T0895_1_129 - CASP12 - GREMLIN Contacts

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T0895_1_129 - T0895 1-129

ID:	45	Sequences: MNKYLFELPYERSEPGWTIRSYFDLMYNENRFLDAVENIVNKESYILDGIYCNFPDMNSYDESEHFEGVEFAVGYPPDEDDIVIVSEETCFEYVRLACEKYLQLHPEDTEKVNKLLSKIPSAGHHHHHH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (111)
Sequences:	98 (86)
Seq/√Len:	8.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_V	116_L	3.677	0.96
22_Y	69_V	2.323	0.71
16_G	112_V	2.299	0.70
42_K	84_I	2.244	0.68
60_Y	85_V	2.228	0.67
52_C	68_G	2.169	0.65
33_L	102_L	2.145	0.64
109_T	112_V	2.142	0.64
34_D	38_N	2.121	0.63
109_T	114_K	2.050	0.61
54_F	76_P	2.044	0.60
24_D	44_S	2.041	0.60
55_P	68_G	2.002	0.59
62_E	84_I	1.991	0.58
86_S	89_T	1.913	0.55
22_Y	76_P	1.822	0.51
29_E	32_F	1.805	0.51
23_F	71_F	1.748	0.48
48_D	74_G	1.718	0.47
52_C	84_I	1.645	0.44
59_S	87_E	1.645	0.44
55_P	65_H	1.590	0.42
44_S	54_F	1.589	0.42
62_E	79_E	1.556	0.40
64_E	99_E	1.533	0.39
71_F	85_V	1.486	0.38
41_N	114_K	1.451	0.36
32_F	42_K	1.412	0.35
65_H	105_H	1.401	0.34
28_N	91_F	1.325	0.32
36_V	119_I	1.314	0.31
92_E	109_T	1.281	0.30
22_Y	35_A	1.269	0.30
56_D	123_G	1.242	0.29
39_I	45_Y	1.237	0.29
71_F	105_H	1.199	0.27
115_L	119_I	1.193	0.27
39_I	112_V	1.183	0.27
26_M	56_D	1.169	0.26
111_K	115_L	1.166	0.26
80_D	84_I	1.160	0.26
110_E	114_K	1.138	0.25
49_G	105_H	1.138	0.25
19_I	38_N	1.130	0.25
33_L	38_N	1.129	0.25
19_I	35_A	1.115	0.25
102_L	106_P	1.113	0.25
94_V	104_L	1.113	0.25
23_F	91_F	1.112	0.24
19_I	118_K	1.095	0.24
41_N	88_E	1.083	0.24
57_M	94_V	1.052	0.23
13_S	96_L	1.019	0.22
94_V	113_N	1.014	0.22
23_F	67_E	1.005	0.21
13_S	69_V	1.004	0.21
107_E	121_S	1.001	0.21
26_M	67_E	0.996	0.21
12_R	16_G	0.983	0.21
99_E	105_H	0.982	0.21
30_N	39_I	0.967	0.20
80_D	105_H	0.963	0.20
38_N	41_N	0.946	0.20
99_E	104_L	0.936	0.19
88_E	92_E	0.932	0.19
13_S	41_N	0.930	0.19
34_D	47_L	0.928	0.19
17_W	103_Q	0.909	0.19
23_F	107_E	0.909	0.19
66_F	97_A	0.909	0.19
30_N	63_S	0.901	0.19
37_E	45_Y	0.900	0.19
48_D	64_E	0.899	0.19
40_V	91_F	0.897	0.18
28_N	63_S	0.889	0.18
17_W	30_N	0.885	0.18
24_D	73_V	0.884	0.18
102_L	108_D	0.880	0.18
36_V	39_I	0.878	0.18
50_I	57_M	0.874	0.18
33_L	67_E	0.874	0.18
24_D	107_E	0.864	0.18
30_N	45_Y	0.856	0.17
87_E	122_A	0.849	0.17
84_I	101_Y	0.838	0.17
61_D	73_V	0.833	0.17
45_Y	54_F	0.823	0.17
86_S	117_S	0.822	0.17
90_C	94_V	0.806	0.16
12_R	117_S	0.804	0.16
26_M	90_C	0.797	0.16
13_S	110_E	0.792	0.16
19_I	44_S	0.786	0.16
69_V	90_C	0.783	0.16
30_N	35_A	0.775	0.16
96_L	120_P	0.773	0.16
115_L	121_S	0.769	0.16
40_V	45_Y	0.769	0.16
74_G	77_P	0.765	0.15
120_P	123_G	0.747	0.15
36_V	114_K	0.743	0.15
39_I	55_P	0.738	0.15
52_C	101_Y	0.737	0.15
32_F	66_F	0.731	0.15
39_I	69_V	0.723	0.15
18_T	77_P	0.719	0.14
23_F	83_V	0.717	0.14
13_S	83_V	0.712	0.14
15_P	90_C	0.707	0.14
56_D	67_E	0.703	0.14
71_F	107_E	0.702	0.14
36_V	70_E	0.702	0.14
26_M	91_F	0.700	0.14
42_K	99_E	0.699	0.14
68_G	84_I	0.694	0.14
34_D	92_E	0.692	0.14
46_I	54_F	0.687	0.14
24_D	61_D	0.687	0.14
95_R	123_G	0.683	0.14
35_A	43_E	0.672	0.14
36_V	45_Y	0.668	0.13
60_Y	106_P	0.666	0.13
86_S	93_Y	0.663	0.13
30_N	83_V	0.659	0.13
55_P	71_F	0.659	0.13
23_F	55_P	0.651	0.13
111_K	119_I	0.644	0.13
34_D	102_L	0.632	0.13
55_P	66_F	0.629	0.13
39_I	71_F	0.628	0.13
51_Y	72_A	0.627	0.13
100_K	121_S	0.614	0.12
13_S	112_V	0.612	0.12
17_W	76_P	0.610	0.12
14_E	20_R	0.607	0.12
49_G	59_S	0.604	0.12
64_E	74_G	0.604	0.12
50_I	76_P	0.603	0.12
47_L	50_I	0.602	0.12
31_R	47_L	0.602	0.12
68_G	87_E	0.601	0.12
100_K	123_G	0.599	0.12
47_L	93_Y	0.592	0.12
104_L	113_N	0.588	0.12
59_S	112_V	0.582	0.12
97_A	106_P	0.580	0.12
20_R	83_V	0.566	0.12
90_C	112_V	0.564	0.12
76_P	86_S	0.557	0.11
113_N	118_K	0.551	0.11
66_F	95_R	0.547	0.11
42_K	88_E	0.547	0.11
48_D	122_A	0.546	0.11
107_E	123_G	0.545	0.11
32_F	71_F	0.541	0.11
22_Y	88_E	0.531	0.11
88_E	93_Y	0.527	0.11
79_E	88_E	0.523	0.11
102_L	113_N	0.523	0.11
15_P	20_R	0.519	0.11
52_C	55_P	0.519	0.11
84_I	119_I	0.517	0.11
63_S	113_N	0.507	0.11
55_P	67_E	0.507	0.11
43_E	47_L	0.505	0.11
28_N	100_K	0.500	0.11

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
4q7o_A	1	0.9147	41.1	0.91	Contact Map
2guk_A	1	0.5736	7.4	0.936	Contact Map
2jul_A	1	0.3333	3.8	0.945	Contact Map
1zvd_A	1	0.2946	3.5	0.945	Contact Map
3dd4_A	1	0.3333	3.3	0.946	Contact Map
1s6c_A	1	0.0155	3	0.947	Contact Map
4b8r_A	1	0.7054	2.5	0.949	Contact Map
4guk_A	1	0.3333	2.5	0.95	Contact Map
1goi_A	1	0.8837	2.5	0.95	Contact Map
1fpw_A	1	0.3333	2.4	0.95	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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