DUF3526 - PFAM28P - GREMLIN Contacts

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DUF3526 - Domain of unknown function (DUF3526)

PFAM:	PF12040	Sequences: RIEFLAQREAGHNPWDPPFAALKDKFLARYPEWGVDSVEDLPWNWYGAVQQEGEEESAEVYDAYAEKLERQNRLARRLGLLSPALALQRLSMALAGTDLAAHLRFLDQAEAYREDLRRFFYPKIFRDYRVDAEDWASLPDFEYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	144 (138)
Sequences:	2903 (2210)
Seq/√Len:	188.1
META:	0.821

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_S	40_D	4.293	1.00
93_A	98_D	3.290	1.00
52_E	55_E	3.003	1.00
102_H	106_L	2.970	1.00
51_Q	55_E	2.632	1.00
114_E	118_R	2.526	1.00
88_Q	92_M	2.499	1.00
20_A	23_K	2.474	1.00
25_K	29_R	2.469	1.00
43_W	48_A	2.449	1.00
36_D	40_D	2.380	1.00
114_E	117_R	2.361	1.00
98_D	101_A	2.233	1.00
58_A	62_D	2.223	1.00
24_D	28_A	2.156	1.00
73_R	77_R	2.123	1.00
20_A	24_D	2.076	1.00
22_L	48_A	1.989	1.00
29_R	55_E	1.803	1.00
115_D	119_F	1.786	1.00
62_D	66_E	1.772	1.00
104_R	108_Q	1.709	1.00
21_A	25_K	1.673	1.00
69_E	100_A	1.660	1.00
26_F	48_A	1.625	1.00
130_V	134_D	1.577	1.00
132_A	136_A	1.534	1.00
116_L	120_F	1.517	1.00
117_R	120_F	1.484	1.00
13_N	17_P	1.473	1.00
63_A	67_K	1.458	1.00
13_N	16_D	1.380	1.00
117_R	121_Y	1.299	1.00
72_N	76_R	1.275	1.00
121_Y	124_I	1.258	1.00
56_E	59_E	1.246	1.00
76_R	89_R	1.214	1.00
122_P	125_F	1.212	1.00
134_D	137_S	1.200	1.00
133_E	137_S	1.183	1.00
104_R	143_Y	1.164	1.00
107_D	111_A	1.161	1.00
59_E	62_D	1.146	1.00
114_E	121_Y	1.146	1.00
119_F	123_K	1.136	1.00
87_L	90_L	1.135	1.00
123_K	128_Y	1.123	1.00
70_R	73_R	1.119	1.00
35_V	42_P	1.098	1.00
38_V	45_W	1.096	1.00
121_Y	125_F	1.087	1.00
108_Q	141_F	1.086	1.00
41_L	47_G	1.059	1.00
131_D	134_D	1.056	1.00
118_R	121_Y	1.054	1.00
73_R	76_R	1.050	1.00
72_N	99_L	1.044	1.00
4_F	7_Q	1.033	1.00
47_G	50_Q	1.030	1.00
30_Y	43_W	1.028	1.00
15_W	18_P	1.026	1.00
4_F	9_E	1.023	1.00
59_E	63_A	1.009	1.00
23_K	27_L	1.007	1.00
78_L	85_L	1.005	0.99
119_F	122_P	1.004	0.99
36_D	39_E	1.000	0.99
5_L	9_E	1.000	0.99
26_F	29_R	0.996	0.99
123_K	134_D	0.991	0.99
64_Y	67_K	0.986	0.99
19_F	23_K	0.979	0.99
45_W	53_G	0.979	0.99
22_L	26_F	0.964	0.99
54_E	113_R	0.959	0.99
35_V	40_D	0.947	0.99
72_N	90_L	0.940	0.99
79_G	85_L	0.939	0.99
27_L	34_G	0.939	0.99
103_L	107_D	0.936	0.99
79_G	89_R	0.928	0.99
6_A	10_A	0.924	0.99
7_Q	10_A	0.922	0.99
39_E	42_P	0.920	0.99
11_G	15_W	0.916	0.99
108_Q	111_A	0.912	0.99
77_R	80_L	0.906	0.99
74_L	77_R	0.902	0.99
12_H	16_D	0.901	0.99
119_F	128_Y	0.897	0.99
99_L	103_L	0.892	0.99
122_P	126_R	0.890	0.99
57_S	61_Y	0.890	0.99
50_Q	57_S	0.887	0.99
120_F	124_I	0.886	0.99
69_E	73_R	0.875	0.99
16_D	19_F	0.872	0.99
30_Y	55_E	0.872	0.99
50_Q	54_E	0.868	0.99
116_L	121_Y	0.863	0.98
68_L	72_N	0.859	0.98
77_R	81_L	0.858	0.98
132_A	138_L	0.858	0.98
52_E	56_E	0.853	0.98
11_G	18_P	0.852	0.98
86_A	92_M	0.843	0.98
115_D	118_R	0.840	0.98
79_G	86_A	0.839	0.98
91_S	113_R	0.821	0.98
105_F	109_A	0.820	0.98
41_L	45_W	0.816	0.98
120_F	123_K	0.810	0.98
4_F	8_R	0.808	0.98
103_L	106_L	0.792	0.97
14_P	18_P	0.786	0.97
116_L	119_F	0.785	0.97
13_N	21_A	0.783	0.97
133_E	136_A	0.782	0.97
53_G	57_S	0.778	0.97
17_P	21_A	0.772	0.97
47_G	53_G	0.760	0.97
43_W	46_Y	0.756	0.96
114_E	127_D	0.748	0.96
117_R	122_P	0.748	0.96
21_A	111_A	0.747	0.96
69_E	103_L	0.741	0.96
46_Y	126_R	0.740	0.96
96_G	101_A	0.738	0.96
118_R	123_K	0.731	0.96
108_Q	143_Y	0.730	0.96
120_F	125_F	0.718	0.95
119_F	125_F	0.714	0.95
75_A	85_L	0.712	0.95
124_I	127_D	0.710	0.95
11_G	53_G	0.708	0.95
5_L	10_A	0.708	0.95
65_A	68_L	0.700	0.95
120_F	128_Y	0.697	0.94
43_W	47_G	0.694	0.94
46_Y	50_Q	0.685	0.94
123_K	126_R	0.680	0.94
64_Y	68_L	0.675	0.93
11_G	22_L	0.669	0.93
131_D	137_S	0.669	0.93
8_R	15_W	0.669	0.93
130_V	138_L	0.661	0.93
75_A	92_M	0.660	0.93
15_W	26_F	0.659	0.93
54_E	57_S	0.655	0.92
41_L	44_N	0.653	0.92
130_V	135_W	0.648	0.92
102_H	138_L	0.645	0.92
132_A	137_S	0.644	0.92
125_F	128_Y	0.641	0.92
65_A	106_L	0.638	0.91
59_E	69_E	0.621	0.90
67_K	70_R	0.621	0.90
62_D	65_A	0.620	0.90
65_A	107_D	0.614	0.90
109_A	113_R	0.614	0.90
66_E	70_R	0.611	0.90
43_W	54_E	0.604	0.89
131_D	136_A	0.595	0.88
26_F	53_G	0.593	0.88
5_L	8_R	0.591	0.88
117_R	128_Y	0.590	0.88
49_V	106_L	0.581	0.87
62_D	100_A	0.575	0.87
121_Y	127_D	0.574	0.87
15_W	19_F	0.567	0.86
128_Y	134_D	0.564	0.86
82_S	85_L	0.563	0.85
113_R	121_Y	0.554	0.85
46_Y	125_F	0.553	0.84
50_Q	117_R	0.553	0.84
23_K	37_S	0.552	0.84
128_Y	132_A	0.551	0.84
90_L	111_A	0.550	0.84
18_P	21_A	0.548	0.84
70_R	77_R	0.542	0.83
44_N	54_E	0.540	0.83
79_G	101_A	0.534	0.82
45_W	49_V	0.532	0.82
23_K	38_V	0.531	0.82
49_V	52_E	0.525	0.81
114_E	119_F	0.522	0.81
82_S	86_A	0.522	0.81
108_Q	112_Y	0.520	0.81
116_L	124_I	0.518	0.80
21_A	24_D	0.518	0.80
49_V	54_E	0.518	0.80
131_D	135_W	0.516	0.80
11_G	14_P	0.515	0.80
56_E	68_L	0.514	0.80
48_A	52_E	0.513	0.80
18_P	45_W	0.513	0.80
23_K	110_E	0.513	0.80
15_W	20_A	0.510	0.79
15_W	45_W	0.508	0.79
56_E	60_V	0.507	0.79
110_E	113_R	0.506	0.79
112_Y	139_P	0.505	0.79
23_K	85_L	0.503	0.78
10_A	85_L	0.502	0.78
27_L	38_V	0.501	0.78
95_A	133_E	0.501	0.78
84_A	88_Q	0.500	0.78

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
3ieeA	1	0.7917	5.4	0.923	Contact Map
1y66A	3	0.3472	5.3	0.923	Contact Map
2etdA	1	0.7292	4.1	0.927	Contact Map
3rh3A	1	0.8611	3.7	0.929	Contact Map
1x3kA	1	0.3819	3.5	0.93	Contact Map
4f4fA	1	0.3681	2.9	0.933	Contact Map
3w4uA	2	0.3611	2.6	0.934	Contact Map
1wddA	4	0.3681	2.5	0.935	Contact Map
1it2A	1	0.4236	2.5	0.935	Contact Map
3bomA	2	0.3611	2.1	0.937	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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