DUF3780 - PFAM28P - GREMLIN Contacts

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DUF3780 - Protein of unknown function (DUF3780)

PFAM:	PF12635	Sequences: KRKTLGFGFPPEESPHHFLVEIPAGRTGPVLISEHFGWDGDEEGIPDDELRVILDRPKWSAIADEVRREFNRRLKAAGLKTGRWKTGENPVDRLLGKELCVLAWAIEDADPELIPVAIRNWLGLRPEERWWLFTMTAAATGHAEDGGRGWRKALRYALTENPVSELLRKRRPRPKKKKEERPDLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	185 (166)
Sequences:	710 (401)
Seq/√Len:	31.1
META:	0.887

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
101_V	154_L	5.823	1.00
62_I	103_A	4.034	1.00
66_V	99_L	3.911	1.00
32_I	103_A	3.638	1.00
52_V	103_A	3.597	1.00
54_L	103_A	3.234	1.00
136_T	154_L	2.874	1.00
73_R	126_P	2.755	1.00
152_K	160_E	2.593	1.00
4_T	10_P	2.579	1.00
51_R	137_A	2.502	0.99
50_L	143_A	2.474	0.99
100_C	154_L	2.462	0.99
62_I	106_I	2.386	0.99
94_L	135_M	2.223	0.99
6_G	90_P	2.189	0.99
21_E	88_E	2.158	0.98
20_V	91_V	2.085	0.98
52_V	100_C	2.016	0.97
71_N	82_G	1.972	0.97
152_K	156_Y	1.877	0.96
9_F	14_S	1.784	0.95
55_D	58_K	1.773	0.95
82_G	89_N	1.770	0.95
153_A	157_A	1.732	0.94
123_G	160_E	1.731	0.94
67_R	84_W	1.689	0.93
79_L	133_F	1.651	0.92
97_K	134_T	1.585	0.91
36_F	51_R	1.572	0.90
35_H	47_D	1.564	0.90
65_E	68_R	1.481	0.87
69_E	138_A	1.478	0.87
152_K	159_T	1.458	0.87
136_T	141_G	1.448	0.86
117_A	120_N	1.391	0.84
9_F	15_P	1.359	0.82
31_L	50_L	1.355	0.82
51_R	126_P	1.346	0.82
108_D	146_G	1.311	0.80
117_A	159_T	1.254	0.77
155_R	159_T	1.231	0.75
113_L	160_E	1.204	0.74
147_G	154_L	1.201	0.74
110_D	123_G	1.197	0.73
29_P	53_I	1.188	0.73
11_P	161_N	1.183	0.73
22_I	89_N	1.174	0.72
24_A	52_V	1.173	0.72
79_L	147_G	1.170	0.72
108_D	147_G	1.166	0.71
119_R	135_M	1.156	0.71
113_L	152_K	1.155	0.71
63_A	67_R	1.153	0.71
16_H	36_F	1.146	0.70
124_L	129_R	1.136	0.69
9_F	51_R	1.135	0.69
150_W	153_A	1.126	0.69
91_V	94_L	1.123	0.68
106_I	123_G	1.111	0.68
9_F	13_E	1.101	0.67
101_V	125_R	1.099	0.67
6_G	91_V	1.097	0.67
63_A	99_L	1.089	0.66
37_G	49_E	1.086	0.66
60_S	63_A	1.077	0.65
66_V	117_A	1.077	0.65
66_V	118_I	1.067	0.64
120_N	161_N	1.055	0.64
134_T	138_A	1.036	0.62
117_A	140_T	1.034	0.62
25_G	57_P	1.020	0.61
21_E	31_L	1.019	0.61
65_E	148_R	1.015	0.60
50_L	133_F	1.011	0.60
39_D	58_K	1.011	0.60
20_V	82_G	1.007	0.60
109_A	113_L	1.004	0.60
54_L	62_I	1.003	0.60
3_K	10_P	0.997	0.59
4_T	80_K	0.990	0.59
45_I	51_R	0.952	0.56
113_L	159_T	0.939	0.54
117_A	135_M	0.927	0.54
140_T	162_P	0.927	0.54
106_I	120_N	0.923	0.53
45_I	89_N	0.919	0.53
46_P	89_N	0.918	0.53
83_R	133_F	0.914	0.52
120_N	162_P	0.912	0.52
70_F	84_W	0.912	0.52
51_R	109_A	0.905	0.52
106_I	117_A	0.900	0.51
41_D	133_F	0.899	0.51
4_T	81_T	0.898	0.51
61_A	119_R	0.888	0.50
46_P	143_A	0.874	0.49
92_D	145_D	0.868	0.49
7_F	70_F	0.864	0.48
51_R	61_A	0.859	0.48
63_A	83_R	0.857	0.48
120_N	140_T	0.856	0.48
42_E	53_I	0.852	0.47
6_G	117_A	0.847	0.47
54_L	84_W	0.847	0.47
64_D	152_K	0.845	0.47
17_H	120_N	0.839	0.46
91_V	135_M	0.834	0.46
120_N	134_T	0.829	0.46
22_I	87_G	0.824	0.45
92_D	100_C	0.816	0.45
64_D	67_R	0.816	0.45
93_R	125_R	0.812	0.44
7_F	20_V	0.810	0.44
41_D	46_P	0.809	0.44
25_G	81_T	0.807	0.44
89_N	125_R	0.802	0.43
76_A	139_A	0.798	0.43
67_R	126_P	0.795	0.43
64_D	95_L	0.795	0.43
42_E	45_I	0.794	0.43
123_G	161_N	0.791	0.43
28_G	43_E	0.790	0.43
6_G	49_E	0.789	0.42
15_P	60_S	0.783	0.42
66_V	91_V	0.782	0.42
117_A	155_R	0.780	0.42
90_P	111_P	0.772	0.41
23_P	26_R	0.771	0.41
48_D	58_K	0.758	0.40
20_V	32_I	0.757	0.40
118_I	140_T	0.750	0.39
149_G	153_A	0.750	0.39
25_G	30_V	0.745	0.39
23_P	87_G	0.743	0.39
30_V	118_I	0.742	0.39
36_F	89_N	0.739	0.39
31_L	53_I	0.737	0.38
120_N	139_A	0.735	0.38
110_D	113_L	0.735	0.38
31_L	75_K	0.734	0.38
10_P	92_D	0.732	0.38
16_H	34_E	0.727	0.38
41_D	45_I	0.725	0.37
16_H	19_L	0.721	0.37
140_T	148_R	0.715	0.37
15_P	40_G	0.707	0.36
74_L	95_L	0.707	0.36
123_G	137_A	0.707	0.36
21_E	35_H	0.706	0.36
69_E	72_R	0.705	0.36
27_T	86_T	0.701	0.36
4_T	51_R	0.698	0.35
115_P	165_E	0.697	0.35
108_D	155_R	0.692	0.35
89_N	94_L	0.688	0.35
42_E	81_T	0.686	0.35
4_T	15_P	0.686	0.35
102_L	107_E	0.685	0.34
8_G	18_F	0.680	0.34
37_G	82_G	0.674	0.34
10_P	68_R	0.668	0.33
138_A	161_N	0.665	0.33
82_G	124_L	0.664	0.33
147_G	152_K	0.664	0.33
153_A	158_L	0.663	0.33
148_R	160_E	0.662	0.33
80_K	148_R	0.655	0.32
25_G	28_G	0.653	0.32
31_L	41_D	0.650	0.32
52_V	133_F	0.650	0.32
97_K	135_M	0.646	0.32
118_I	123_G	0.645	0.32
111_P	114_I	0.642	0.31
134_T	159_T	0.638	0.31
93_R	139_A	0.635	0.31
115_P	140_T	0.633	0.31
140_T	155_R	0.633	0.31
12_E	27_T	0.626	0.30
14_S	38_W	0.625	0.30
23_P	89_N	0.625	0.30
19_L	29_P	0.619	0.30
61_A	135_M	0.618	0.30
49_E	139_A	0.616	0.30
134_T	161_N	0.615	0.30
101_V	116_V	0.611	0.29
30_V	136_T	0.610	0.29
74_L	82_G	0.607	0.29
47_D	106_I	0.607	0.29
80_K	144_E	0.606	0.29
97_K	136_T	0.603	0.29
20_V	23_P	0.601	0.29
17_H	20_V	0.597	0.28
79_L	86_T	0.596	0.28
49_E	101_V	0.595	0.28
8_G	11_P	0.592	0.28
10_P	77_A	0.592	0.28
160_E	163_V	0.591	0.28
49_E	76_A	0.590	0.28
131_W	157_A	0.587	0.28
58_K	114_I	0.587	0.28
67_R	75_K	0.585	0.28
20_V	84_W	0.583	0.27
41_D	44_G	0.582	0.27
162_P	165_E	0.581	0.27
49_E	133_F	0.578	0.27
57_P	61_A	0.577	0.27
51_R	101_V	0.572	0.27
120_N	123_G	0.572	0.27
119_R	140_T	0.569	0.27
136_T	156_Y	0.568	0.27
126_P	133_F	0.566	0.26
70_F	126_P	0.564	0.26
14_S	17_H	0.563	0.26
50_L	53_I	0.563	0.26
58_K	94_L	0.560	0.26
58_K	111_P	0.559	0.26
61_A	115_P	0.558	0.26
32_I	91_V	0.557	0.26
62_I	80_K	0.556	0.26
32_I	60_S	0.555	0.26
132_L	154_L	0.555	0.26
37_G	51_R	0.555	0.26
35_H	51_R	0.552	0.26
3_K	53_I	0.549	0.25
7_F	17_H	0.548	0.25
28_G	41_D	0.544	0.25
94_L	133_F	0.544	0.25
16_H	52_V	0.542	0.25
99_L	113_L	0.541	0.25
8_G	12_E	0.540	0.25
58_K	155_R	0.540	0.25
57_P	81_T	0.535	0.24
138_A	162_P	0.529	0.24
11_P	83_R	0.528	0.24
6_G	85_K	0.526	0.24
58_K	108_D	0.524	0.24
72_R	133_F	0.523	0.24
23_P	68_R	0.523	0.24
97_K	120_N	0.522	0.24
114_I	119_R	0.517	0.23
97_K	138_A	0.516	0.23
55_D	155_R	0.515	0.23
58_K	162_P	0.513	0.23
80_K	137_A	0.511	0.23
4_T	79_L	0.508	0.23
3_K	80_K	0.505	0.23
54_L	109_A	0.500	0.22
19_L	33_S	0.500	0.22

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
4bxoA	1	0.4054	11.3	0.965	Contact Map
3pzjA	2	0.3189	10	0.966	Contact Map
2z10A	2	0.3784	9.7	0.966	Contact Map
1yreA	2	0.3784	8.3	0.967	Contact Map
1wdkA	2	0.3243	7.7	0.968	Contact Map
4avaA	1	0.4324	5.4	0.97	Contact Map
1nslA	3	0.3135	4.4	0.971	Contact Map
1nltA	1	0.3027	4.3	0.972	Contact Map
2wtgA	2	0.3243	4.1	0.972	Contact Map
5bo7A	2	0.3135	4	0.972	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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