T0936_126_205 - CASP12 - GREMLIN Contacts

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T0936_126_205 - T0936 126-205

ID:	105	Sequences: VRPCMRDAACEHALFDMNRYYEKLRARMPADSRQTLVAAQREWAAFSDAMTPLVSEGERVDLIGARVATLKRFSETVNNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (66)
Sequences:	1366 (1003)
Seq/√Len:	123.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_D	71_K	3.461	1.00
50_M	62_L	2.868	1.00
20_Y	67_V	2.319	1.00
13_A	60_V	2.271	1.00
25_R	37_V	2.228	1.00
37_V	41_R	2.096	1.00
18_N	21_Y	1.771	1.00
20_Y	71_K	1.767	1.00
22_E	26_A	1.743	1.00
20_Y	74_S	1.743	1.00
18_N	44_A	1.702	1.00
15_F	19_R	1.659	1.00
39_A	46_F	1.627	1.00
61_D	65_A	1.445	1.00
46_F	50_M	1.398	1.00
45_A	49_A	1.394	1.00
42_E	49_A	1.367	1.00
65_A	69_T	1.311	1.00
16_D	20_Y	1.305	1.00
42_E	45_A	1.258	1.00
25_R	33_R	1.214	0.99
29_P	32_S	1.159	0.99
13_A	67_V	1.149	0.99
58_E	63_I	1.137	0.99
16_D	64_G	1.126	0.99
56_E	59_R	1.114	0.99
14_L	48_D	1.108	0.99
29_P	33_R	1.108	0.99
21_Y	37_V	1.105	0.99
37_V	44_A	1.103	0.99
18_N	41_R	1.077	0.99
20_Y	24_L	1.027	0.98
14_L	63_I	1.013	0.98
51_T	54_V	0.994	0.98
19_R	23_K	0.984	0.97
24_L	28_M	0.983	0.97
44_A	63_I	0.961	0.97
44_A	48_D	0.941	0.97
13_A	64_G	0.933	0.96
66_R	69_T	0.922	0.96
28_M	32_S	0.895	0.95
68_A	72_R	0.887	0.95
53_L	57_G	0.885	0.95
20_Y	70_L	0.881	0.95
14_L	44_A	0.879	0.95
46_F	62_L	0.875	0.95
19_R	34_Q	0.867	0.95
52_P	60_V	0.866	0.94
21_Y	25_R	0.860	0.94
21_Y	44_A	0.849	0.94
18_N	63_I	0.849	0.94
39_A	50_M	0.848	0.94
60_V	64_G	0.842	0.94
64_G	68_A	0.838	0.93
62_L	65_A	0.829	0.93
24_L	74_S	0.817	0.93
14_L	17_M	0.809	0.92
14_L	41_R	0.804	0.92
46_F	69_T	0.801	0.92
40_Q	66_R	0.781	0.91
21_Y	28_M	0.779	0.91
13_A	63_I	0.779	0.91
55_S	59_R	0.771	0.90
13_A	16_D	0.770	0.90
71_K	75_E	0.752	0.89
34_Q	38_A	0.742	0.89
14_L	18_N	0.736	0.88
52_P	56_E	0.718	0.87
57_G	61_D	0.700	0.85
23_K	74_S	0.695	0.85
24_L	73_F	0.689	0.85
59_R	63_I	0.681	0.84
44_A	47_S	0.681	0.84
17_M	40_Q	0.665	0.82
39_A	66_R	0.661	0.82
34_Q	37_V	0.640	0.80
15_F	22_E	0.615	0.77
12_H	16_D	0.612	0.77
68_A	71_K	0.602	0.76
27_R	56_E	0.591	0.74
17_M	41_R	0.590	0.74
46_F	73_F	0.583	0.73
21_Y	36_L	0.573	0.72
57_G	65_A	0.564	0.71
62_L	69_T	0.559	0.70
38_A	72_R	0.555	0.70
56_E	67_V	0.553	0.70
23_K	27_R	0.553	0.70
38_A	49_A	0.549	0.69
27_R	30_A	0.540	0.68
12_H	41_R	0.532	0.67
14_L	36_L	0.527	0.66
41_R	44_A	0.527	0.66
16_D	19_R	0.522	0.65
53_L	56_E	0.520	0.65
48_D	59_R	0.516	0.64
33_R	37_V	0.508	0.63
21_Y	41_R	0.502	0.62
51_T	55_S	0.500	0.62

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
3gi7_A	1	0.95	99.2	0.364	Contact Map
3lxu_X	1	0.975	13	0.869	Contact Map
2yay_A	1	0.25	4.7	0.893	Contact Map
2y9m_A	1	0.3375	2.7	0.906	Contact Map
3csk_A	1	1	2.7	0.906	Contact Map
2rno_A	1	0.4125	2.5	0.907	Contact Map
3jb6_A	1	0.35	2	0.912	Contact Map
4p72_A	1	0.4625	1.9	0.913	Contact Map
3pco_B	1	0.475	1.9	0.913	Contact Map
1deq_A	1	0.9875	1.8	0.915	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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