DUF4291 - PFAM28P - GREMLIN Contacts

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DUF4291 - Domain of unknown function (DUF4291)

PFAM:	PF14124	Sequences: QIRAQYDDDTIVVYQAYRPAIADPAVAHGRFGGPPFSFDRMTWIKPSFLWMMYRSGWGTKEGQERVLAIRITREGFEWALAHAVLSSFDPGVYASREEWKRALARSPVRVQWDPERDPRGAPLERRAIQLGLRGEALRRYVDEWIVSIEDITPFVREQRALVRAGDLDEARALLPVERVY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	180 (179)
Sequences:	2192 (1654)
Seq/√Len:	123.6
META:	0.713

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_S	66_V	3.393	1.00
117_D	121_A	3.380	1.00
56_G	60_K	3.306	1.00
23_D	65_R	3.027	1.00
166_D	169_E	2.650	1.00
78_W	139_R	2.611	1.00
12_V	70_R	2.559	1.00
42_T	137_L	2.557	1.00
159_R	163_R	2.509	1.00
22_A	65_R	2.432	1.00
75_G	144_W	2.403	1.00
20_A	35_P	2.390	1.00
70_R	147_S	2.350	1.00
139_R	143_E	2.339	1.00
73_R	77_E	2.309	1.00
96_R	100_K	2.306	1.00
10_T	146_V	2.299	1.00
38_F	141_V	2.279	1.00
18_R	62_G	2.070	1.00
132_L	136_A	2.047	1.00
32_G	35_P	2.031	1.00
7_D	70_R	1.969	1.00
78_W	82_H	1.894	1.00
58_G	66_V	1.893	1.00
95_S	98_E	1.827	1.00
69_I	148_I	1.781	1.00
162_V	167_L	1.770	1.00
38_F	142_D	1.764	1.00
68_A	151_I	1.756	1.00
58_G	152_T	1.729	1.00
85_L	92_V	1.708	1.00
22_A	26_V	1.704	1.00
138_R	142_D	1.695	1.00
23_D	27_A	1.682	1.00
24_P	28_H	1.680	1.00
115_E	127_A	1.677	1.00
156_R	159_R	1.626	1.00
24_P	30_R	1.620	1.00
19_P	23_D	1.611	1.00
85_L	93_Y	1.561	1.00
77_E	180_Y	1.558	1.00
72_T	75_G	1.514	1.00
52_M	155_V	1.500	1.00
69_I	140_Y	1.473	1.00
83_A	110_V	1.473	1.00
69_I	145_I	1.452	1.00
30_R	145_I	1.436	1.00
30_R	142_D	1.431	1.00
100_K	103_L	1.401	1.00
151_I	155_V	1.398	1.00
94_A	98_E	1.394	1.00
72_T	146_V	1.303	1.00
151_I	154_F	1.301	1.00
76_F	130_L	1.290	1.00
85_L	89_D	1.280	1.00
24_P	32_G	1.271	1.00
6_Y	178_R	1.265	1.00
26_V	151_I	1.263	1.00
107_P	135_E	1.259	1.00
79_A	144_W	1.255	1.00
66_V	152_T	1.255	1.00
93_Y	102_A	1.246	1.00
19_P	65_R	1.235	0.99
145_I	148_I	1.230	0.99
28_H	32_G	1.212	0.99
162_V	166_D	1.204	0.99
38_F	138_R	1.187	0.99
19_P	64_E	1.182	0.99
135_E	138_R	1.174	0.99
42_T	141_V	1.173	0.99
159_R	162_V	1.152	0.99
17_Y	36_F	1.134	0.99
49_L	52_M	1.134	0.99
65_R	152_T	1.132	0.99
47_S	116_R	1.116	0.99
59_T	159_R	1.112	0.99
101_R	105_R	1.111	0.99
31_F	140_Y	1.110	0.99
115_E	125_R	1.083	0.99
88_F	99_W	1.076	0.99
5_Q	12_V	1.073	0.98
89_D	92_V	1.050	0.98
23_D	26_V	1.043	0.98
59_T	156_R	1.041	0.98
98_E	101_R	1.027	0.98
78_W	136_A	1.026	0.98
135_E	139_R	1.022	0.98
12_V	68_A	1.016	0.98
84_V	106_S	1.014	0.98
117_D	123_L	1.013	0.98
160_A	163_R	1.007	0.98
88_F	93_Y	1.005	0.98
86_S	109_R	0.985	0.97
6_Y	73_R	0.970	0.97
49_L	57_W	0.964	0.97
38_F	75_G	0.963	0.97
107_P	133_R	0.959	0.97
42_T	132_L	0.950	0.97
158_Q	170_A	0.943	0.97
100_K	104_A	0.934	0.96
161_L	169_E	0.931	0.96
119_R	167_L	0.917	0.96
41_M	109_R	0.907	0.96
79_A	130_L	0.902	0.96
152_T	156_R	0.901	0.96
75_G	79_A	0.900	0.96
10_T	70_R	0.898	0.95
106_S	133_R	0.896	0.95
3_R	115_E	0.889	0.95
26_V	65_R	0.885	0.95
53_Y	120_G	0.882	0.95
18_R	35_P	0.875	0.95
48_F	155_V	0.874	0.95
79_A	136_A	0.873	0.95
56_G	59_T	0.872	0.95
110_V	130_L	0.868	0.95
29_G	148_I	0.866	0.94
139_R	144_W	0.862	0.94
161_L	166_D	0.859	0.94
120_G	155_V	0.859	0.94
107_P	136_A	0.858	0.94
31_F	69_I	0.849	0.94
118_P	174_L	0.839	0.94
7_D	10_T	0.836	0.93
160_A	164_A	0.834	0.93
82_H	136_A	0.833	0.93
52_M	57_W	0.830	0.93
88_F	95_S	0.822	0.93
114_P	126_R	0.819	0.93
98_E	102_A	0.819	0.93
53_Y	122_P	0.809	0.92
58_G	156_R	0.808	0.92
36_F	140_Y	0.798	0.92
82_H	135_E	0.797	0.92
20_A	62_G	0.795	0.92
78_W	81_A	0.792	0.91
19_P	26_V	0.790	0.91
26_V	29_G	0.786	0.91
102_A	106_S	0.784	0.91
169_E	172_A	0.771	0.90
51_M	109_R	0.770	0.90
58_G	65_R	0.764	0.90
9_D	74_E	0.763	0.90
75_G	141_V	0.756	0.89
84_V	102_A	0.755	0.89
73_R	180_Y	0.744	0.89
31_F	34_P	0.739	0.88
91_G	94_A	0.734	0.88
93_Y	98_E	0.733	0.88
18_R	37_S	0.727	0.88
84_V	103_L	0.726	0.87
108_V	132_L	0.723	0.87
89_D	94_A	0.723	0.87
53_Y	116_R	0.723	0.87
101_R	104_A	0.721	0.87
65_R	150_D	0.716	0.87
103_L	133_R	0.711	0.86
82_H	107_P	0.704	0.86
118_P	158_Q	0.702	0.86
157_E	173_L	0.700	0.85
154_F	158_Q	0.699	0.85
153_P	157_E	0.695	0.85
86_S	106_S	0.695	0.85
59_T	66_V	0.695	0.85
68_A	149_E	0.690	0.85
107_P	134_G	0.688	0.84
61_E	64_E	0.684	0.84
55_S	59_T	0.678	0.84
76_F	128_I	0.677	0.84
137_L	141_V	0.675	0.83
138_R	143_E	0.665	0.82
88_F	96_R	0.664	0.82
1_Q	5_Q	0.656	0.82
97_E	101_R	0.652	0.81
5_Q	70_R	0.647	0.81
158_Q	161_L	0.647	0.81
119_R	162_V	0.633	0.79
109_R	126_R	0.632	0.79
42_T	75_G	0.625	0.78
89_D	93_Y	0.625	0.78
70_R	149_E	0.622	0.78
118_P	170_A	0.620	0.78
29_G	147_S	0.619	0.78
165_G	178_R	0.615	0.77
167_L	170_A	0.614	0.77
22_A	58_G	0.614	0.77
18_R	24_P	0.611	0.77
79_A	132_L	0.610	0.77
57_W	73_R	0.608	0.76
16_A	55_S	0.608	0.76
4_A	7_D	0.605	0.76
97_E	100_K	0.605	0.76
34_P	38_F	0.604	0.76
99_W	106_S	0.601	0.76
1_Q	4_A	0.599	0.75
49_L	174_L	0.592	0.75
82_H	139_R	0.592	0.75
177_E	180_Y	0.589	0.74
44_I	79_A	0.587	0.74
51_M	126_R	0.586	0.74
141_V	144_W	0.586	0.74
56_G	126_R	0.585	0.74
53_Y	126_R	0.584	0.74
3_R	47_S	0.584	0.74
99_W	103_L	0.582	0.73
102_A	105_R	0.579	0.73
77_E	80_L	0.577	0.73
113_D	129_Q	0.577	0.73
18_R	64_E	0.576	0.73
86_S	103_L	0.576	0.73
3_R	125_R	0.576	0.73
143_E	146_V	0.575	0.72
26_V	68_A	0.574	0.72
65_R	68_A	0.573	0.72
7_D	73_R	0.570	0.72
71_I	132_L	0.566	0.71
90_P	98_E	0.564	0.71
78_W	107_P	0.563	0.71
31_F	36_F	0.563	0.71
30_R	141_V	0.563	0.71
36_F	137_L	0.561	0.71
79_A	128_I	0.560	0.70
56_G	109_R	0.558	0.70
87_S	110_V	0.556	0.70
84_V	87_S	0.555	0.70
108_V	137_L	0.553	0.70
53_Y	56_G	0.553	0.70
134_G	137_L	0.553	0.70
48_F	57_W	0.552	0.69
42_T	79_A	0.549	0.69
89_D	96_R	0.549	0.69
161_L	170_A	0.548	0.69
60_K	66_V	0.548	0.69
90_P	96_R	0.547	0.69
57_W	155_V	0.547	0.69
66_V	156_R	0.545	0.68
49_L	118_P	0.544	0.68
24_P	34_P	0.542	0.68
22_A	35_P	0.541	0.68
17_Y	20_A	0.540	0.68
55_S	152_T	0.537	0.67
1_Q	47_S	0.534	0.67
57_W	120_G	0.534	0.67
1_Q	125_R	0.528	0.66
110_V	116_R	0.528	0.66
167_L	171_R	0.525	0.66
58_G	64_E	0.525	0.66
168_D	171_R	0.523	0.65
29_G	116_R	0.523	0.65
133_R	137_L	0.522	0.65
64_E	88_F	0.521	0.65
24_P	35_P	0.521	0.65
2_I	80_L	0.521	0.65
75_G	139_R	0.520	0.65
38_F	42_T	0.518	0.65
116_R	120_G	0.518	0.65
37_S	86_S	0.516	0.64
84_V	107_P	0.514	0.64
28_H	34_P	0.512	0.64
140_Y	145_I	0.511	0.64
60_K	117_D	0.510	0.63
49_L	122_P	0.509	0.63
118_P	171_R	0.508	0.63
91_G	98_E	0.506	0.63
81_A	138_R	0.503	0.62
48_F	52_M	0.502	0.62
4_A	11_I	0.501	0.62
101_R	168_D	0.500	0.62

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
4m70R	1	0.0056	6	0.969	Contact Map
2wb0X	1	0.4667	4.1	0.972	Contact Map
2nvnA	2	0.3778	3.2	0.973	Contact Map
4cylA	1	0.3333	3.1	0.973	Contact Map
1q9uA	2	0.4167	2.8	0.974	Contact Map
3a9sA	5	0.3278	2.6	0.974	Contact Map
3shgB	1	0.2889	2.5	0.974	Contact Map
2it9A	2	0.3722	2.3	0.975	Contact Map
3uqsA	4	0.2278	2.3	0.975	Contact Map
2kz3A	1	0.1556	2.1	0.975	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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