DUF3362 - PFAM28P - GREMLIN Contacts

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DUF3362 - Domain of unknown function (DUF3362)

PFAM:	PF11842	Sequences: DQVQDFYPSPMALATAMYYTGKNPLTKVTRKSEPVYVPKGPRERRLHKALLRYHDPENWPLVREALKKMGRADLIGNGKKCLIPPRQPKGTGKARYQSARRKNSTKGKKKKKRKKKKKKGKRKKAGKGRKSKKKPKKGRILTQHTGLPPR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	150 (135)
Sequences:	3354 (2520)
Seq/√Len:	216.9
META:	0.757

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_N	85_P	4.921	1.00
42_R	64_E	3.624	1.00
67_K	72_A	3.052	1.00
22_K	32_S	2.855	1.00
22_K	34_P	2.847	1.00
63_R	67_K	2.803	1.00
63_R	83_I	2.577	1.00
59_W	63_R	2.450	1.00
72_A	75_I	2.446	1.00
50_L	62_V	2.440	1.00
36_Y	43_E	2.232	1.00
41_P	45_R	2.213	1.00
26_T	33_E	2.179	1.00
64_E	68_K	2.137	1.00
96_Y	99_A	2.071	1.00
29_T	32_S	1.906	1.00
22_K	28_V	1.836	1.00
109_K	112_K	1.786	1.00
23_N	26_T	1.764	1.00
38_P	43_E	1.742	1.00
111_K	114_K	1.717	1.00
59_W	83_I	1.702	1.00
13_L	16_A	1.657	1.00
108_K	111_K	1.631	1.00
46_L	65_A	1.621	1.00
63_R	84_P	1.586	1.00
9_S	13_L	1.572	1.00
7_Y	15_T	1.536	1.00
16_A	20_T	1.532	1.00
21_G	34_P	1.500	1.00
131_S	134_K	1.442	1.00
5_D	38_P	1.402	1.00
25_L	32_S	1.398	1.00
104_S	107_G	1.397	1.00
77_N	86_R	1.386	1.00
62_V	69_M	1.379	1.00
48_K	52_R	1.349	1.00
124_K	127_K	1.339	1.00
110_K	113_R	1.309	1.00
112_K	115_K	1.248	1.00
98_S	102_K	1.247	1.00
17_M	24_P	1.243	1.00
99_A	103_N	1.220	1.00
113_R	116_K	1.214	1.00
13_L	25_L	1.211	1.00
127_K	130_K	1.200	1.00
21_G	39_K	1.196	1.00
75_I	83_I	1.192	1.00
11_M	51_L	1.156	1.00
107_G	110_K	1.153	1.00
50_L	65_A	1.134	1.00
112_K	116_K	1.098	1.00
125_A	130_K	1.079	1.00
131_S	135_P	1.076	1.00
53_Y	59_W	1.054	1.00
17_M	37_V	1.050	1.00
100_R	103_N	1.045	1.00
97_Q	101_R	1.045	1.00
53_Y	58_N	1.042	1.00
7_Y	11_M	1.039	1.00
22_K	27_K	1.033	1.00
9_S	12_A	1.027	1.00
23_N	33_E	1.023	1.00
116_K	119_K	0.993	1.00
78_G	81_C	0.986	1.00
106_K	111_K	0.980	1.00
129_R	132_K	0.973	1.00
110_K	114_K	0.966	1.00
49_A	65_A	0.963	1.00
124_K	129_R	0.963	1.00
11_M	16_A	0.947	1.00
123_K	127_K	0.945	1.00
9_S	15_T	0.943	1.00
40_G	45_R	0.942	1.00
124_K	128_G	0.934	0.99
11_M	40_G	0.930	0.99
126_G	130_K	0.927	0.99
124_K	133_K	0.925	0.99
101_R	104_S	0.916	0.99
76_G	82_L	0.884	0.99
107_G	111_K	0.883	0.99
16_A	38_P	0.873	0.99
95_R	100_R	0.871	0.99
129_R	134_K	0.853	0.99
128_G	132_K	0.850	0.99
114_K	117_K	0.839	0.99
121_K	124_K	0.838	0.99
111_K	115_K	0.832	0.99
18_Y	45_R	0.826	0.99
7_Y	41_P	0.824	0.99
50_L	71_R	0.822	0.99
9_S	41_P	0.816	0.99
25_L	54_H	0.816	0.99
122_R	125_A	0.814	0.99
12_A	15_T	0.811	0.99
117_K	120_G	0.806	0.99
49_A	61_L	0.803	0.98
125_A	128_G	0.799	0.98
130_K	133_K	0.798	0.98
40_G	43_E	0.797	0.98
106_K	109_K	0.796	0.98
130_K	134_K	0.792	0.98
84_P	88_P	0.784	0.98
59_W	86_R	0.780	0.98
60_P	63_R	0.779	0.98
42_R	68_K	0.778	0.98
122_R	127_K	0.775	0.98
103_N	108_K	0.775	0.98
130_K	135_P	0.775	0.98
98_S	101_R	0.760	0.98
126_G	129_R	0.756	0.98
27_K	31_K	0.751	0.98
106_K	110_K	0.750	0.98
90_G	93_K	0.736	0.97
110_K	115_K	0.725	0.97
60_P	86_R	0.725	0.97
96_Y	103_N	0.715	0.97
111_K	116_K	0.713	0.97
55_D	60_P	0.712	0.97
11_M	25_L	0.709	0.97
127_K	133_K	0.708	0.97
60_P	87_Q	0.707	0.97
7_Y	51_L	0.700	0.96
26_T	29_T	0.697	0.96
108_K	112_K	0.695	0.96
21_G	36_Y	0.684	0.96
87_Q	90_G	0.682	0.96
121_K	125_A	0.681	0.96
56_P	86_R	0.674	0.96
98_S	104_S	0.672	0.95
36_Y	41_P	0.672	0.95
28_V	31_K	0.668	0.95
18_Y	51_L	0.666	0.95
123_K	128_G	0.659	0.95
5_D	36_Y	0.658	0.95
129_R	135_P	0.656	0.95
5_D	44_R	0.652	0.95
40_G	46_L	0.652	0.95
124_K	130_K	0.646	0.94
53_Y	60_P	0.634	0.94
102_K	105_T	0.633	0.94
99_A	105_T	0.632	0.94
61_L	65_A	0.630	0.94
77_N	88_P	0.629	0.94
100_R	104_S	0.629	0.94
127_K	132_K	0.624	0.93
109_K	113_R	0.623	0.93
54_H	84_P	0.622	0.93
95_R	98_S	0.622	0.93
61_L	64_E	0.620	0.93
128_G	131_S	0.618	0.93
17_M	58_N	0.618	0.93
52_R	58_N	0.617	0.93
30_R	43_E	0.616	0.93
79_K	87_Q	0.611	0.93
99_A	102_K	0.610	0.93
113_R	117_K	0.609	0.92
132_K	135_P	0.607	0.92
96_Y	100_R	0.606	0.92
28_V	34_P	0.604	0.92
127_K	134_K	0.601	0.92
5_D	41_P	0.599	0.92
121_K	126_G	0.592	0.91
114_K	120_G	0.589	0.91
5_D	47_H	0.586	0.91
11_M	44_R	0.580	0.91
98_S	105_T	0.579	0.90
122_R	126_G	0.578	0.90
90_G	95_R	0.578	0.90
50_L	69_M	0.578	0.90
1_D	52_R	0.571	0.90
50_L	73_D	0.570	0.90
27_K	32_S	0.568	0.90
7_Y	13_L	0.566	0.89
125_A	131_S	0.566	0.89
51_L	54_H	0.564	0.89
83_I	86_R	0.560	0.89
26_T	32_S	0.560	0.89
76_G	81_C	0.559	0.89
122_R	132_K	0.559	0.89
7_Y	12_A	0.549	0.88
119_K	122_R	0.548	0.88
24_P	27_K	0.546	0.88
126_G	132_K	0.545	0.88
91_T	94_A	0.543	0.87
95_R	105_T	0.538	0.87
6_F	15_T	0.532	0.86
13_L	23_N	0.530	0.86
23_N	54_H	0.530	0.86
9_S	44_R	0.529	0.86
115_K	118_K	0.525	0.86
127_K	131_S	0.521	0.85
63_R	86_R	0.519	0.85
28_V	33_E	0.518	0.85
102_K	107_G	0.513	0.84
97_Q	103_N	0.511	0.84
55_D	58_N	0.509	0.84
108_K	114_K	0.506	0.84
97_Q	100_R	0.503	0.83
121_K	128_G	0.502	0.83
45_R	61_L	0.502	0.83
45_R	51_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
3fn5A	1	0.3667	11.9	0.951	Contact Map
3heiB	1	0.2867	11.6	0.951	Contact Map
3fayA	1	0.4867	9.9	0.953	Contact Map
4pkdB	1	0.6867	9.5	0.953	Contact Map
3g5bA	1	0.4733	9.2	0.953	Contact Map
4g1hA	1	0.2267	8.7	0.954	Contact Map
4o8tA	2	0.3667	7.4	0.956	Contact Map
3zg9A	1	0.2733	7.3	0.956	Contact Map
3pn3A	2	0.3867	7.1	0.956	Contact Map
3g66A	1	0.2467	6.9	0.956	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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