DUF1405 - PFAM28P - GREMLIN Contacts

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DUF1405 - Protein of unknown function (DUF1405)

PFAM:	PF07187	Sequences: TIYGYYWYGPQLAETPPWFWPFVPDSPTASLFFTLALLLLLLGRNSPLLEALAFVTLIKYGLWAVVMLLLFAAQGGSLTQGWMLIVSHLGMAVEALLYARFYRFKVWALAVAAAWTLLNDVVDYVFGFHPWLYSPLDDYLAAIGAFTFWLSILSLAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	157 (156)
Sequences:	1194 (829)
Seq/√Len:	66.4
META:	0.58

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_T	23_V	5.127	1.00
39_L	46_S	3.056	1.00
122_V	128_F	2.881	1.00
55_V	109_L	2.772	1.00
56_T	116_T	2.660	1.00
6_Y	9_G	2.592	1.00
59_K	120_D	2.430	1.00
145_A	148_F	2.415	1.00
18_W	21_P	2.245	1.00
35_L	49_L	2.189	1.00
107_W	111_V	2.143	1.00
36_A	50_E	2.088	1.00
35_L	39_L	2.078	1.00
9_G	13_A	2.040	1.00
26_S	29_A	2.022	1.00
121_V	126_F	1.924	1.00
11_Q	15_T	1.881	1.00
145_A	149_W	1.878	1.00
48_L	107_W	1.818	1.00
69_L	73_A	1.790	1.00
121_V	125_V	1.789	1.00
113_A	155_L	1.774	1.00
29_A	56_T	1.740	1.00
105_K	108_A	1.738	1.00
16_P	128_F	1.686	0.99
69_L	85_I	1.653	0.99
52_L	112_A	1.649	0.99
36_A	40_L	1.608	0.99
48_L	111_V	1.564	0.99
26_S	53_A	1.550	0.99
147_T	151_S	1.549	0.99
50_E	102_Y	1.541	0.99
55_V	116_T	1.532	0.99
66_V	146_F	1.509	0.99
58_I	96_L	1.491	0.99
50_E	101_F	1.488	0.99
84_L	87_S	1.487	0.99
17_P	21_P	1.483	0.99
129_H	140_L	1.465	0.98
36_A	101_F	1.455	0.98
65_V	85_I	1.449	0.98
29_A	53_A	1.436	0.98
36_A	98_Y	1.436	0.98
114_A	118_L	1.397	0.98
26_S	91_M	1.393	0.98
122_V	126_F	1.368	0.98
54_F	95_A	1.367	0.98
22_F	122_V	1.345	0.97
57_L	94_E	1.331	0.97
19_F	122_V	1.312	0.97
34_T	38_L	1.302	0.97
80_Q	83_M	1.301	0.97
68_L	72_A	1.278	0.96
62_L	92_A	1.272	0.96
22_F	118_L	1.244	0.96
10_P	13_A	1.227	0.95
56_T	115_W	1.218	0.95
141_A	148_F	1.214	0.95
36_A	39_L	1.197	0.95
25_D	130_P	1.184	0.94
38_L	42_L	1.183	0.94
39_L	49_L	1.164	0.94
117_L	152_I	1.161	0.94
54_F	96_L	1.157	0.94
144_G	148_F	1.148	0.93
153_L	156_A	1.145	0.93
83_M	87_S	1.138	0.93
62_L	89_L	1.127	0.93
141_A	145_A	1.110	0.92
58_I	62_L	1.108	0.92
125_V	130_P	1.104	0.92
68_L	81_G	1.095	0.92
114_A	117_L	1.086	0.91
65_V	89_L	1.083	0.91
50_E	98_Y	1.080	0.91
82_W	85_I	1.075	0.91
26_S	30_S	1.075	0.91
30_S	34_T	1.059	0.90
129_H	132_L	1.045	0.90
126_F	142_A	1.034	0.89
63_W	124_Y	1.019	0.88
110_A	156_A	1.010	0.88
17_P	20_W	0.988	0.87
117_L	120_D	0.976	0.86
79_T	82_W	0.974	0.86
90_G	93_V	0.973	0.86
1_T	30_S	0.961	0.85
118_L	131_W	0.949	0.84
9_G	20_W	0.942	0.84
128_F	133_Y	0.936	0.84
64_A	68_L	0.922	0.83
51_A	112_A	0.908	0.82
137_D	140_L	0.907	0.82
123_D	130_P	0.904	0.81
45_N	50_E	0.901	0.81
4_G	8_Y	0.896	0.81
14_E	132_L	0.893	0.81
135_P	138_D	0.884	0.80
16_P	20_W	0.865	0.78
137_D	141_A	0.861	0.78
108_A	112_A	0.859	0.78
33_F	37_L	0.859	0.78
141_A	144_G	0.858	0.78
72_A	81_G	0.856	0.78
53_A	57_L	0.851	0.77
136_L	139_Y	0.851	0.77
79_T	86_V	0.846	0.77
3_Y	7_W	0.843	0.77
64_A	67_M	0.841	0.77
34_T	57_L	0.840	0.76
116_T	120_D	0.838	0.76
74_Q	139_Y	0.830	0.76
5_Y	28_T	0.824	0.75
96_L	134_S	0.822	0.75
144_G	150_L	0.808	0.74
55_V	155_L	0.804	0.73
11_Q	23_V	0.799	0.73
53_A	94_E	0.799	0.73
6_Y	10_P	0.791	0.72
74_Q	138_D	0.788	0.72
58_I	92_A	0.786	0.72
72_A	82_W	0.781	0.71
98_Y	101_F	0.778	0.71
149_W	152_I	0.776	0.71
3_Y	84_L	0.772	0.70
129_H	137_D	0.769	0.70
64_A	133_Y	0.768	0.70
16_P	37_L	0.764	0.69
82_W	86_V	0.762	0.69
71_F	76_G	0.759	0.69
78_L	82_W	0.758	0.69
7_W	68_L	0.751	0.68
78_L	81_G	0.747	0.68
57_L	91_M	0.746	0.68
73_A	81_G	0.743	0.67
118_L	145_A	0.741	0.67
96_L	99_A	0.732	0.66
64_A	116_T	0.728	0.66
3_Y	98_Y	0.722	0.65
94_E	156_A	0.718	0.65
47_P	104_F	0.717	0.64
1_T	31_L	0.712	0.64
21_P	118_L	0.708	0.63
142_A	146_F	0.708	0.63
117_L	151_S	0.705	0.63
12_L	60_Y	0.691	0.62
143_I	146_F	0.688	0.61
29_A	119_N	0.687	0.61
89_L	93_V	0.687	0.61
121_V	148_F	0.686	0.61
72_A	95_A	0.684	0.61
9_G	14_E	0.673	0.60
68_L	71_F	0.671	0.59
76_G	80_Q	0.658	0.58
107_W	110_A	0.658	0.58
47_P	50_E	0.653	0.57
36_A	102_Y	0.646	0.56
86_V	90_G	0.645	0.56
5_Y	24_P	0.645	0.56
42_L	96_L	0.642	0.56
71_F	85_I	0.641	0.56
14_E	77_S	0.641	0.56
140_L	143_I	0.639	0.56
12_L	20_W	0.638	0.56
35_L	45_N	0.634	0.55
32_F	87_S	0.631	0.55
71_F	133_Y	0.630	0.55
152_I	156_A	0.629	0.54
86_V	115_W	0.629	0.54
25_D	32_F	0.629	0.54
13_A	16_P	0.627	0.54
53_A	87_S	0.624	0.54
58_I	102_Y	0.622	0.54
30_S	87_S	0.620	0.53
37_L	90_G	0.620	0.53
17_P	106_V	0.619	0.53
76_G	79_T	0.617	0.53
18_W	38_L	0.615	0.53
24_P	84_L	0.613	0.53
127_G	141_A	0.612	0.52
135_P	143_I	0.611	0.52
151_S	155_L	0.609	0.52
25_D	123_D	0.605	0.52
112_A	155_L	0.594	0.50
2_I	6_Y	0.587	0.50
77_S	80_Q	0.585	0.49
21_P	26_S	0.584	0.49
20_W	128_F	0.581	0.49
72_A	78_L	0.576	0.48
106_V	109_L	0.575	0.48
112_A	130_P	0.568	0.47
118_L	121_V	0.568	0.47
30_S	33_F	0.566	0.47
3_Y	6_Y	0.558	0.46
86_V	89_L	0.557	0.46
141_A	156_A	0.556	0.46
57_L	68_L	0.554	0.46
150_L	153_L	0.554	0.46
135_P	140_L	0.552	0.45
42_L	45_N	0.551	0.45
143_I	149_W	0.548	0.45
27_P	84_L	0.548	0.45
72_A	90_G	0.545	0.45
49_L	53_A	0.544	0.44
60_Y	116_T	0.539	0.44
96_L	153_L	0.538	0.44
7_W	30_S	0.537	0.44
37_L	67_M	0.536	0.44
3_Y	11_Q	0.535	0.43
11_Q	84_L	0.535	0.43
127_G	140_L	0.535	0.43
141_A	147_T	0.532	0.43
118_L	149_W	0.532	0.43
66_V	70_L	0.530	0.43
5_Y	64_A	0.530	0.43
29_A	116_T	0.529	0.43
21_P	77_S	0.527	0.43
58_I	154_S	0.522	0.42
29_A	57_L	0.522	0.42
52_L	95_A	0.519	0.42
60_Y	65_V	0.517	0.41
53_A	89_L	0.516	0.41
89_L	116_T	0.514	0.41
135_P	139_Y	0.513	0.41
75_G	79_T	0.513	0.41
20_W	134_S	0.512	0.41
58_I	153_L	0.511	0.41
113_A	117_L	0.510	0.41
44_R	106_V	0.507	0.40
82_W	147_T	0.505	0.40
151_S	154_S	0.505	0.40
24_P	122_V	0.502	0.40
14_E	17_P	0.500	0.39
55_V	94_E	0.500	0.39

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
3tw5A	1	0.3312	1.2	0.966	Contact Map
4hkrA	3	0.2548	1	0.968	Contact Map
2mfrA	1	0.3439	1	0.968	Contact Map
2hfrA	1	0.172	1	0.968	Contact Map
2jp3A	1	0.2293	0.9	0.969	Contact Map
4m64A	1	0.3567	0.9	0.969	Contact Map
3wu2T	1	0.1338	0.8	0.97	Contact Map
2l6wA	2	0.1592	0.8	0.97	Contact Map
2jwaA	2	0.1529	0.7	0.971	Contact Map
2k1aA	1	0.242	0.7	0.971	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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