T0925_1_87 - CASP12 - GREMLIN Contacts

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T0925_1_87 - T0925 1-87

ID:	91	Sequences: GEFEDLSRVNATVQETNDLLHNSTMTTLLAGRKMKDMEMQANLLLDRLKPLKTLEENLSRNLSEIKLLISRARKQAASIKVAVSADR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (78)
Sequences:	155 (117)
Seq/√Len:	13.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_I	68_L	4.804	1.00
72_A	76_A	3.086	0.97
67_L	71_R	1.892	0.74
29_L	37_M	1.869	0.73
77_A	82_A	1.769	0.69
10_N	13_V	1.656	0.64
69_I	76_A	1.644	0.63
82_A	85_A	1.583	0.60
25_M	30_A	1.575	0.60
12_T	15_E	1.555	0.59
36_D	40_Q	1.547	0.58
17_N	21_H	1.532	0.57
42_N	78_S	1.524	0.57
36_D	39_M	1.452	0.53
42_N	85_A	1.431	0.52
68_L	71_R	1.426	0.52
16_T	79_I	1.408	0.51
14_Q	21_H	1.390	0.50
65_I	71_R	1.373	0.49
18_D	36_D	1.356	0.48
71_R	79_I	1.348	0.48
55_E	83_V	1.348	0.48
43_L	70_S	1.323	0.46
27_T	30_A	1.322	0.46
22_N	27_T	1.313	0.46
27_T	31_G	1.297	0.45
25_M	29_L	1.292	0.45
62_L	84_S	1.249	0.43
69_I	72_A	1.235	0.42
82_A	87_R	1.206	0.40
61_N	72_A	1.166	0.38
33_K	37_M	1.152	0.38
15_E	22_N	1.141	0.37
14_Q	46_D	1.135	0.37
38_E	58_L	1.135	0.37
47_R	53_T	1.091	0.35
41_A	54_L	1.078	0.34
71_R	76_A	1.070	0.34
23_S	49_K	1.061	0.33
13_V	17_N	1.054	0.33
31_G	42_N	1.051	0.33
20_L	77_A	1.043	0.32
57_N	65_I	1.040	0.32
66_K	73_R	1.032	0.32
65_I	82_A	0.987	0.30
19_L	23_S	0.984	0.30
25_M	28_L	0.973	0.29
32_R	43_L	0.963	0.29
14_Q	20_L	0.941	0.28
56_E	80_K	0.924	0.27
73_R	76_A	0.923	0.27
24_T	30_A	0.921	0.27
19_L	25_M	0.898	0.26
11_A	15_E	0.897	0.26
33_K	42_N	0.892	0.26
55_E	84_S	0.891	0.26
10_N	32_R	0.885	0.26
21_H	24_T	0.883	0.26
33_K	61_N	0.864	0.25
23_S	37_M	0.863	0.25
61_N	69_I	0.860	0.25
10_N	14_Q	0.853	0.24
10_N	35_K	0.842	0.24
31_G	58_L	0.833	0.24
46_D	52_K	0.820	0.23
11_A	14_Q	0.818	0.23
33_K	62_L	0.814	0.23
66_K	76_A	0.812	0.23
39_M	46_D	0.796	0.22
14_Q	17_N	0.782	0.22
73_R	77_A	0.776	0.21
37_M	59_S	0.757	0.21
70_S	85_A	0.744	0.20
23_S	72_A	0.744	0.20
61_N	87_R	0.728	0.20
74_K	79_I	0.728	0.20
47_R	86_D	0.726	0.20
55_E	64_E	0.726	0.20
21_H	32_R	0.722	0.20
67_L	84_S	0.722	0.20
10_N	18_D	0.701	0.19
58_L	83_V	0.700	0.19
48_L	68_L	0.690	0.19
15_E	21_H	0.690	0.19
29_L	34_M	0.690	0.19
11_A	17_N	0.686	0.18
11_A	21_H	0.681	0.18
41_A	86_D	0.680	0.18
17_N	37_M	0.677	0.18
54_L	72_A	0.659	0.18
68_L	78_S	0.658	0.18
62_L	86_D	0.653	0.17
30_A	81_V	0.653	0.17
13_V	20_L	0.652	0.17
42_N	47_R	0.650	0.17
20_L	53_T	0.639	0.17
11_A	18_D	0.620	0.16
10_N	16_T	0.620	0.16
35_K	84_S	0.608	0.16
26_T	65_I	0.603	0.16
19_L	26_T	0.598	0.16
57_N	69_I	0.596	0.16
34_M	62_L	0.595	0.16
75_Q	80_K	0.594	0.16
67_L	76_A	0.587	0.16
36_D	46_D	0.587	0.16
41_A	55_E	0.575	0.15
79_I	83_V	0.560	0.15
34_M	68_L	0.558	0.15
63_S	67_L	0.555	0.15
48_L	61_N	0.544	0.14
70_S	74_K	0.534	0.14
64_E	83_V	0.533	0.14
71_R	82_A	0.517	0.14
75_Q	81_V	0.506	0.13
36_D	77_A	0.506	0.13
24_T	47_R	0.500	0.13

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
3c9i_A	1	1	85.8	0.765	Contact Map
5bu8_A	1	0.1609	80.2	0.779	Contact Map
4q4g_X	1	0	79.4	0.781	Contact Map
4cgk_A	1	0.8506	78.5	0.783	Contact Map
2yko_A	1	0.6092	44.2	0.827	Contact Map
4lin_A	1	1	39.9	0.831	Contact Map
5amo_A	1	0	37	0.834	Contact Map
2ch7_A	1	0.9195	34.8	0.837	Contact Map
4uxv_A	1	0.9655	30.5	0.841	Contact Map
4rh7_A	1	0.954	29.2	0.843	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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