T0908_1_137 - CASP12 - GREMLIN Contacts

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T0908_1_137 - T0908 1-137

ID:	61	Sequences: MQVQLVESGGGLVQAGGSLRLSCAASGRTFSSYVMGWFRQAPGKEREFVTAISWSGGSIHYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYTCVAGFAGYGSFTSRSARDSDKYDYWGQGTKVTVSSHHHHHH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (117)
Sequences:	2040 (1255)
Seq/√Len:	116.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
122_G	125_T	3.254	1.00
69_F	84_M	3.216	1.00
13_V	87_L	2.739	1.00
19_L	127_V	2.471	1.00
121_W	127_V	2.440	1.00
37_W	82_L	2.378	1.00
49_V	69_F	2.376	1.00
39_R	93_A	2.321	1.00
7_E	122_G	2.269	1.00
121_W	124_G	2.269	1.00
25_A	35_M	2.162	1.00
35_M	80_V	2.149	1.00
40_Q	46_R	2.094	1.00
14_Q	17_G	2.057	1.00
118_Y	126_K	2.041	1.00
20_R	81_Y	1.922	1.00
38_F	48_F	1.858	1.00
91_D	95_Y	1.803	1.00
123_Q	128_T	1.782	1.00
13_V	17_G	1.779	1.00
101_F	104_Y	1.719	1.00
120_Y	123_Q	1.698	1.00
119_D	126_K	1.628	1.00
117_K	126_K	1.436	1.00
20_R	83_Q	1.403	1.00
49_V	65_V	1.400	1.00
18_S	87_L	1.390	1.00
24_A	79_T	1.386	1.00
125_T	129_V	1.351	1.00
117_K	120_Y	1.347	1.00
67_G	70_T	1.327	1.00
121_W	126_K	1.327	1.00
34_V	51_A	1.321	1.00
118_Y	121_W	1.317	1.00
39_R	47_E	1.298	1.00
124_G	127_V	1.289	1.00
50_T	71_I	1.258	0.99
43_G	46_R	1.248	0.99
23_C	97_C	1.239	0.99
51_A	60_H	1.232	0.99
44_K	85_N	1.217	0.99
120_Y	126_K	1.201	0.99
120_Y	128_T	1.200	0.99
32_S	55_S	1.180	0.99
56_G	59_I	1.175	0.99
40_Q	82_L	1.169	0.99
25_A	30_F	1.168	0.99
119_D	128_T	1.167	0.99
34_V	53_S	1.160	0.99
81_Y	90_E	1.129	0.99
84_M	94_V	1.122	0.99
121_W	125_T	1.110	0.99
5_L	37_W	1.103	0.98
30_F	35_M	1.100	0.98
7_E	125_T	1.092	0.98
25_A	78_N	1.090	0.98
124_G	129_V	1.089	0.98
37_W	97_C	1.081	0.98
91_D	96_T	1.056	0.98
34_V	60_H	1.049	0.98
33_Y	58_S	1.034	0.98
63_D	66_K	1.016	0.97
71_I	84_M	1.015	0.97
7_E	11_G	1.003	0.97
49_V	73_R	0.995	0.97
61_Y	65_V	0.981	0.97
40_Q	43_G	0.972	0.97
100_G	103_G	0.956	0.96
56_G	60_H	0.951	0.96
11_G	19_L	0.948	0.96
102_A	117_K	0.944	0.96
84_M	88_K	0.940	0.96
68_R	88_K	0.916	0.95
123_Q	126_K	0.892	0.94
51_A	58_S	0.874	0.94
16_G	67_G	0.859	0.93
117_K	121_W	0.856	0.93
36_G	48_F	0.847	0.93
24_A	81_Y	0.845	0.93
21_L	37_W	0.843	0.93
5_L	75_N	0.833	0.92
54_W	100_G	0.832	0.92
102_A	105_G	0.832	0.92
69_F	82_L	0.831	0.92
2_Q	104_Y	0.820	0.92
119_D	124_G	0.805	0.91
5_L	78_N	0.797	0.90
86_S	94_V	0.796	0.90
96_T	124_G	0.793	0.90
30_F	78_N	0.787	0.90
65_V	69_F	0.782	0.89
122_G	127_V	0.777	0.89
53_S	60_H	0.773	0.89
28_R	32_S	0.768	0.89
60_H	63_D	0.762	0.88
16_G	20_R	0.761	0.88
7_E	10_G	0.759	0.88
64_S	72_S	0.757	0.88
123_Q	127_V	0.756	0.88
95_Y	98_V	0.750	0.87
24_A	42_P	0.749	0.87
35_M	69_F	0.733	0.86
67_G	87_L	0.728	0.86
121_W	129_V	0.708	0.84
33_Y	102_A	0.703	0.84
38_F	99_A	0.702	0.84
68_R	84_M	0.701	0.84
19_L	83_Q	0.699	0.83
36_G	98_V	0.699	0.83
17_G	81_Y	0.697	0.83
23_C	37_W	0.696	0.83
10_G	88_K	0.692	0.83
119_D	123_Q	0.689	0.83
25_A	48_F	0.687	0.82
62_A	79_T	0.683	0.82
51_A	80_V	0.683	0.82
122_G	129_V	0.675	0.81
17_G	89_P	0.675	0.81
81_Y	88_K	0.667	0.81
82_L	95_Y	0.652	0.79
28_R	80_V	0.652	0.79
68_R	86_S	0.650	0.79
15_A	87_L	0.650	0.79
91_D	97_C	0.644	0.78
36_G	60_H	0.634	0.77
126_K	129_V	0.632	0.77
26_S	49_V	0.630	0.77
36_G	51_A	0.619	0.75
9_G	123_Q	0.618	0.75
77_K	81_Y	0.614	0.75
4_Q	61_Y	0.611	0.74
55_S	58_S	0.606	0.74
29_T	38_F	0.604	0.74
33_Y	99_A	0.601	0.73
11_G	14_Q	0.594	0.72
101_F	105_G	0.593	0.72
36_G	80_V	0.593	0.72
100_G	104_Y	0.591	0.72
31_S	100_G	0.584	0.71
36_G	79_T	0.583	0.71
39_R	61_Y	0.583	0.71
9_G	12_L	0.582	0.71
2_Q	6_V	0.582	0.71
18_S	83_Q	0.581	0.71
2_Q	51_A	0.577	0.70
13_V	19_L	0.575	0.70
20_R	87_L	0.575	0.70
66_K	70_T	0.571	0.69
41_A	90_E	0.571	0.69
90_E	94_V	0.570	0.69
18_S	27_G	0.566	0.69
8_S	11_G	0.558	0.68
25_A	75_N	0.557	0.68
51_A	70_T	0.556	0.67
75_N	78_N	0.553	0.67
24_A	77_K	0.552	0.67
52_I	73_R	0.551	0.67
3_V	44_K	0.548	0.66
46_R	96_T	0.543	0.66
120_Y	125_T	0.539	0.65
68_R	95_Y	0.539	0.65
32_S	101_F	0.538	0.65
24_A	41_A	0.537	0.65
28_R	31_S	0.536	0.65
40_Q	83_Q	0.534	0.64
15_A	96_T	0.532	0.64
53_S	58_S	0.532	0.64
49_V	105_G	0.528	0.63
100_G	119_D	0.527	0.63
51_A	56_G	0.526	0.63
25_A	93_A	0.523	0.63
27_G	127_V	0.516	0.62
96_T	100_G	0.510	0.61
65_V	75_N	0.504	0.60
79_T	102_A	0.501	0.59
101_F	117_K	0.500	0.59

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
4pfe_A	1	0.0584	99.8	0.224	Contact Map
2yc1_A	1	0.854	99.8	0.264	Contact Map
4b41_A	1	0.854	99.8	0.274	Contact Map
4qo1_A	1	0.927	99.8	0.276	Contact Map
3k74_B	1	0.8394	99.8	0.278	Contact Map
4ut7_H	1	0.9781	99.8	0.278	Contact Map
4lgp_B	1	0.8467	99.8	0.283	Contact Map
1yjd_C	1	0.8394	99.8	0.285	Contact Map
4jvp_A	1	0.9562	99.8	0.287	Contact Map
1zvy_A	1	0.9124	99.8	0.289	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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