DUF1777 - PFAM28P - GREMLIN Contacts

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DUF1777 - Protein of unknown function (DUF1777)

PFAM:	PF08648	Sequences: RSRSRDRRDRRRDRRRDRRDRDRRDRDRDRDRRRRRRRRDRSRSRDRSRRRRDRSRSRDRSRRRRRSRRRRRRSRRRPRRRSRSPSRERSRSREDSKSKKDSAAKDEDEEEEDLEGDDDEEAEMMKMMGFGGFDTTKGKKVPGNDVGGVRKEKKRKYRQYMNRKGGFNRPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (167)
Sequences:	596 (547)
Seq/√Len:	42.3
META:	0.141

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
144_N	147_G	4.369	1.00
123_E	126_K	3.627	1.00
141_V	144_N	3.304	1.00
155_R	164_K	2.725	1.00
46_D	49_R	2.723	1.00
134_D	139_K	2.621	1.00
160_Y	163_R	2.525	1.00
135_T	138_G	2.461	1.00
138_G	148_G	2.267	1.00
19_R	22_D	2.198	1.00
136_T	141_V	2.164	1.00
152_E	155_R	1.999	0.99
140_K	157_Y	1.953	0.99
67_S	70_R	1.952	0.99
152_E	156_K	1.915	0.99
150_R	156_K	1.876	0.99
13_D	16_R	1.815	0.98
147_G	153_K	1.815	0.98
9_D	12_R	1.798	0.98
144_N	153_K	1.779	0.98
149_V	154_K	1.766	0.98
130_F	164_K	1.751	0.98
142_P	147_G	1.696	0.97
152_E	157_Y	1.667	0.97
168_N	171_L	1.661	0.97
167_F	171_L	1.639	0.97
130_F	157_Y	1.605	0.96
12_R	15_R	1.596	0.96
16_R	19_R	1.594	0.96
140_K	143_G	1.579	0.96
56_R	62_R	1.578	0.96
8_R	11_R	1.551	0.95
156_K	164_K	1.530	0.95
11_R	14_R	1.527	0.95
121_E	125_M	1.518	0.95
122_A	153_K	1.507	0.95
130_F	153_K	1.479	0.94
166_G	171_L	1.477	0.94
132_G	147_G	1.476	0.94
145_D	152_E	1.411	0.92
140_K	164_K	1.397	0.92
66_R	69_R	1.388	0.92
154_K	157_Y	1.366	0.91
13_D	19_R	1.351	0.91
64_R	67_S	1.321	0.90
37_R	40_D	1.315	0.89
14_R	18_R	1.297	0.89
166_G	169_R	1.292	0.89
10_R	16_R	1.278	0.88
45_R	48_S	1.269	0.88
75_R	78_P	1.254	0.87
17_D	20_D	1.243	0.87
72_R	75_R	1.240	0.86
77_R	80_R	1.235	0.86
144_N	157_Y	1.205	0.85
150_R	164_K	1.202	0.85
151_K	164_K	1.187	0.84
153_K	157_Y	1.185	0.84
15_R	18_R	1.183	0.84
151_K	156_K	1.182	0.84
13_D	18_R	1.182	0.84
126_K	134_D	1.162	0.83
122_A	144_N	1.153	0.82
146_V	152_E	1.145	0.82
127_M	132_G	1.141	0.81
48_S	51_R	1.114	0.80
125_M	141_V	1.111	0.80
126_K	132_G	1.102	0.79
142_P	150_R	1.100	0.79
140_K	153_K	1.091	0.78
109_E	112_E	1.080	0.78
14_R	17_D	1.078	0.77
138_G	155_R	1.074	0.77
140_K	147_G	1.057	0.76
10_R	18_R	1.046	0.75
27_D	30_R	1.041	0.75
121_E	155_R	1.040	0.75
145_D	154_K	1.034	0.74
163_R	171_L	1.032	0.74
163_R	168_N	1.029	0.74
159_Q	162_N	1.020	0.73
134_D	147_G	1.009	0.73
163_R	167_F	1.004	0.72
48_S	53_D	1.002	0.72
107_E	110_E	0.993	0.71
111_E	114_L	0.987	0.71
151_K	154_K	0.983	0.71
75_R	79_R	0.972	0.70
62_R	65_R	0.970	0.70
105_K	110_E	0.970	0.70
10_R	13_D	0.969	0.70
9_D	13_D	0.968	0.69
110_E	113_D	0.963	0.69
160_Y	171_L	0.963	0.69
151_K	157_Y	0.955	0.68
144_N	152_E	0.954	0.68
61_S	71_R	0.954	0.68
122_A	125_M	0.952	0.68
25_D	30_R	0.949	0.68
43_R	46_D	0.948	0.68
160_Y	168_N	0.945	0.68
160_Y	167_F	0.919	0.65
36_R	40_D	0.918	0.65
150_R	154_K	0.918	0.65
25_D	29_D	0.915	0.65
122_A	134_D	0.912	0.65
82_S	85_P	0.910	0.65
141_V	152_E	0.907	0.64
151_K	155_R	0.906	0.64
120_E	143_G	0.900	0.64
121_E	126_K	0.895	0.63
131_G	153_K	0.891	0.63
12_R	19_R	0.886	0.63
34_R	37_R	0.884	0.62
123_E	156_K	0.877	0.62
19_R	23_R	0.876	0.62
166_G	170_P	0.875	0.62
146_V	150_R	0.869	0.61
167_F	170_P	0.867	0.61
124_M	134_D	0.867	0.61
105_K	108_D	0.865	0.61
50_R	135_T	0.862	0.60
31_D	38_R	0.855	0.60
89_R	93_R	0.851	0.59
122_A	131_G	0.849	0.59
60_R	68_R	0.842	0.59
152_E	164_K	0.834	0.58
6_D	9_D	0.832	0.58
37_R	45_R	0.830	0.57
165_G	168_N	0.828	0.57
120_E	127_M	0.822	0.57
132_G	136_T	0.822	0.57
150_R	157_Y	0.819	0.56
114_L	117_D	0.818	0.56
22_D	135_T	0.811	0.56
19_R	24_R	0.810	0.56
122_A	126_K	0.802	0.55
163_R	169_R	0.802	0.55
134_D	153_K	0.799	0.55
65_R	68_R	0.798	0.54
25_D	40_D	0.795	0.54
165_G	171_L	0.781	0.53
137_K	144_N	0.780	0.53
12_R	17_D	0.776	0.52
59_D	62_R	0.771	0.52
144_N	151_K	0.767	0.52
5_R	8_R	0.762	0.51
12_R	16_R	0.759	0.51
125_M	136_T	0.759	0.51
163_R	166_G	0.756	0.51
158_R	161_M	0.756	0.51
160_Y	169_R	0.750	0.50
160_Y	165_G	0.745	0.49
143_G	153_K	0.740	0.49
137_K	143_G	0.739	0.49
119_D	123_E	0.733	0.48
146_V	154_K	0.731	0.48
138_G	153_K	0.730	0.48
38_R	48_S	0.729	0.48
40_D	48_S	0.724	0.48
83_R	87_R	0.723	0.47
38_R	43_R	0.721	0.47
150_R	155_R	0.708	0.46
122_A	130_F	0.707	0.46
97_K	101_D	0.702	0.45
130_F	152_E	0.701	0.45
11_R	17_D	0.701	0.45
139_K	147_G	0.701	0.45
122_A	127_M	0.697	0.45
165_G	169_R	0.692	0.45
81_R	84_S	0.691	0.44
78_P	83_R	0.686	0.44
59_D	66_R	0.684	0.44
121_E	134_D	0.682	0.44
80_R	83_R	0.682	0.44
96_S	99_K	0.678	0.43
109_E	114_L	0.675	0.43
84_S	87_R	0.672	0.43
130_F	140_K	0.671	0.43
158_R	163_R	0.671	0.43
27_D	32_R	0.669	0.42
87_R	90_S	0.658	0.41
120_E	123_E	0.656	0.41
92_S	95_D	0.654	0.41
123_E	127_M	0.649	0.41
6_D	10_R	0.643	0.40
30_R	34_R	0.640	0.40
32_R	44_S	0.639	0.40
144_N	150_R	0.638	0.40
12_R	18_R	0.631	0.39
160_Y	166_G	0.630	0.39
113_D	116_G	0.624	0.38
140_K	144_N	0.623	0.38
8_R	15_R	0.622	0.38
145_D	157_Y	0.622	0.38
85_P	93_R	0.617	0.38
78_P	81_R	0.616	0.38
89_R	92_S	0.614	0.37
127_M	134_D	0.613	0.37
125_M	151_K	0.611	0.37
131_G	147_G	0.609	0.37
74_S	77_R	0.609	0.37
91_R	99_K	0.604	0.37
134_D	152_E	0.603	0.36
100_K	105_K	0.598	0.36
142_P	155_R	0.596	0.36
143_G	155_R	0.595	0.36
146_V	157_Y	0.595	0.36
81_R	85_P	0.593	0.36
126_K	147_G	0.590	0.35
128_M	131_G	0.587	0.35
23_R	30_R	0.587	0.35
132_G	144_N	0.586	0.35
95_D	102_S	0.585	0.35
145_D	148_G	0.584	0.35
39_R	42_S	0.581	0.35
35_R	38_R	0.579	0.34
43_R	71_R	0.578	0.34
127_M	131_G	0.576	0.34
161_M	166_G	0.570	0.34
159_Q	167_F	0.563	0.33
73_R	78_P	0.563	0.33
126_K	153_K	0.562	0.33
128_M	132_G	0.560	0.33
40_D	44_S	0.558	0.33
140_K	155_R	0.550	0.32
36_R	39_R	0.549	0.32
110_E	114_L	0.548	0.32
116_G	122_A	0.548	0.32
159_Q	163_R	0.548	0.32
15_R	20_D	0.541	0.31
116_G	125_M	0.536	0.31
158_R	166_G	0.533	0.31
122_A	164_K	0.529	0.30
132_G	137_K	0.526	0.30
100_K	104_A	0.526	0.30
153_K	164_K	0.525	0.30
29_D	32_R	0.524	0.30
157_Y	164_K	0.522	0.30
27_D	35_R	0.521	0.30
63_R	70_R	0.520	0.30
63_R	67_S	0.517	0.29
134_D	138_G	0.514	0.29
141_V	153_K	0.514	0.29
150_R	153_K	0.509	0.29
147_G	150_R	0.508	0.29
36_R	64_R	0.507	0.29
22_D	27_D	0.505	0.28
125_M	134_D	0.502	0.28
104_A	107_E	0.500	0.28

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
3pgwS	1	0	51.9	0.918	Contact Map
3sv0A	1	0.3333	8.7	0.944	Contact Map
3vn9A	1	0.345	7.9	0.945	Contact Map
3e3pA	2	0.3158	6.2	0.948	Contact Map
4u6rA	1	0.345	5.8	0.948	Contact Map
2r5tA	2	0.3392	5.8	0.948	Contact Map
4oo6B	1	0.0468	5.6	0.949	Contact Map
2wjvD	1	0.1579	5.3	0.949	Contact Map
3warA	1	0.5088	5	0.95	Contact Map
4x7qB	1	0.2924	4.6	0.951	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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