T0885_1_116 - CASP12 - GREMLIN Contacts

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T0885_1_116 - T0885 1-116

ID:	32	Sequences: MTMRYQEPARIPNAEIDHVLASGNPEAIADACLSIAYYEDDWEWAFKRLKSVAFDLNRPDSLRSLAVTCVGHLARRIHDLDVAMAEEFLLSLGGDQAVASAASDALDDLRIFRMSD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (103)
Sequences:	128 (111)
Seq/√Len:	10.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_L	73_L	3.096	0.95
55_D	70_V	2.974	0.94
65_L	69_C	2.908	0.93
72_H	75_R	2.815	0.92
31_A	89_L	2.397	0.84
63_R	93_G	2.121	0.75
75_R	100_S	2.066	0.73
72_H	108_D	1.988	0.70
20_L	70_V	1.830	0.64
75_R	78_H	1.821	0.63
45_A	73_L	1.732	0.59
63_R	105_A	1.691	0.57
37_Y	72_H	1.683	0.57
71_G	104_D	1.635	0.55
46_F	81_D	1.628	0.54
72_H	100_S	1.623	0.54
34_S	45_A	1.602	0.53
25_P	66_A	1.516	0.49
95_D	98_V	1.505	0.48
26_E	90_L	1.482	0.47
75_R	108_D	1.477	0.47
46_F	49_L	1.467	0.47
33_L	69_C	1.460	0.46
49_L	80_L	1.409	0.44
36_A	69_C	1.398	0.43
36_A	98_V	1.382	0.43
68_T	104_D	1.371	0.42
87_E	111_I	1.352	0.41
66_A	71_G	1.347	0.41
33_L	68_T	1.338	0.40
74_A	80_L	1.333	0.40
31_A	106_L	1.330	0.40
55_D	88_F	1.258	0.37
33_L	75_R	1.233	0.36
40_D	93_G	1.212	0.35
75_R	104_D	1.195	0.34
20_L	24_N	1.191	0.34
19_V	45_A	1.170	0.33
25_P	88_F	1.165	0.33
35_I	76_R	1.164	0.33
73_L	102_A	1.142	0.32
23_G	58_R	1.136	0.32
36_A	64_S	1.128	0.31
57_N	105_A	1.113	0.31
36_A	76_R	1.111	0.31
68_T	98_V	1.111	0.31
31_A	77_I	1.105	0.30
29_A	67_V	1.086	0.30
28_I	32_C	1.086	0.30
65_L	92_L	1.081	0.29
91_S	110_R	1.074	0.29
59_P	82_V	1.053	0.28
28_I	54_F	1.052	0.28
82_V	110_R	1.051	0.28
15_E	31_A	1.045	0.28
18_H	94_G	1.036	0.28
41_D	58_R	1.029	0.27
55_D	69_C	1.020	0.27
54_F	82_V	0.993	0.26
87_E	93_G	0.991	0.26
15_E	34_S	0.989	0.26
104_D	108_D	0.986	0.26
81_D	107_D	0.970	0.25
63_R	95_D	0.965	0.25
88_F	92_L	0.957	0.25
76_R	87_E	0.943	0.24
63_R	102_A	0.928	0.24
9_A	113_R	0.928	0.24
32_C	69_C	0.926	0.24
57_N	62_L	0.925	0.24
42_W	80_L	0.925	0.24
44_W	68_T	0.907	0.23
58_R	70_V	0.887	0.22
11_I	57_N	0.881	0.22
32_C	83_A	0.870	0.22
62_L	74_A	0.865	0.22
63_R	99_A	0.862	0.21
28_I	74_A	0.857	0.21
23_G	86_E	0.853	0.21
66_A	79_D	0.851	0.21
33_L	37_Y	0.839	0.21
35_I	40_D	0.838	0.21
67_V	88_F	0.834	0.21
69_C	89_L	0.830	0.20
74_A	107_D	0.827	0.20
84_M	96_Q	0.826	0.20
102_A	106_L	0.825	0.20
41_D	108_D	0.797	0.19
43_E	81_D	0.793	0.19
32_C	54_F	0.790	0.19
63_R	98_V	0.786	0.19
22_S	68_T	0.770	0.19
66_A	73_L	0.767	0.19
44_W	96_Q	0.767	0.19
85_A	109_L	0.765	0.18
59_P	79_D	0.763	0.18
87_E	113_R	0.759	0.18
37_Y	58_R	0.754	0.18
32_C	57_N	0.749	0.18
83_A	107_D	0.743	0.18
20_L	55_D	0.733	0.18
11_I	29_A	0.711	0.17
78_H	108_D	0.708	0.17
68_T	75_R	0.704	0.17
43_E	69_C	0.698	0.17
70_V	101_A	0.694	0.17
30_D	69_C	0.690	0.16
101_A	104_D	0.682	0.16
71_G	105_A	0.681	0.16
45_A	66_A	0.677	0.16
68_T	78_H	0.676	0.16
72_H	81_D	0.660	0.16
20_L	23_G	0.644	0.15
22_S	103_S	0.642	0.15
33_L	80_L	0.640	0.15
35_I	97_A	0.631	0.15
80_L	86_E	0.630	0.15
64_S	101_A	0.625	0.15
15_E	18_H	0.622	0.15
68_T	89_L	0.619	0.15
55_D	77_I	0.603	0.14
43_E	64_S	0.601	0.14
28_I	91_S	0.599	0.14
47_K	63_R	0.594	0.14
46_F	88_F	0.594	0.14
42_W	46_F	0.587	0.14
16_I	102_A	0.579	0.14
40_D	50_K	0.578	0.14
65_L	105_A	0.575	0.14
29_A	86_E	0.574	0.14
11_I	19_V	0.565	0.13
39_E	66_A	0.564	0.13
60_D	104_D	0.561	0.13
9_A	23_G	0.556	0.13
25_P	102_A	0.554	0.13
18_H	56_L	0.552	0.13
99_A	102_A	0.548	0.13
72_H	104_D	0.545	0.13
39_E	96_Q	0.544	0.13
47_K	69_C	0.544	0.13
37_Y	75_R	0.543	0.13
22_S	34_S	0.540	0.13
100_S	104_D	0.537	0.13
73_L	81_D	0.535	0.13
36_A	57_N	0.534	0.13
13_N	44_W	0.529	0.13
35_I	45_A	0.527	0.13
37_Y	100_S	0.518	0.12
21_A	53_A	0.517	0.12
78_H	100_S	0.511	0.12
103_S	107_D	0.508	0.12
71_G	98_V	0.507	0.12
108_D	112_F	0.504	0.12
17_D	73_L	0.500	0.12

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
2db0_A	1	0.9397	97.3	0.784	Contact Map
4jw2_A	1	0.6121	97.2	0.789	Contact Map
5frp_A	1	0.9741	97.2	0.789	Contact Map
1te4_A	1	0.7328	97.1	0.792	Contact Map
4l7m_A	1	0.8534	97	0.794	Contact Map
2vgl_B	1	0.9828	96.5	0.806	Contact Map
4g3a_A	1	0.9138	96.5	0.807	Contact Map
2vgl_A	1	0.9828	96.4	0.808	Contact Map
3ltj_A	1	0.8448	96.4	0.809	Contact Map
4p6z_G	1	0.9741	96.4	0.809	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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