DUF2017 - PFAM28P - GREMLIN Contacts

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DUF2017 - Domain of unknown function (DUF2017)

PFAM:	PF09438	Sequences: RRGGGVVARLDPVEAALLRSLVGQLLELLGPRAAEAPDADPLAALLGIRTGPSEPPEDPVLARLLPDAYRDDPEAAAEFRRLTEPDLRDAKRAAARTVLDTLPAAGGRGVELDEEQAQAWLRALNDVRLALGTRLGITEDDDAELERLPDDDPRAPLLAVYDWLGWLQESLVEALM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (173)
Sequences:	2270 (1390)
Seq/√Len:	105.7
META:	0.705

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_V	130_A	5.345	1.00
113_D	116_Q	4.426	1.00
25_L	127_V	3.874	1.00
94_A	122_R	3.204	1.00
20_S	24_Q	3.182	1.00
101_T	120_W	2.989	1.00
169_E	173_E	2.975	1.00
101_T	116_Q	2.962	1.00
84_E	88_R	2.737	1.00
97_T	119_A	2.673	1.00
22_V	127_V	2.664	1.00
29_L	65_L	2.545	1.00
98_V	123_A	2.538	1.00
72_D	75_A	2.377	1.00
161_Y	165_G	2.375	1.00
22_V	98_V	2.236	1.00
58_D	134_R	2.210	1.00
97_T	116_Q	2.132	1.00
68_A	79_F	2.091	1.00
22_V	99_L	1.930	1.00
60_V	133_T	1.895	1.00
94_A	119_A	1.803	1.00
97_T	101_T	1.799	1.00
2_R	5_G	1.760	1.00
89_D	93_A	1.759	1.00
133_T	138_T	1.755	1.00
69_Y	75_A	1.744	1.00
65_L	91_K	1.738	1.00
91_K	126_D	1.738	1.00
19_R	103_P	1.727	1.00
67_D	76_A	1.725	1.00
60_V	134_R	1.650	1.00
80_R	84_E	1.625	1.00
98_V	120_W	1.600	1.00
26_L	96_R	1.589	1.00
26_L	92_R	1.563	1.00
42_L	47_G	1.560	1.00
139_E	142_D	1.557	1.00
42_L	46_L	1.542	1.00
78_E	81_R	1.535	1.00
25_L	65_L	1.531	1.00
42_L	45_L	1.499	1.00
23_G	99_L	1.495	1.00
104_A	116_Q	1.473	1.00
79_F	83_T	1.466	1.00
156_P	160_V	1.403	1.00
30_G	92_R	1.402	1.00
139_E	158_L	1.378	1.00
91_K	168_Q	1.370	1.00
165_G	169_E	1.365	1.00
166_W	170_S	1.325	0.99
162_D	165_G	1.308	0.99
23_G	26_L	1.300	0.99
76_A	80_R	1.285	0.99
67_D	73_P	1.270	0.99
96_R	100_D	1.252	0.99
59_P	133_T	1.245	0.99
32_R	88_R	1.231	0.99
43_A	46_L	1.215	0.99
67_D	80_R	1.201	0.99
5_G	111_E	1.191	0.99
91_K	123_A	1.189	0.99
123_A	127_V	1.183	0.99
76_A	79_F	1.140	0.98
45_L	48_I	1.124	0.98
95_A	99_L	1.122	0.98
22_V	123_A	1.120	0.98
125_N	132_G	1.103	0.98
165_G	168_Q	1.102	0.98
100_D	116_Q	1.095	0.98
26_L	30_G	1.082	0.98
103_P	107_G	1.068	0.97
83_T	88_R	1.066	0.97
90_A	94_A	1.053	0.97
21_L	127_V	1.053	0.97
51_G	55_P	1.049	0.97
41_P	48_I	1.049	0.97
76_A	83_T	1.041	0.97
68_A	81_R	1.040	0.97
2_R	9_R	1.032	0.97
138_T	142_D	1.028	0.97
132_G	136_G	1.028	0.97
162_D	166_W	1.014	0.96
133_T	137_I	1.010	0.96
92_R	96_R	0.997	0.96
55_P	67_D	0.973	0.95
78_E	82_L	0.966	0.95
105_A	109_G	0.964	0.95
155_A	159_A	0.964	0.95
24_Q	87_L	0.961	0.95
42_L	48_I	0.959	0.95
103_P	106_G	0.946	0.95
126_D	168_Q	0.938	0.94
19_R	99_L	0.925	0.94
68_A	78_E	0.924	0.94
21_L	24_Q	0.923	0.94
55_P	62_A	0.916	0.94
24_Q	130_A	0.908	0.93
141_D	158_L	0.905	0.93
132_G	137_I	0.881	0.92
79_F	82_L	0.862	0.92
14_E	18_L	0.850	0.91
80_R	83_T	0.847	0.91
30_G	96_R	0.839	0.90
95_A	123_A	0.839	0.90
69_Y	120_W	0.838	0.90
15_A	95_A	0.837	0.90
148_L	153_P	0.827	0.90
28_L	61_L	0.827	0.90
6_V	95_A	0.825	0.90
44_A	47_G	0.823	0.90
148_L	151_D	0.823	0.90
86_D	89_D	0.813	0.89
10_L	167_L	0.806	0.89
45_L	51_G	0.800	0.88
150_D	155_A	0.792	0.88
61_L	84_E	0.792	0.88
7_V	11_D	0.791	0.88
27_E	30_G	0.783	0.87
17_L	21_L	0.779	0.87
117_A	174_A	0.777	0.87
13_V	20_S	0.776	0.87
125_N	139_E	0.774	0.87
163_W	172_V	0.754	0.85
135_L	161_Y	0.745	0.84
15_A	19_R	0.744	0.84
50_T	53_S	0.742	0.84
41_P	46_L	0.733	0.83
163_W	167_L	0.732	0.83
13_V	16_A	0.727	0.83
78_E	83_T	0.722	0.83
43_A	48_I	0.718	0.82
122_R	125_N	0.716	0.82
61_L	156_P	0.707	0.81
148_L	154_R	0.705	0.81
166_W	169_E	0.705	0.81
17_L	160_V	0.705	0.81
28_L	130_A	0.704	0.81
29_L	88_R	0.702	0.81
148_L	152_D	0.699	0.80
6_V	114_E	0.692	0.80
7_V	111_E	0.690	0.80
65_L	84_E	0.690	0.80
76_A	87_L	0.686	0.79
118_Q	122_R	0.685	0.79
116_Q	119_A	0.683	0.79
85_P	89_D	0.681	0.79
75_A	82_L	0.678	0.78
4_G	175_L	0.673	0.78
48_I	53_S	0.672	0.78
95_A	159_A	0.671	0.78
75_A	79_F	0.669	0.77
23_G	27_E	0.667	0.77
147_R	151_D	0.666	0.77
2_R	111_E	0.663	0.77
75_A	78_E	0.662	0.77
130_A	133_T	0.661	0.77
172_V	175_L	0.659	0.76
89_D	114_E	0.657	0.76
121_L	172_V	0.654	0.76
46_L	81_R	0.654	0.76
69_Y	82_L	0.653	0.76
68_A	83_T	0.651	0.76
3_G	7_V	0.648	0.75
89_D	118_Q	0.647	0.75
29_L	92_R	0.643	0.75
41_P	57_E	0.642	0.75
70_R	76_A	0.640	0.74
145_L	148_L	0.637	0.74
65_L	88_R	0.637	0.74
69_Y	163_W	0.635	0.74
136_G	139_E	0.635	0.74
15_A	107_G	0.626	0.73
5_G	11_D	0.626	0.73
87_L	126_D	0.623	0.72
43_A	47_G	0.619	0.72
117_A	175_L	0.610	0.71
56_P	61_L	0.606	0.70
8_A	112_L	0.605	0.70
101_T	112_L	0.603	0.70
143_A	158_L	0.601	0.70
145_L	165_G	0.599	0.69
91_K	125_N	0.596	0.69
155_A	160_V	0.595	0.69
132_G	165_G	0.594	0.69
94_A	126_D	0.594	0.69
26_L	95_A	0.592	0.68
125_N	159_A	0.590	0.68
125_N	138_T	0.590	0.68
135_L	165_G	0.589	0.68
101_T	113_D	0.588	0.68
98_V	121_L	0.587	0.68
48_I	89_D	0.585	0.68
112_L	126_D	0.583	0.67
69_Y	79_F	0.582	0.67
121_L	165_G	0.578	0.67
122_R	126_D	0.578	0.67
9_R	15_A	0.577	0.67
39_A	45_L	0.576	0.66
57_E	62_A	0.575	0.66
132_G	164_L	0.575	0.66
125_N	129_L	0.571	0.66
39_A	47_G	0.568	0.65
165_G	172_V	0.566	0.65
69_Y	81_R	0.564	0.65
25_L	130_A	0.564	0.65
68_A	88_R	0.562	0.64
114_E	118_Q	0.560	0.64
27_E	82_L	0.555	0.64
11_D	18_L	0.554	0.63
15_A	130_A	0.551	0.63
48_I	52_P	0.550	0.63
137_I	165_G	0.549	0.63
69_Y	78_E	0.548	0.63
6_V	117_A	0.547	0.62
158_L	165_G	0.545	0.62
59_P	136_G	0.544	0.62
3_G	6_V	0.544	0.62
118_Q	175_L	0.543	0.62
34_A	37_P	0.541	0.62
35_E	39_A	0.540	0.61
140_D	171_L	0.540	0.61
73_P	111_E	0.540	0.61
56_P	80_R	0.540	0.61
80_R	168_Q	0.540	0.61
120_W	163_W	0.540	0.61
146_E	149_P	0.537	0.61
7_V	26_L	0.537	0.61
57_E	111_E	0.536	0.61
156_P	159_A	0.533	0.60
70_R	75_A	0.531	0.60
76_A	91_K	0.531	0.60
132_G	138_T	0.529	0.60
40_D	45_L	0.527	0.60
39_A	70_R	0.526	0.59
25_L	123_A	0.525	0.59
137_I	162_D	0.524	0.59
33_A	37_P	0.524	0.59
12_P	105_A	0.524	0.59
101_T	106_G	0.523	0.59
21_L	129_L	0.523	0.59
39_A	46_L	0.523	0.59
90_A	93_A	0.522	0.59
151_D	155_A	0.519	0.58
159_A	162_D	0.519	0.58
159_A	166_W	0.518	0.58
157_L	162_D	0.518	0.58
40_D	48_I	0.516	0.58
16_A	123_A	0.516	0.58
145_L	149_P	0.514	0.58
117_A	126_D	0.513	0.58
33_A	39_A	0.512	0.57
35_E	38_D	0.510	0.57
24_Q	28_L	0.507	0.57
162_D	173_E	0.507	0.57
39_A	44_A	0.506	0.57
132_G	139_E	0.502	0.56
2_R	7_V	0.501	0.56
69_Y	133_T	0.501	0.56
113_D	118_Q	0.500	0.56

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
1ofdA	1	0.3636	5.2	0.952	Contact Map
2qibA	2	0.3864	3.2	0.956	Contact Map
2kkeA	2	0.2614	3.2	0.957	Contact Map
1kyqA	2	0.4318	2.6	0.959	Contact Map
1g2yA	4	0.0966	2.3	0.96	Contact Map
3oq9A	3	0.3295	2.1	0.961	Contact Map
3encA	2	0.2045	2	0.961	Contact Map
2o71A	1	0.3864	1.8	0.962	Contact Map
2of5A	5	0.3864	1.8	0.962	Contact Map
1gcvB	1	0.75	1.5	0.964	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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