (4874)
Seq/√Len:	370.6
META:	0.929

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_K	155_A	3.953	1.00
70_W	135_L	3.424	1.00
101_D	104_L	3.413	1.00
157_A	166_L	3.164	1.00
120_G	137_I	2.839	1.00
109_A	124_V	2.586	1.00
125_V	135_L	2.552	1.00
22_P	27_D	2.381	1.00
115_E	125_V	2.281	1.00
31_D	34_G	2.248	1.00
87_H	92_K	2.217	1.00
62_K	159_D	2.170	1.00
77_P	158_E	2.111	1.00
141_G	147_A	2.026	1.00
117_L	123_S	1.878	1.00
12_E	20_T	1.820	1.00
128_A	169_L	1.820	1.00
106_L	110_E	1.798	1.00
117_L	135_L	1.785	1.00
67_S	155_A	1.755	1.00
121_D	140_E	1.719	1.00
106_L	116_P	1.688	1.00
102_P	140_E	1.684	1.00
106_L	122_A	1.674	1.00
14_D	20_T	1.662	1.00
20_T	27_D	1.654	1.00
88_K	92_K	1.620	1.00
56_H	165_D	1.610	1.00
4_E	8_R	1.610	1.00
11_A	21_L	1.608	1.00
68_G	154_D	1.574	1.00
117_L	125_V	1.541	1.00
106_L	124_V	1.538	1.00
115_E	127_P	1.523	1.00
164_E	167_A	1.459	1.00
104_L	107_E	1.418	1.00
2_P	19_L	1.417	1.00
71_I	76_L	1.405	1.00
92_K	96_K	1.388	1.00
90_A	151_I	1.381	1.00
107_E	110_E	1.373	1.00
54_L	129_L	1.369	1.00
23_F	50_E	1.355	1.00
28_Y	54_L	1.346	1.00
82_Y	89_R	1.322	1.00
64_T	159_D	1.305	1.00
136_L	174_V	1.300	1.00
76_L	157_A	1.273	1.00
127_P	133_P	1.268	1.00
108_A	111_K	1.256	1.00
95_A	149_A	1.253	1.00
11_A	19_L	1.251	1.00
14_D	17_G	1.248	1.00
133_P	156_S	1.232	1.00
126_F	173_L	1.229	1.00
21_L	28_Y	1.229	1.00
132_V	157_A	1.213	1.00
103_E	107_E	1.204	1.00
136_L	173_L	1.202	1.00
24_L	128_A	1.200	1.00
84_P	88_K	1.185	1.00
167_A	171_E	1.176	1.00
72_S	83_F	1.171	1.00
102_P	122_A	1.167	1.00
110_E	124_V	1.166	1.00
72_S	75_E	1.160	1.00
69_K	75_E	1.156	1.00
26_R	39_D	1.129	1.00
6_A	19_L	1.128	1.00
21_L	30_V	1.121	1.00
99_G	147_A	1.108	1.00
125_V	133_P	1.102	1.00
20_T	29_R	1.100	1.00
53_L	129_L	1.096	1.00
4_E	7_R	1.090	1.00
109_A	126_F	1.087	1.00
133_P	154_D	1.086	1.00
23_F	128_A	1.086	1.00
12_E	27_D	1.082	1.00
5_V	19_L	1.079	1.00
102_P	106_L	1.076	1.00
85_A	167_A	1.061	1.00
83_F	87_H	1.056	1.00
74_R	83_F	1.054	1.00
56_H	162_P	1.039	1.00
66_L	133_P	1.036	1.00
82_Y	85_A	1.031	1.00
17_G	29_R	1.027	1.00
162_P	165_D	1.022	1.00
30_V	37_I	1.019	1.00
76_L	166_L	1.014	1.00
32_P	35_G	1.012	1.00
19_L	58_L	1.006	1.00
29_R	40_G	1.002	1.00
99_G	138_L	0.997	1.00
5_V	8_R	0.995	1.00
73_F	86_F	0.994	1.00
76_L	163_T	0.991	1.00
134_L	173_L	0.990	1.00
73_F	167_A	0.990	1.00
131_R	160_Y	0.982	1.00
29_R	38_S	0.980	1.00
79_G	163_T	0.965	1.00
120_G	139_W	0.961	1.00
8_R	63_G	0.956	1.00
161_L	165_D	0.952	1.00
137_I	152_L	0.951	1.00
107_E	111_K	0.945	1.00
6_A	13_Y	0.939	1.00
61_A	160_Y	0.932	1.00
90_A	93_P	0.931	1.00
142_D	145_F	0.928	1.00
3_E	15_G	0.922	1.00
110_E	116_P	0.922	1.00
64_T	156_S	0.916	1.00
106_L	109_A	0.915	1.00
19_L	32_P	0.910	1.00
65_P	131_R	0.910	1.00
91_E	150_N	0.897	1.00
13_Y	16_D	0.894	1.00
49_W	171_E	0.888	1.00
2_P	13_Y	0.881	1.00
53_L	168_V	0.870	1.00
73_F	163_T	0.867	1.00
86_F	170_G	0.861	1.00
15_G	18_G	0.859	1.00
164_E	168_V	0.858	1.00
85_A	88_K	0.857	1.00
28_Y	46_V	0.853	1.00
26_R	41_D	0.844	1.00
86_F	90_A	0.844	1.00
100_G	141_G	0.841	1.00
60_N	162_P	0.840	1.00
119_L	137_I	0.831	1.00
22_P	130_P	0.819	1.00
105_L	124_V	0.817	1.00
128_A	133_P	0.814	1.00
122_A	140_E	0.811	1.00
2_P	32_P	0.807	1.00
20_T	40_G	0.805	1.00
31_D	36_E	0.804	1.00
170_G	173_L	0.802	1.00
98_F	108_A	0.796	1.00
56_H	164_E	0.791	1.00
158_E	163_T	0.789	1.00
6_A	11_A	0.787	1.00
70_W	125_V	0.783	1.00
21_L	54_L	0.780	1.00
27_D	40_G	0.780	1.00
13_Y	19_L	0.778	1.00
94_L	149_A	0.777	1.00
46_V	51_Q	0.769	1.00
119_L	123_S	0.767	1.00
123_S	137_I	0.764	1.00
57_Y	131_R	0.760	1.00
66_L	156_S	0.754	1.00
67_S	156_S	0.753	1.00
78_G	81_F	0.752	1.00
40_G	43_G	0.749	1.00
153_F	170_G	0.749	1.00
103_E	106_L	0.747	1.00
99_G	141_G	0.746	1.00
114_G	126_F	0.742	1.00
168_V	171_E	0.734	1.00
14_D	18_G	0.732	1.00
167_A	170_G	0.731	1.00
86_F	153_F	0.720	1.00
9_L	61_A	0.717	1.00
102_P	105_L	0.716	1.00
170_G	174_V	0.708	0.99
9_L	58_L	0.707	0.99
100_G	140_E	0.705	0.99
119_L	135_L	0.700	0.99
30_V	58_L	0.699	0.99
2_P	5_V	0.699	0.99
165_D	168_V	0.697	0.99
94_L	174_V	0.696	0.99
85_A	89_R	0.695	0.99
13_Y	18_G	0.687	0.99
28_Y	39_D	0.685	0.99
87_H	91_E	0.682	0.99
22_P	113_G	0.679	0.99
78_G	163_T	0.677	0.99
67_S	154_D	0.672	0.99
136_L	151_I	0.672	0.99
63_G	160_Y	0.668	0.99
116_P	124_V	0.667	0.99
103_E	140_E	0.666	0.99
63_G	131_R	0.662	0.99
47_P	50_E	0.662	0.99
3_E	7_R	0.661	0.99
73_F	85_A	0.660	0.99
171_E	174_V	0.659	0.99
141_G	145_F	0.659	0.99
50_E	54_L	0.659	0.99
74_R	80_A	0.654	0.99
93_P	96_K	0.650	0.99
118_D	123_S	0.649	0.99
28_Y	37_I	0.649	0.99
81_F	85_A	0.642	0.99
97_R	104_L	0.638	0.99
108_A	112_L	0.634	0.99
23_F	54_L	0.632	0.99
168_V	172_L	0.620	0.99
5_V	9_L	0.614	0.99
98_F	138_L	0.611	0.98
90_A	167_A	0.611	0.98
99_G	140_E	0.605	0.98
109_A	113_G	0.604	0.98
23_F	172_L	0.603	0.98
82_Y	168_V	0.603	0.98
90_A	174_V	0.602	0.98
109_A	114_G	0.599	0.98
84_P	87_H	0.596	0.98
81_F	84_P	0.591	0.98
132_V	169_L	0.589	0.98
48_P	51_Q	0.588	0.98
77_P	163_T	0.586	0.98
89_R	165_D	0.582	0.98
86_F	91_E	0.580	0.98
3_E	13_Y	0.580	0.98
3_E	6_A	0.579	0.98
162_P	168_V	0.578	0.98
92_K	95_A	0.576	0.98
56_H	60_N	0.575	0.98
73_F	82_Y	0.575	0.98
73_F	90_A	0.572	0.98
149_A	174_V	0.563	0.97
142_D	146_P	0.558	0.97
60_N	160_Y	0.558	0.97
86_F	89_R	0.558	0.97
67_S	159_D	0.558	0.97
10_G	131_R	0.557	0.97
66_L	154_D	0.556	0.97
145_F	148_S	0.555	0.97
134_L	153_F	0.552	0.97
6_A	9_L	0.550	0.97
39_D	42_G	0.545	0.97
74_R	81_F	0.544	0.97
55_L	58_L	0.544	0.97
134_L	151_I	0.543	0.97
39_D	44_E	0.534	0.96
50_E	172_L	0.532	0.96
52_I	56_H	0.530	0.96
82_Y	167_A	0.528	0.96
165_D	171_E	0.528	0.96
101_D	105_L	0.526	0.96
31_D	38_S	0.526	0.96
17_G	31_D	0.525	0.96
93_P	174_V	0.523	0.96
47_P	172_L	0.521	0.96
120_G	123_S	0.520	0.96
13_Y	17_G	0.516	0.96
151_I	170_G	0.514	0.96
9_L	19_L	0.511	0.95
2_P	6_A	0.509	0.95
53_L	165_D	0.506	0.95
89_R	171_E	0.506	0.95
157_A	161_L	0.501	0.95
24_L	173_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
4g6vB	1	0.3352	6.7	0.946	Contact Map
3kf8B	1	0.625	6.1	0.947	Contact Map
1ghhA	1	0.1591	5.7	0.947	Contact Map
1yo5C	1	0.2955	3.3	0.953	Contact Map
4g32A	1	0.9318	3	0.954	Contact Map
1wwxA	1	0.3693	3	0.954	Contact Map
2kz3A	1	0.2784	3	0.954	Contact Map
1fi2A	5	0.5909	2.9	0.955	Contact Map
2uvaG	3	0.8409	2.7	0.955	Contact Map
3zenD	6	0.8864	2.7	0.955	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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