DUF3842 - PFAM28P - GREMLIN Contacts

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DUF3842 - Domain of unknown function (DUF3842)

PFAM:	PF12953	Sequences: RIAVIDGQGGGIGKAIIEKLREELPEAVEIIALGTNAIATSAMLKAGANRGATGENAIVVNVRKADVIIGPIGIVIANSMLGEITPAMAEAVASSPAKKILLPLNQCNVEIVGVSDEPLPHLIDEAVEKI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	130 (129)
Sequences:	2528 (1681)
Seq/√Len:	148.0
META:	0.899

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_K	96_P	2.893	1.00
19_K	124_D	2.820	1.00
40_T	53_T	2.815	1.00
98_K	110_E	2.742	1.00
3_A	65_A	2.689	1.00
78_N	94_S	2.670	1.00
21_R	49_N	2.492	1.00
40_T	51_G	2.360	1.00
87_A	90_E	2.304	1.00
59_V	87_A	2.276	1.00
60_V	78_N	2.071	1.00
68_I	95_S	2.057	1.00
90_E	94_S	2.031	1.00
50_R	81_L	1.947	1.00
70_G	74_I	1.831	1.00
100_I	126_A	1.793	1.00
33_L	58_I	1.793	1.00
69_I	126_A	1.756	1.00
14_K	18_E	1.751	1.00
75_V	93_A	1.733	1.00
56_N	78_N	1.724	1.00
69_I	100_I	1.690	1.00
77_A	86_P	1.688	1.00
3_A	33_L	1.632	1.00
100_I	112_V	1.618	1.00
118_P	121_H	1.601	1.00
15_A	123_I	1.578	1.00
16_I	126_A	1.571	1.00
78_N	90_E	1.570	1.00
72_I	111_I	1.564	1.00
75_V	101_L	1.554	1.00
5_I	92_V	1.543	1.00
117_E	125_E	1.537	1.00
112_V	125_E	1.444	1.00
110_E	129_K	1.432	1.00
115_S	125_E	1.397	1.00
29_E	50_R	1.375	1.00
55_E	87_A	1.357	1.00
62_V	68_I	1.355	1.00
1_R	31_I	1.335	1.00
16_I	69_I	1.331	1.00
37_A	53_T	1.322	1.00
76_I	109_V	1.321	1.00
44_L	51_G	1.299	1.00
35_T	84_I	1.278	1.00
4_V	17_I	1.272	1.00
60_V	64_K	1.264	1.00
58_I	88_M	1.264	1.00
31_I	50_R	1.237	1.00
19_K	23_E	1.221	1.00
63_R	96_P	1.218	1.00
117_E	121_H	1.203	1.00
56_N	60_V	1.183	1.00
74_I	101_L	1.179	1.00
32_A	43_M	1.178	1.00
1_R	64_K	1.177	1.00
2_I	28_V	1.165	1.00
76_I	93_A	1.160	1.00
84_I	88_M	1.160	1.00
98_K	108_N	1.160	1.00
23_E	128_E	1.151	1.00
75_V	109_V	1.143	1.00
38_I	41_S	1.120	0.99
21_R	30_I	1.103	0.99
24_L	28_V	1.060	0.99
99_K	109_V	1.049	0.99
57_A	85_T	1.048	0.99
24_L	27_A	1.044	0.99
11_G	80_M	1.040	0.99
63_R	78_N	1.039	0.99
12_I	104_L	1.015	0.99
32_A	48_A	0.998	0.99
57_A	61_N	0.987	0.99
17_I	32_A	0.984	0.99
63_R	94_S	0.984	0.99
11_G	57_A	0.973	0.98
31_I	61_N	0.970	0.98
99_K	108_N	0.958	0.98
121_H	124_D	0.927	0.98
1_R	29_E	0.923	0.98
34_G	40_T	0.919	0.98
73_G	107_C	0.919	0.98
50_R	106_Q	0.908	0.98
125_E	129_K	0.906	0.98
3_A	62_V	0.889	0.97
70_G	101_L	0.887	0.97
60_V	63_R	0.884	0.97
18_E	22_E	0.873	0.97
3_A	31_I	0.862	0.97
25_P	28_V	0.826	0.96
69_I	127_V	0.818	0.95
86_P	94_S	0.816	0.95
89_A	92_V	0.812	0.95
20_L	100_I	0.809	0.95
4_V	16_I	0.808	0.95
104_L	117_E	0.795	0.95
102_L	112_V	0.785	0.94
66_D	96_P	0.777	0.94
30_I	59_V	0.770	0.94
52_A	56_N	0.765	0.94
1_R	65_A	0.754	0.93
20_L	30_I	0.752	0.93
23_E	127_V	0.750	0.93
4_V	30_I	0.740	0.92
38_I	42_A	0.738	0.92
122_L	125_E	0.733	0.92
29_E	49_N	0.730	0.92
77_A	111_I	0.726	0.92
5_I	58_I	0.717	0.91
84_I	92_V	0.715	0.91
37_A	52_A	0.710	0.91
67_V	98_K	0.707	0.91
117_E	120_P	0.696	0.90
113_G	122_L	0.691	0.90
42_A	46_A	0.687	0.89
17_I	25_P	0.686	0.89
33_L	51_G	0.682	0.89
124_D	128_E	0.678	0.89
12_I	119_L	0.674	0.88
24_L	127_V	0.673	0.88
112_V	122_L	0.663	0.88
102_L	122_L	0.663	0.88
67_V	97_A	0.660	0.87
115_S	122_L	0.656	0.87
72_I	105_N	0.655	0.87
11_G	18_E	0.654	0.87
88_M	91_A	0.651	0.87
126_A	129_K	0.650	0.87
59_V	91_A	0.650	0.87
20_L	69_I	0.647	0.86
61_N	64_K	0.647	0.86
11_G	14_K	0.644	0.86
35_T	88_M	0.635	0.85
47_G	73_G	0.634	0.85
12_I	71_P	0.633	0.85
30_I	49_N	0.623	0.84
26_E	49_N	0.620	0.84
3_A	51_G	0.619	0.84
33_L	57_A	0.616	0.83
31_I	64_K	0.607	0.83
40_T	44_L	0.604	0.82
30_I	47_G	0.604	0.82
71_P	80_M	0.597	0.82
16_I	20_L	0.594	0.81
62_V	95_S	0.590	0.81
99_K	106_Q	0.590	0.81
15_A	18_E	0.589	0.81
77_A	93_A	0.588	0.81
60_V	85_T	0.588	0.81
27_A	38_I	0.586	0.80
65_A	97_A	0.581	0.80
62_V	92_V	0.581	0.80
116_D	128_E	0.579	0.80
81_L	85_T	0.578	0.79
33_L	65_A	0.571	0.79
104_L	115_S	0.569	0.78
124_D	127_V	0.569	0.78
7_G	118_P	0.566	0.78
21_R	28_V	0.565	0.78
77_A	94_S	0.564	0.78
78_N	86_P	0.562	0.78
8_Q	85_T	0.561	0.77
17_I	24_L	0.561	0.77
89_A	93_A	0.559	0.77
36_N	83_E	0.557	0.77
86_P	89_A	0.557	0.77
76_I	94_S	0.550	0.76
21_R	24_L	0.543	0.75
30_I	69_I	0.537	0.74
4_V	13_G	0.536	0.74
62_V	88_M	0.535	0.74
64_K	108_N	0.533	0.74
19_K	123_I	0.532	0.74
60_V	90_E	0.530	0.73
81_L	104_L	0.528	0.73
22_E	26_E	0.526	0.73
95_S	99_K	0.525	0.73
15_A	19_K	0.524	0.73
121_H	125_E	0.523	0.72
60_V	94_S	0.519	0.72
10_G	56_N	0.519	0.72
61_N	81_L	0.518	0.72
14_K	106_Q	0.518	0.72
68_I	74_I	0.517	0.72
107_C	111_I	0.516	0.71
14_K	50_R	0.515	0.71
31_I	65_A	0.514	0.71
10_G	13_G	0.513	0.71
2_I	27_A	0.510	0.71
84_I	89_A	0.510	0.71
49_N	121_H	0.504	0.70
98_K	129_K	0.502	0.69
14_K	42_A	0.501	0.69
18_E	106_Q	0.500	0.69

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
2jl1A	2	0.9615	66.2	0.918	Contact Map
3istA	2	0.9846	64.3	0.919	Contact Map
2dwuA	2	0.9231	63.1	0.919	Contact Map
2jfqA	2	0.9769	61.5	0.92	Contact Map
1zuwA	2	0.9769	60.6	0.921	Contact Map
3e48A	2	0.9692	60.3	0.921	Contact Map
2vvtA	2	0.9769	60.3	0.921	Contact Map
2gzmA	3	0.9769	59.5	0.921	Contact Map
4ppmA	2	0	58	0.922	Contact Map
1yqdA	2	0.9462	57.4	0.922	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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