Y3061 - HALSA - GREMLIN Contacts

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Y3061 - UPF0033 protein VNG_5061C/VNG_5236C/VNG_6059C/VNG_6467C

UniProt:	O54608	Sequences: MSADYDITETLDVKGASCPMPVVKTKSAIDDLAEGEILEVLATDSGSMSDIDGWASGTAGVELVDQEEGDDVYKHYVRKTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	81 (73)
Sequences:	1054 (651)
Seq/√Len:	76.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_E	78_R	3.631	1.00
33_A	36_E	3.179	1.00
14_K	72_V	3.176	1.00
8_T	36_E	3.166	1.00
39_E	74_K	2.730	1.00
10_T	39_E	2.368	1.00
14_K	41_L	2.152	1.00
9_E	31_D	2.080	1.00
9_E	32_L	1.857	1.00
55_A	77_V	1.807	1.00
37_I	76_Y	1.789	1.00
37_I	64_V	1.668	1.00
68_E	71_D	1.629	1.00
41_L	72_V	1.565	0.99
32_L	36_E	1.501	0.99
58_T	61_V	1.455	0.99
14_K	43_T	1.451	0.99
29_I	54_W	1.438	0.99
52_D	56_S	1.390	0.99
25_T	51_I	1.336	0.98
23_V	54_W	1.332	0.98
16_A	24_K	1.302	0.98
47_S	75_H	1.263	0.97
7_I	39_E	1.227	0.97
63_L	75_H	1.227	0.97
47_S	73_Y	1.194	0.96
10_T	41_L	1.179	0.96
9_E	36_E	1.128	0.95
48_M	68_E	1.097	0.94
20_M	23_V	1.092	0.94
48_M	66_Q	1.087	0.94
42_A	47_S	1.087	0.94
26_K	30_D	1.058	0.93
66_Q	75_H	1.026	0.92
20_M	24_K	1.021	0.92
8_T	32_L	1.000	0.91
48_M	73_Y	0.987	0.90
22_V	57_G	0.971	0.89
40_V	51_I	0.960	0.89
25_T	40_V	0.948	0.88
25_T	38_L	0.937	0.88
45_S	73_Y	0.935	0.88
34_E	79_K	0.934	0.88
67_E	74_K	0.912	0.86
41_L	74_K	0.903	0.86
26_K	46_G	0.898	0.85
42_A	73_Y	0.897	0.85
65_D	76_Y	0.897	0.85
48_M	52_D	0.878	0.84
11_L	38_L	0.863	0.83
23_V	29_I	0.855	0.82
16_A	20_M	0.849	0.82
27_S	31_D	0.840	0.81
17_S	26_K	0.831	0.81
28_A	32_L	0.828	0.80
11_L	28_A	0.793	0.77
22_V	26_K	0.781	0.76
37_I	78_R	0.770	0.75
55_A	59_A	0.762	0.75
27_S	59_A	0.753	0.74
6_D	71_D	0.748	0.73
52_D	66_Q	0.729	0.71
41_L	76_Y	0.723	0.71
52_D	75_H	0.696	0.68
28_A	31_D	0.693	0.67
29_I	57_G	0.691	0.67
32_L	79_K	0.689	0.67
9_E	28_A	0.686	0.67
7_I	37_I	0.685	0.67
29_I	32_L	0.682	0.66
9_E	38_L	0.662	0.64
28_A	40_V	0.647	0.62
26_K	47_S	0.647	0.62
39_E	76_Y	0.642	0.62
63_L	73_Y	0.627	0.60
13_V	71_D	0.612	0.58
32_L	38_L	0.611	0.58
11_L	25_T	0.604	0.57
69_G	72_V	0.600	0.56
69_G	74_K	0.599	0.56
55_A	63_L	0.595	0.56
7_I	76_Y	0.590	0.55
67_E	76_Y	0.590	0.55
46_G	53_G	0.572	0.53
46_G	54_W	0.566	0.52
22_V	25_T	0.565	0.52
10_T	74_K	0.558	0.51
26_K	58_T	0.555	0.51
22_V	58_T	0.554	0.51
23_V	47_S	0.540	0.49
66_Q	76_Y	0.536	0.48
15_G	69_G	0.536	0.48
6_D	9_E	0.533	0.48
11_L	40_V	0.532	0.48
13_V	53_G	0.529	0.47
13_V	42_A	0.528	0.47
55_A	58_T	0.523	0.47
72_V	78_R	0.522	0.47
65_D	75_H	0.520	0.46
23_V	57_G	0.518	0.46
16_A	34_E	0.517	0.46
47_S	55_A	0.513	0.45
30_D	57_G	0.513	0.45
25_T	79_K	0.511	0.45
33_A	69_G	0.509	0.45
24_K	27_S	0.508	0.45
45_S	57_G	0.508	0.45
49_S	58_T	0.507	0.45
64_V	70_D	0.506	0.45
6_D	56_S	0.500	0.44

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
1je3A	1	0.9506	99.9	0.332	Contact Map
1jdqA	1	0.9753	99.9	0.341	Contact Map
1pavA	1	0.963	99.9	0.346	Contact Map
3lvjC	1	0.9259	99.9	0.379	Contact Map
3hz7A	1	0.9012	99.9	0.388	Contact Map
2lxrA	1	0.8642	99.8	0.443	Contact Map
1okgA	1	0.7284	98.6	0.698	Contact Map
2l3mA	1	0.7531	24.6	0.911	Contact Map
1rcqA	2	0.9136	20.9	0.914	Contact Map
1oz2A	1	0.8889	19.6	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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