DUF788 - PFAM28P - GREMLIN Contacts

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DUF788 - Protein of unknown function (DUF788)

PFAM:	PF05620	Sequences: MANKGAKKIAEENAATLKFLHLIILGVNALYLLLRFLFRRSSFTSRSLLLYLLLSLPYLACYYYLERMARPKYDEDGELLDAGEDLNAEGLTEYMFDVIYLTWFVQVLSSLFSNKFWWLYLVIPAYAAYKLWGLLGPWLGGFAGGAEAAEEPEATSKRQEKLEKRGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	167 (166)
Sequences:	565 (447)
Seq/√Len:	34.7
META:	0.195

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_Y	79_L	6.081	1.00
126_Y	130_K	3.329	1.00
23_I	103_W	3.260	1.00
134_L	137_P	3.111	1.00
28_N	58_Y	2.715	1.00
157_K	161_K	2.634	1.00
3_N	8_K	2.461	1.00
104_F	119_L	2.405	1.00
16_T	19_F	2.373	0.99
156_S	161_K	2.166	0.99
49_L	53_L	2.116	0.99
94_Y	126_Y	2.044	0.98
45_S	49_L	2.043	0.98
1_M	7_K	1.952	0.98
35_R	114_N	1.932	0.98
161_K	165_R	1.924	0.98
62_Y	66_E	1.916	0.98
113_S	116_F	1.912	0.98
28_N	51_Y	1.909	0.98
132_W	137_P	1.882	0.97
64_Y	68_M	1.802	0.96
103_W	120_Y	1.771	0.96
90_G	100_Y	1.768	0.96
155_T	160_E	1.755	0.96
88_A	92_T	1.740	0.96
18_K	22_L	1.690	0.95
25_L	29_A	1.675	0.95
145_G	148_A	1.666	0.94
61_C	65_L	1.657	0.94
128_A	132_W	1.656	0.94
1_M	8_K	1.654	0.94
36_F	143_A	1.644	0.94
13_N	85_D	1.638	0.94
102_T	120_Y	1.561	0.92
144_G	150_E	1.559	0.92
105_V	120_Y	1.558	0.92
34_L	38_F	1.537	0.92
108_L	116_F	1.535	0.92
24_I	62_Y	1.531	0.92
20_L	100_Y	1.466	0.90
10_A	69_A	1.462	0.90
6_A	90_G	1.460	0.89
4_K	8_K	1.424	0.88
156_S	160_E	1.422	0.88
13_N	17_L	1.372	0.86
94_Y	115_K	1.364	0.86
156_S	164_K	1.335	0.85
26_G	30_L	1.328	0.84
102_T	117_W	1.325	0.84
26_G	139_L	1.317	0.84
146_A	151_E	1.301	0.83
20_L	96_F	1.274	0.82
160_E	165_R	1.256	0.81
118_W	121_L	1.242	0.80
28_N	31_Y	1.241	0.80
58_Y	69_A	1.231	0.80
21_H	62_Y	1.218	0.79
69_A	113_S	1.218	0.79
60_A	146_A	1.215	0.79
6_A	82_A	1.171	0.76
30_L	34_L	1.159	0.75
10_A	82_A	1.157	0.75
16_T	96_F	1.152	0.75
102_T	127_A	1.148	0.75
127_A	131_L	1.145	0.74
17_L	159_Q	1.141	0.74
151_E	158_R	1.100	0.71
96_F	100_Y	1.089	0.71
55_S	59_L	1.087	0.70
26_G	147_E	1.077	0.70
69_A	81_D	1.072	0.69
27_V	91_L	1.066	0.69
6_A	161_K	1.061	0.68
19_F	23_I	1.060	0.68
162_L	165_R	1.049	0.68
154_A	159_Q	1.039	0.67
149_A	152_P	1.038	0.67
131_L	134_L	1.037	0.67
65_L	127_A	1.032	0.66
121_L	125_A	1.024	0.66
141_G	146_A	1.020	0.65
125_A	129_Y	1.010	0.65
101_L	104_F	1.007	0.64
20_L	23_I	1.007	0.64
156_S	165_R	1.000	0.64
6_A	9_I	0.993	0.63
121_L	148_A	0.993	0.63
32_L	111_L	0.989	0.63
53_L	57_P	0.985	0.63
92_T	95_M	0.981	0.62
86_L	92_T	0.970	0.61
103_W	158_R	0.954	0.60
53_L	120_Y	0.941	0.59
14_A	53_L	0.940	0.59
50_L	105_V	0.939	0.59
64_Y	132_W	0.926	0.58
30_L	81_D	0.919	0.57
156_S	159_Q	0.918	0.57
106_Q	109_S	0.913	0.57
100_Y	156_S	0.908	0.56
8_K	20_L	0.908	0.56
4_K	120_Y	0.895	0.55
143_A	148_A	0.884	0.54
69_A	105_V	0.879	0.54
13_N	90_G	0.870	0.53
5_G	8_K	0.864	0.53
15_A	107_V	0.859	0.52
65_L	96_F	0.858	0.52
104_F	136_G	0.857	0.52
74_D	80_L	0.856	0.52
26_G	150_E	0.842	0.51
12_E	19_F	0.838	0.50
79_L	120_Y	0.831	0.50
87_N	96_F	0.831	0.50
83_G	86_L	0.825	0.49
5_G	9_I	0.822	0.49
69_A	82_A	0.816	0.48
125_A	152_P	0.810	0.48
22_L	26_G	0.810	0.48
2_A	7_K	0.804	0.47
74_D	78_E	0.797	0.47
69_A	112_F	0.795	0.47
30_L	108_L	0.793	0.47
85_D	117_W	0.790	0.46
15_A	19_F	0.787	0.46
64_Y	95_M	0.785	0.46
66_E	70_R	0.783	0.46
9_I	87_N	0.783	0.46
58_Y	103_W	0.783	0.46
33_L	73_Y	0.780	0.45
34_L	112_F	0.780	0.45
45_S	56_L	0.779	0.45
5_G	11_E	0.761	0.44
9_I	96_F	0.760	0.44
162_L	166_G	0.759	0.44
1_M	5_G	0.758	0.44
17_L	73_Y	0.755	0.43
141_G	147_E	0.743	0.42
122_V	147_E	0.742	0.42
142_F	146_A	0.739	0.42
138_W	149_A	0.737	0.42
141_G	152_P	0.737	0.42
30_L	82_A	0.737	0.42
146_A	150_E	0.735	0.42
100_Y	104_F	0.735	0.42
98_V	123_I	0.734	0.42
101_L	108_L	0.734	0.42
49_L	122_V	0.734	0.42
23_I	100_Y	0.729	0.41
34_L	39_R	0.724	0.41
38_F	44_T	0.721	0.40
17_L	21_H	0.719	0.40
140_G	143_A	0.719	0.40
93_E	96_F	0.717	0.40
16_T	20_L	0.709	0.40
38_F	101_L	0.708	0.39
13_N	100_Y	0.702	0.39
4_K	12_E	0.700	0.39
5_G	48_L	0.697	0.39
74_D	89_E	0.697	0.39
123_I	130_K	0.696	0.38
78_E	81_D	0.688	0.38
23_I	129_Y	0.687	0.38
145_G	152_P	0.684	0.37
152_P	156_S	0.682	0.37
28_N	106_Q	0.682	0.37
125_A	134_L	0.680	0.37
47_S	51_Y	0.678	0.37
31_Y	109_S	0.677	0.37
141_G	150_E	0.674	0.37
108_L	122_V	0.672	0.37
86_L	159_Q	0.669	0.36
42_S	114_N	0.668	0.36
114_N	125_A	0.664	0.36
107_V	111_L	0.660	0.36
55_S	77_G	0.655	0.35
130_K	134_L	0.652	0.35
33_L	49_L	0.647	0.35
14_A	18_K	0.638	0.34
161_K	164_K	0.635	0.34
24_I	104_F	0.632	0.33
158_R	162_L	0.632	0.33
163_E	166_G	0.631	0.33
9_I	13_N	0.631	0.33
29_A	33_L	0.625	0.33
48_L	57_P	0.622	0.33
121_L	150_E	0.621	0.33
46_R	50_L	0.621	0.33
133_G	136_G	0.611	0.32
156_S	162_L	0.607	0.32
65_L	103_W	0.607	0.32
144_G	152_P	0.602	0.31
104_F	129_Y	0.599	0.31
18_K	127_A	0.599	0.31
144_G	147_E	0.599	0.31
69_A	72_K	0.599	0.31
12_E	87_N	0.599	0.31
9_I	92_T	0.594	0.31
92_T	96_F	0.593	0.31
91_L	94_Y	0.587	0.30
63_Y	158_R	0.586	0.30
154_A	158_R	0.583	0.30
14_A	52_L	0.578	0.29
74_D	77_G	0.578	0.29
51_Y	92_T	0.577	0.29
131_L	153_E	0.572	0.29
25_L	45_S	0.571	0.29
158_R	166_G	0.569	0.29
76_D	89_E	0.566	0.29
45_S	105_V	0.561	0.28
109_S	131_L	0.560	0.28
136_G	143_A	0.559	0.28
112_F	116_F	0.559	0.28
28_N	55_S	0.558	0.28
159_Q	162_L	0.554	0.28
115_K	118_W	0.548	0.27
13_N	20_L	0.548	0.27
142_F	148_A	0.547	0.27
39_R	45_S	0.545	0.27
9_I	19_F	0.544	0.27
65_L	100_Y	0.541	0.27
75_E	139_L	0.540	0.27
94_Y	124_P	0.537	0.27
80_L	98_V	0.536	0.27
51_Y	58_Y	0.533	0.26
30_L	151_E	0.533	0.26
19_F	87_N	0.529	0.26
28_N	71_P	0.529	0.26
160_E	164_K	0.528	0.26
111_L	146_A	0.525	0.26
60_A	122_V	0.523	0.26
99_I	123_I	0.522	0.26
36_F	45_S	0.522	0.26
157_K	160_E	0.520	0.26
18_K	30_L	0.520	0.26
72_K	125_A	0.516	0.25
80_L	83_G	0.515	0.25
57_P	113_S	0.515	0.25
119_L	152_P	0.513	0.25
142_F	158_R	0.510	0.25
38_F	112_F	0.510	0.25
110_S	144_G	0.508	0.25
77_G	123_I	0.508	0.25
71_P	112_F	0.507	0.25
56_L	60_A	0.506	0.25
56_L	98_V	0.505	0.25
15_A	54_L	0.504	0.24
132_W	136_G	0.500	0.24
16_T	108_L	0.500	0.24

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
3sjdD	1	0.0898	14	0.942	Contact Map
3mk7C	2	0.6587	11.6	0.944	Contact Map
3zs9C	1	0.0958	11	0.945	Contact Map
1qfqB	1	0.0958	8.8	0.947	Contact Map
1jzpA	1	0.1198	6.1	0.951	Contact Map
4cylA	1	0.1856	5.2	0.953	Contact Map
3ukxC	1	0.0479	4.7	0.953	Contact Map
4ltoA	3	0.7006	4.7	0.953	Contact Map
3tx3A	2	0.9222	4.3	0.954	Contact Map
3qapA	1	0.4371	4	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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