DUF2992 - PFAM28P - GREMLIN Contacts

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DUF2992 - Protein of unknown function (DUF2992)

PFAM:	PF11208	Sequences: LTVFFEDPFWVGVFERIEDGKLSVCKVTFGAEPKDYEVYEFVLKNYYRLRFSPAVEAEVKEEKKINPKRLQREARKQLQNTGIGTKAQQALKLQQEQNKKERKKRSREQREAEKERKFELKQQKKKEKHRGH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	132 (132)
Sequences:	1400 (1075)
Seq/√Len:	93.6
META:	0.711

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_K	95_Q	5.436	1.00
45_N	48_R	3.995	1.00
85_T	88_Q	3.408	1.00
118_F	122_Q	2.663	1.00
4_F	11_V	2.545	1.00
40_E	44_K	2.517	1.00
116_R	120_L	2.505	1.00
16_R	23_S	2.491	1.00
14_F	46_Y	2.324	1.00
115_E	119_E	2.316	1.00
122_Q	125_K	2.302	1.00
84_G	89_Q	2.300	1.00
14_F	42_V	2.250	1.00
108_E	112_A	2.201	1.00
22_L	87_A	2.198	1.00
14_F	27_V	2.115	1.00
39_Y	43_L	2.108	1.00
123_Q	127_E	2.091	1.00
89_Q	92_K	1.879	1.00
105_R	109_Q	1.857	1.00
106_S	109_Q	1.802	1.00
70_L	74_A	1.756	1.00
5_F	8_P	1.734	1.00
1_L	12_G	1.703	1.00
84_G	88_Q	1.609	1.00
113_E	116_R	1.589	1.00
12_G	29_F	1.566	1.00
22_L	55_V	1.509	1.00
1_L	14_F	1.464	1.00
94_Q	97_Q	1.445	1.00
13_V	82_G	1.443	1.00
64_K	70_L	1.415	0.99
65_I	70_L	1.387	0.99
111_E	115_E	1.384	0.99
65_I	73_E	1.345	0.99
18_E	23_S	1.325	0.99
117_K	120_L	1.315	0.99
53_P	94_Q	1.313	0.99
94_Q	98_N	1.303	0.99
107_R	111_E	1.290	0.99
121_K	125_K	1.279	0.99
71_Q	74_A	1.270	0.99
25_C	49_L	1.259	0.99
112_A	116_R	1.250	0.99
75_R	78_L	1.249	0.99
127_E	132_H	1.245	0.99
69_R	72_R	1.209	0.98
18_E	21_K	1.208	0.98
127_E	130_R	1.208	0.98
95_Q	98_N	1.196	0.98
101_E	104_K	1.191	0.98
13_V	22_L	1.187	0.98
118_F	121_K	1.169	0.98
46_Y	51_F	1.145	0.97
111_E	114_K	1.144	0.97
113_E	117_K	1.139	0.97
106_S	110_R	1.129	0.97
129_H	132_H	1.124	0.97
4_F	13_V	1.097	0.97
25_C	51_F	1.091	0.97
41_F	45_N	1.073	0.96
5_F	10_W	1.069	0.96
6_E	26_K	1.061	0.96
114_K	117_K	1.041	0.96
128_K	131_G	1.029	0.95
110_R	114_K	1.028	0.95
4_F	22_L	1.026	0.95
74_A	77_Q	1.015	0.95
1_L	42_V	1.013	0.95
125_K	129_H	0.955	0.93
73_E	77_Q	0.945	0.93
10_W	32_E	0.941	0.93
86_K	94_Q	0.932	0.92
53_P	97_Q	0.928	0.92
67_P	75_R	0.927	0.92
14_F	23_S	0.919	0.92
92_K	96_E	0.885	0.90
104_K	108_E	0.878	0.90
85_T	89_Q	0.876	0.90
120_L	129_H	0.871	0.89
36_Y	40_E	0.863	0.89
34_K	38_V	0.858	0.89
37_E	41_F	0.826	0.87
63_K	87_A	0.810	0.86
107_R	124_K	0.809	0.86
67_P	72_R	0.807	0.85
17_I	57_A	0.807	0.85
126_K	132_H	0.797	0.85
98_N	109_Q	0.796	0.85
8_P	11_V	0.796	0.85
109_Q	112_A	0.789	0.84
63_K	70_L	0.785	0.84
93_L	97_Q	0.784	0.84
83_I	92_K	0.777	0.83
125_K	130_R	0.752	0.81
74_A	78_L	0.748	0.81
70_L	73_E	0.746	0.81
60_K	116_R	0.744	0.80
27_V	45_N	0.736	0.80
55_V	58_E	0.732	0.79
64_K	73_E	0.724	0.79
46_Y	125_K	0.721	0.78
98_N	101_E	0.712	0.77
1_L	10_W	0.709	0.77
98_N	105_R	0.703	0.77
14_F	51_F	0.703	0.77
2_T	10_W	0.702	0.76
46_Y	76_K	0.699	0.76
15_E	22_L	0.697	0.76
57_A	60_K	0.696	0.76
84_G	90_A	0.688	0.75
34_K	37_E	0.679	0.74
17_I	21_K	0.679	0.74
120_L	123_Q	0.670	0.73
78_L	81_T	0.667	0.73
21_K	54_A	0.666	0.73
73_E	76_K	0.661	0.72
71_Q	86_K	0.658	0.72
118_F	125_K	0.657	0.72
47_Y	80_N	0.657	0.72
40_E	63_K	0.655	0.71
4_F	12_G	0.652	0.71
27_V	42_V	0.652	0.71
55_V	87_A	0.649	0.71
92_K	98_N	0.648	0.71
50_R	97_Q	0.645	0.70
125_K	128_K	0.643	0.70
86_K	118_F	0.642	0.70
48_R	112_A	0.640	0.70
51_F	86_K	0.637	0.69
56_E	59_V	0.636	0.69
61_E	79_Q	0.625	0.68
17_I	87_A	0.619	0.67
91_L	94_Q	0.615	0.67
102_R	106_S	0.611	0.66
1_L	38_V	0.610	0.66
61_E	65_I	0.605	0.65
38_V	67_P	0.600	0.65
11_V	26_K	0.599	0.64
11_V	25_C	0.599	0.64
61_E	64_K	0.597	0.64
124_K	128_K	0.596	0.64
89_Q	93_L	0.593	0.64
16_R	51_F	0.585	0.63
46_Y	50_R	0.585	0.63
3_V	16_R	0.582	0.62
65_I	74_A	0.582	0.62
119_E	123_Q	0.580	0.62
50_R	107_R	0.578	0.62
27_V	51_F	0.576	0.61
26_K	61_E	0.576	0.61
108_E	114_K	0.576	0.61
80_N	114_K	0.571	0.61
9_F	28_T	0.564	0.60
118_F	132_H	0.564	0.60
47_Y	81_T	0.563	0.60
2_T	15_E	0.563	0.60
70_L	78_L	0.563	0.60
9_F	103_K	0.562	0.60
88_Q	96_E	0.562	0.60
3_V	13_V	0.561	0.59
26_K	29_F	0.558	0.59
102_R	113_E	0.557	0.59
17_I	22_L	0.557	0.59
100_K	106_S	0.555	0.59
29_F	35_D	0.552	0.58
2_T	132_H	0.549	0.58
28_T	71_Q	0.547	0.58
105_R	108_E	0.547	0.58
42_V	47_Y	0.543	0.57
84_G	92_K	0.542	0.57
53_P	120_L	0.536	0.56
17_I	20_G	0.535	0.56
55_V	94_Q	0.533	0.56
115_E	123_Q	0.532	0.56
58_E	63_K	0.529	0.55
52_S	55_V	0.525	0.55
24_V	94_Q	0.524	0.54
65_I	79_Q	0.524	0.54
46_Y	75_R	0.522	0.54
15_E	24_V	0.520	0.54
21_K	24_V	0.517	0.53
53_P	56_E	0.516	0.53
23_S	51_F	0.515	0.53
75_R	81_T	0.515	0.53
86_K	90_A	0.513	0.53
60_K	63_K	0.510	0.52
94_Q	129_H	0.510	0.52
5_F	43_L	0.507	0.52
11_V	28_T	0.507	0.52
107_R	129_H	0.506	0.52
3_V	10_W	0.505	0.52
25_C	114_K	0.505	0.52
49_L	89_Q	0.504	0.52
77_Q	126_K	0.503	0.51
27_V	41_F	0.503	0.51
68_K	76_K	0.502	0.51
29_F	41_F	0.500	0.51

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
2oq1A	1	0.4242	44	0.922	Contact Map
2y3aB	1	0.4242	43	0.923	Contact Map
2hdvA	1	0.4318	39.9	0.924	Contact Map
2cs0A	1	0.4697	38.8	0.925	Contact Map
2mk2A	1	0.4091	38.8	0.925	Contact Map
4tziA	1	0.4242	38.7	0.925	Contact Map
4u5wB	2	0.4318	37.6	0.925	Contact Map
1nrvA	1	0.3864	37.6	0.925	Contact Map
2ecdA	1	0.4848	37.1	0.926	Contact Map
1ka6A	1	0.447	36.9	0.926	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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