DUF507 - PFAM28P - GREMLIN Contacts

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DUF507 - Protein of unknown function (DUF507)

PFAM:	PF04368	Sequences: MRLYREKIPYIAREIVRDLVNSGDIETEDGPEEVAEDIEAVLEEYLRVEDELNEEVRDILEQYGEYMRREGVDYQEMFRRIKKKLAEERGVILAGEDRINDISHQILEMLMKSRLVEVFVDDNEVRLKIVKILTKHLAVEEEIDREVREKIKNYKRELIEGTEEWDILYRRYYEEELRKRGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	182 (181)
Sequences:	1368 (724)
Seq/√Len:	53.8
META:	0.937

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_L	85_L	6.099	1.00
34_V	116_V	4.643	1.00
16_V	34_V	3.893	1.00
24_D	128_K	3.581	1.00
121_D	124_E	3.195	1.00
159_I	162_T	3.191	1.00
78_F	82_K	3.003	1.00
144_D	169_Y	2.847	1.00
39_E	43_E	2.404	1.00
35_A	39_E	2.379	1.00
43_E	47_R	2.349	1.00
55_E	89_R	2.273	1.00
38_I	106_I	2.165	1.00
13_R	35_A	2.114	1.00
170_R	174_E	2.051	1.00
45_Y	102_I	2.028	1.00
27_T	31_P	2.009	1.00
158_L	168_L	1.978	1.00
41_V	109_M	1.969	1.00
175_E	179_K	1.902	0.99
84_K	88_E	1.806	0.99
110_L	116_V	1.800	0.99
101_D	105_Q	1.792	0.99
153_N	158_L	1.781	0.99
111_M	118_V	1.770	0.99
154_Y	158_L	1.748	0.99
8_I	46_L	1.699	0.99
17_R	21_N	1.697	0.99
173_Y	176_E	1.689	0.99
144_D	148_R	1.632	0.98
107_L	125_V	1.613	0.98
176_E	179_K	1.613	0.98
154_Y	157_E	1.589	0.98
52_L	56_V	1.509	0.97
154_Y	172_Y	1.500	0.97
85_L	88_E	1.492	0.97
158_L	164_E	1.470	0.97
50_D	57_R	1.464	0.97
12_A	15_I	1.457	0.97
172_Y	175_E	1.449	0.97
56_V	78_F	1.438	0.96
22_S	128_K	1.438	0.96
44_E	47_R	1.429	0.96
37_D	40_A	1.391	0.96
34_V	110_L	1.377	0.95
97_D	104_H	1.347	0.95
173_Y	177_L	1.341	0.95
29_D	34_V	1.338	0.95
57_R	166_D	1.329	0.94
59_I	85_L	1.324	0.94
148_R	160_E	1.312	0.94
100_N	103_S	1.304	0.94
158_L	175_E	1.303	0.94
29_D	32_E	1.292	0.94
45_Y	98_R	1.288	0.94
162_T	169_Y	1.233	0.92
49_E	53_N	1.229	0.92
49_E	98_R	1.221	0.92
116_V	122_D	1.204	0.91
5_R	50_D	1.199	0.91
47_R	53_N	1.189	0.90
20_V	31_P	1.180	0.90
2_R	5_R	1.175	0.90
11_I	15_I	1.174	0.90
168_L	172_Y	1.168	0.90
55_E	147_V	1.157	0.89
125_V	128_K	1.148	0.89
16_V	116_V	1.145	0.89
122_D	153_N	1.142	0.89
59_I	81_I	1.131	0.88
85_L	108_E	1.110	0.87
10_Y	13_R	1.099	0.87
33_E	37_D	1.086	0.86
159_I	164_E	1.085	0.86
53_N	78_F	1.058	0.84
47_R	51_E	1.058	0.84
80_R	151_I	1.056	0.84
41_V	106_I	1.046	0.84
155_K	163_E	1.042	0.84
76_E	80_R	1.027	0.83
48_V	92_I	1.026	0.83
138_A	162_T	1.023	0.82
42_L	46_L	1.023	0.82
55_E	88_E	1.015	0.82
18_D	22_S	1.014	0.82
69_R	72_V	1.007	0.81
67_M	71_G	1.005	0.81
51_E	89_R	0.985	0.80
60_L	81_I	0.984	0.80
8_I	12_A	0.978	0.79
7_K	136_H	0.972	0.79
109_M	124_E	0.962	0.78
52_L	91_V	0.946	0.77
151_I	169_Y	0.937	0.76
143_I	147_V	0.936	0.76
88_E	177_L	0.935	0.76
58_D	61_E	0.932	0.76
25_I	132_I	0.928	0.76
24_D	124_E	0.923	0.75
22_S	120_V	0.917	0.75
178_R	182_L	0.912	0.74
163_E	174_E	0.909	0.74
123_N	127_L	0.904	0.74
144_D	151_I	0.900	0.73
67_M	72_V	0.897	0.73
163_E	167_I	0.895	0.73
96_E	134_T	0.894	0.73
110_L	115_L	0.887	0.72
59_I	84_K	0.880	0.72
111_M	117_E	0.874	0.71
100_N	130_V	0.873	0.71
4_Y	8_I	0.873	0.71
52_L	90_G	0.871	0.71
98_R	102_I	0.860	0.70
170_R	175_E	0.847	0.69
143_I	173_Y	0.846	0.69
157_E	162_T	0.845	0.69
145_R	149_E	0.838	0.68
46_L	78_F	0.837	0.68
52_L	84_K	0.834	0.68
60_L	78_F	0.832	0.67
151_I	172_Y	0.831	0.67
76_E	114_R	0.824	0.67
51_E	55_E	0.820	0.66
144_D	147_V	0.819	0.66
15_I	129_I	0.818	0.66
4_Y	7_K	0.803	0.65
24_D	120_V	0.802	0.65
161_G	166_D	0.799	0.64
2_R	7_K	0.796	0.64
144_D	172_Y	0.792	0.64
9_P	39_E	0.790	0.63
89_R	102_I	0.780	0.62
28_E	119_F	0.774	0.62
97_D	170_R	0.774	0.62
147_V	169_Y	0.770	0.61
100_N	104_H	0.767	0.61
104_H	123_N	0.764	0.61
108_E	119_F	0.763	0.61
5_R	13_R	0.760	0.60
7_K	11_I	0.755	0.60
21_N	24_D	0.755	0.60
91_V	171_R	0.753	0.60
106_I	180_R	0.752	0.60
138_A	142_E	0.748	0.59
24_D	41_V	0.741	0.58
176_E	180_R	0.741	0.58
109_M	112_K	0.740	0.58
28_E	58_D	0.739	0.58
37_D	118_V	0.736	0.58
25_I	110_L	0.735	0.58
168_L	175_E	0.735	0.58
7_K	10_Y	0.735	0.58
92_I	100_N	0.731	0.57
32_E	35_A	0.730	0.57
20_V	35_A	0.728	0.57
2_R	53_N	0.728	0.57
93_L	131_K	0.725	0.57
8_I	139_V	0.723	0.57
80_R	127_L	0.721	0.56
115_L	147_V	0.719	0.56
28_E	81_I	0.717	0.56
98_R	137_L	0.713	0.56
54_E	57_R	0.707	0.55
100_N	129_I	0.707	0.55
60_L	82_K	0.706	0.55
172_Y	176_E	0.704	0.55
105_Q	113_S	0.703	0.55
119_F	122_D	0.696	0.54
107_L	123_N	0.695	0.54
42_L	140_E	0.686	0.53
12_A	58_D	0.679	0.52
58_D	166_D	0.677	0.52
72_V	108_E	0.674	0.51
32_E	39_E	0.670	0.51
139_V	143_I	0.666	0.51
45_Y	48_V	0.661	0.50
170_R	173_Y	0.659	0.50
10_Y	82_K	0.658	0.50
56_V	65_E	0.655	0.49
25_I	128_K	0.654	0.49
8_I	42_L	0.652	0.49
124_E	131_K	0.651	0.49
20_V	27_T	0.650	0.49
8_I	57_R	0.650	0.49
73_D	76_E	0.645	0.48
50_D	132_I	0.645	0.48
41_V	113_S	0.645	0.48
44_E	48_V	0.645	0.48
174_E	180_R	0.644	0.48
86_A	93_L	0.644	0.48
17_R	33_E	0.644	0.48
39_E	102_I	0.643	0.48
153_N	168_L	0.642	0.48
159_I	163_E	0.639	0.48
46_L	154_Y	0.637	0.47
167_I	179_K	0.633	0.47
67_M	74_Y	0.633	0.47
60_L	137_L	0.633	0.47
55_E	58_D	0.632	0.47
78_F	164_E	0.631	0.47
132_I	136_H	0.630	0.47
88_E	145_R	0.630	0.47
61_E	136_H	0.628	0.47
151_I	154_Y	0.628	0.47
50_D	54_E	0.628	0.47
105_Q	146_E	0.627	0.46
41_V	105_Q	0.626	0.46
126_R	160_E	0.623	0.46
37_D	122_D	0.622	0.46
77_M	90_G	0.621	0.46
168_L	171_R	0.617	0.45
86_A	106_I	0.615	0.45
36_E	40_A	0.614	0.45
3_L	137_L	0.613	0.45
65_E	176_E	0.606	0.44
151_I	157_E	0.606	0.44
67_M	77_M	0.603	0.44
43_E	158_L	0.600	0.44
133_L	169_Y	0.600	0.44
72_V	113_S	0.597	0.43
137_L	140_E	0.593	0.43
42_L	137_L	0.592	0.43
43_E	100_N	0.591	0.43
44_E	51_E	0.589	0.42
50_D	147_V	0.588	0.42
37_D	113_S	0.584	0.42
13_R	17_R	0.580	0.42
46_L	53_N	0.573	0.41
77_M	80_R	0.569	0.40
107_L	118_V	0.568	0.40
58_D	78_F	0.565	0.40
55_E	66_Y	0.565	0.40
149_E	152_K	0.562	0.40
86_A	122_D	0.556	0.39
147_V	173_Y	0.555	0.39
71_G	165_W	0.554	0.39
152_K	157_E	0.553	0.39
6_E	17_R	0.551	0.39
102_I	106_I	0.551	0.39
103_S	129_I	0.549	0.38
72_V	94_A	0.548	0.38
173_Y	181_G	0.544	0.38
45_Y	134_T	0.543	0.38
61_E	84_K	0.543	0.38
74_Y	152_K	0.541	0.38
85_L	90_G	0.539	0.37
158_L	161_G	0.539	0.37
52_L	92_I	0.538	0.37
49_E	90_G	0.537	0.37
70_E	157_E	0.533	0.37
24_D	125_V	0.533	0.37
128_K	132_I	0.532	0.37
107_L	178_R	0.531	0.37
8_I	11_I	0.528	0.36
141_E	173_Y	0.525	0.36
104_H	130_V	0.519	0.35
155_K	168_L	0.519	0.35
60_L	97_D	0.517	0.35
125_V	162_T	0.517	0.35
3_L	15_I	0.516	0.35
113_S	162_T	0.516	0.35
101_D	119_F	0.515	0.35
119_F	124_E	0.513	0.35
98_R	150_K	0.511	0.35
71_G	74_Y	0.507	0.34
103_S	171_R	0.507	0.34
76_E	108_E	0.506	0.34
129_I	133_L	0.503	0.34
152_K	172_Y	0.502	0.34
75_Q	78_F	0.502	0.34
16_V	20_V	0.500	0.34

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
3h0lB	1	0.2253	23.2	0.942	Contact Map
3n8iA	1	0.3462	18.7	0.944	Contact Map
4yvqA	2	0.4341	17.5	0.945	Contact Map
2hz7A	1	0	17	0.945	Contact Map
3rofA	1	0.3626	13.8	0.947	Contact Map
1q1vA	1	0.3791	12.9	0.948	Contact Map
3ip4B	1	0.6099	12.3	0.949	Contact Map
1ileA	1	0.3516	12	0.949	Contact Map
3al0B	1	0.5714	11.6	0.949	Contact Map
2gi4A	1	0.3407	10.2	0.95	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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