DUF2115 - PFAM28P - GREMLIN Contacts

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DUF2115 - Uncharacterized protein conserved in archaea (DUF2115)

PFAM:	PF09888	Sequences: TKGELLEILKKEALRYSIFDLQQISGRLEEEIKYLPPPYRERLIPYFTEQLFGTYHEIKLHRQGDFSTMDEPIIDPEELKEFWEMLPEQCFAWDEEDEPRFRLLYYLISAYTMFVLEEPGHPVGTPFPGGFKVEERGGVYYCPVRDKQKDVPYALCPFCPAKQT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	164 (163)
Sequences:	674 (466)
Seq/√Len:	36.5
META:	0.858

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
135_E	138_G	6.957	1.00
30_E	33_K	4.120	1.00
139_V	162_K	3.058	1.00
156_C	159_C	2.916	1.00
21_L	26_G	2.883	1.00
54_T	118_E	2.820	1.00
37_P	41_E	2.700	1.00
42_R	132_K	2.400	1.00
144_V	148_Q	2.289	0.99
46_Y	49_E	2.267	0.99
113_M	120_G	2.205	0.99
134_E	164_T	2.165	0.99
57_E	118_E	2.110	0.99
124_G	133_V	2.012	0.99
77_E	81_E	1.885	0.98
17_S	20_D	1.824	0.97
39_Y	128_P	1.813	0.97
79_L	83_W	1.810	0.97
7_E	11_K	1.809	0.97
4_E	7_E	1.802	0.97
146_D	149_K	1.790	0.97
54_T	112_T	1.753	0.96
148_Q	154_A	1.745	0.96
3_G	6_L	1.738	0.96
49_E	125_T	1.723	0.96
35_L	47_F	1.713	0.96
82_F	113_M	1.701	0.96
3_G	17_S	1.650	0.95
2_K	117_E	1.623	0.95
34_Y	65_D	1.587	0.94
28_L	93_W	1.569	0.93
56_H	60_L	1.567	0.93
82_F	126_P	1.545	0.93
6_L	10_K	1.537	0.93
65_D	69_M	1.520	0.92
5_L	13_A	1.514	0.92
128_P	144_V	1.507	0.92
82_F	114_F	1.494	0.92
42_R	126_P	1.490	0.92
3_G	68_T	1.482	0.91
47_F	155_L	1.471	0.91
39_Y	129_G	1.464	0.91
2_K	9_L	1.436	0.90
145_R	160_P	1.421	0.89
61_H	64_G	1.390	0.88
130_G	158_F	1.351	0.87
109_S	140_Y	1.316	0.85
47_F	52_F	1.308	0.85
129_G	143_P	1.306	0.85
79_L	110_A	1.293	0.84
12_E	114_F	1.212	0.80
24_I	31_E	1.209	0.80
77_E	80_K	1.205	0.80
127_F	133_V	1.174	0.78
101_F	118_E	1.160	0.77
6_L	66_F	1.159	0.77
148_Q	157_P	1.158	0.77
92_A	98_E	1.156	0.77
66_F	69_M	1.144	0.76
142_C	156_C	1.140	0.76
144_V	151_V	1.137	0.76
28_L	47_F	1.136	0.76
69_M	111_Y	1.133	0.76
104_L	108_I	1.129	0.75
81_E	132_K	1.125	0.75
41_E	49_E	1.120	0.75
25_S	54_T	1.101	0.73
157_P	160_P	1.098	0.73
150_D	154_A	1.097	0.73
11_K	70_D	1.078	0.72
156_C	161_A	1.062	0.71
49_E	53_G	1.061	0.71
73_I	79_L	1.051	0.70
82_F	110_A	1.048	0.70
10_K	111_Y	1.043	0.69
78_E	150_D	1.043	0.69
6_L	115_V	1.041	0.69
67_S	70_D	1.037	0.69
75_D	81_E	1.036	0.69
34_Y	51_L	1.023	0.68
36_P	110_A	1.014	0.67
74_I	115_V	1.010	0.67
151_V	157_P	1.010	0.67
145_R	151_V	1.002	0.66
146_D	163_Q	0.979	0.64
11_K	14_L	0.978	0.64
142_C	159_C	0.974	0.64
3_G	69_M	0.962	0.63
21_L	52_F	0.959	0.63
46_Y	125_T	0.945	0.62
123_V	133_V	0.944	0.61
32_I	147_K	0.944	0.61
155_L	160_P	0.939	0.61
27_R	32_I	0.936	0.61
6_L	11_K	0.927	0.60
57_E	65_D	0.921	0.60
9_L	117_E	0.921	0.60
4_E	97_D	0.920	0.59
89_Q	154_A	0.918	0.59
142_C	145_R	0.906	0.58
54_T	108_I	0.904	0.58
4_E	9_L	0.904	0.58
11_K	15_R	0.903	0.58
133_V	160_P	0.898	0.58
83_W	110_A	0.891	0.57
58_I	88_E	0.879	0.56
127_F	130_G	0.876	0.56
143_P	154_A	0.867	0.55
59_K	158_F	0.864	0.55
8_I	77_E	0.854	0.54
15_R	74_I	0.853	0.54
27_R	43_L	0.853	0.54
2_K	54_T	0.845	0.53
118_E	132_K	0.844	0.53
102_R	164_T	0.837	0.52
95_E	98_E	0.835	0.52
36_P	52_F	0.830	0.52
13_A	18_I	0.819	0.51
54_T	58_I	0.810	0.50
129_G	133_V	0.809	0.50
28_L	103_L	0.800	0.49
105_Y	126_P	0.789	0.48
82_F	155_L	0.785	0.48
144_V	154_A	0.772	0.47
145_R	148_Q	0.771	0.46
95_E	117_E	0.771	0.46
91_F	117_E	0.767	0.46
46_Y	52_F	0.765	0.46
93_W	102_R	0.765	0.46
41_E	45_P	0.763	0.46
24_I	104_L	0.757	0.45
37_P	108_I	0.756	0.45
144_V	155_L	0.756	0.45
7_E	67_S	0.752	0.45
149_K	152_P	0.743	0.44
66_F	77_E	0.730	0.43
44_I	48_T	0.730	0.43
70_D	94_D	0.727	0.43
74_I	117_E	0.726	0.43
21_L	24_I	0.723	0.42
160_P	163_Q	0.719	0.42
9_L	31_E	0.715	0.42
154_A	157_P	0.708	0.41
85_M	155_L	0.704	0.41
148_Q	151_V	0.703	0.41
150_D	161_A	0.703	0.41
152_P	163_Q	0.703	0.41
74_I	79_L	0.702	0.41
24_I	148_Q	0.701	0.40
86_L	112_T	0.697	0.40
75_D	114_F	0.696	0.40
149_K	157_P	0.692	0.40
5_L	9_L	0.691	0.40
85_M	115_V	0.690	0.40
143_P	150_D	0.690	0.40
52_F	99_P	0.687	0.39
25_S	122_P	0.678	0.39
23_Q	33_K	0.673	0.38
33_K	101_F	0.671	0.38
105_Y	110_A	0.670	0.38
110_A	113_M	0.670	0.38
25_S	31_E	0.664	0.37
65_D	74_I	0.661	0.37
86_L	150_D	0.654	0.37
100_R	123_V	0.648	0.36
11_K	84_E	0.641	0.36
86_L	154_A	0.640	0.35
17_S	150_D	0.634	0.35
23_Q	98_E	0.632	0.35
36_P	132_K	0.631	0.35
104_L	144_V	0.628	0.34
151_V	154_A	0.626	0.34
83_W	144_V	0.623	0.34
75_D	109_S	0.621	0.34
82_F	160_P	0.616	0.34
108_I	135_E	0.616	0.34
90_C	107_L	0.614	0.33
15_R	19_F	0.614	0.33
31_E	105_Y	0.614	0.33
24_I	27_R	0.613	0.33
148_Q	155_L	0.607	0.33
24_I	89_Q	0.607	0.33
153_Y	157_P	0.599	0.32
125_T	128_P	0.592	0.32
9_L	27_R	0.589	0.31
36_P	82_F	0.589	0.31
7_E	68_T	0.588	0.31
22_Q	58_I	0.585	0.31
26_G	41_E	0.584	0.31
154_A	163_Q	0.582	0.31
81_E	162_K	0.580	0.31
31_E	92_A	0.576	0.30
10_K	60_L	0.574	0.30
57_E	164_T	0.572	0.30
145_R	157_P	0.571	0.30
55_Y	104_L	0.571	0.30
50_Q	141_Y	0.570	0.30
43_L	125_T	0.570	0.30
48_T	100_R	0.567	0.30
58_I	114_F	0.566	0.30
38_P	91_F	0.562	0.29
125_T	163_Q	0.560	0.29
97_D	137_G	0.559	0.29
2_K	6_L	0.557	0.29
152_P	164_T	0.555	0.29
109_S	134_E	0.554	0.29
103_L	107_L	0.553	0.29
3_G	71_E	0.553	0.29
60_L	111_Y	0.551	0.29
6_L	14_L	0.548	0.28
75_D	80_K	0.546	0.28
32_I	114_F	0.546	0.28
47_F	158_F	0.541	0.28
83_W	113_M	0.539	0.28
32_I	44_I	0.535	0.28
37_P	150_D	0.532	0.27
7_E	23_Q	0.532	0.27
19_F	109_S	0.531	0.27
56_H	62_R	0.527	0.27
50_Q	134_E	0.526	0.27
16_Y	21_L	0.525	0.27
57_E	81_E	0.524	0.27
48_T	153_Y	0.524	0.27
18_I	27_R	0.523	0.27
53_G	150_D	0.523	0.27
119_P	140_Y	0.521	0.27
141_Y	162_K	0.520	0.27
28_L	108_I	0.517	0.26
2_K	5_L	0.515	0.26
152_P	155_L	0.514	0.26
46_Y	99_P	0.513	0.26
5_L	124_G	0.512	0.26
20_D	139_V	0.511	0.26
94_D	102_R	0.511	0.26
27_R	122_P	0.510	0.26
113_M	151_V	0.510	0.26
100_R	111_Y	0.508	0.26
3_G	10_K	0.508	0.26
112_T	120_G	0.505	0.25
69_M	162_K	0.504	0.25
35_L	94_D	0.504	0.25
22_Q	134_E	0.504	0.25
85_M	157_P	0.501	0.25
7_E	135_E	0.500	0.25

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
4mzyA	2	0.4329	15.6	0.947	Contact Map
2w9yA	1	0.561	12.3	0.949	Contact Map
4yubA	2	0.3659	10.6	0.951	Contact Map
2rioA	2	0.4146	9.2	0.952	Contact Map
4fixA	3	0.3049	7.1	0.955	Contact Map
1zbtA	1	0.5366	7	0.955	Contact Map
2zfhA	3	0.2744	6.9	0.955	Contact Map
3d5aX	1	0.5732	6.8	0.955	Contact Map
4e98A	3	0.2805	6.7	0.955	Contact Map
2wbmA	1	0.5427	6.1	0.956	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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