Thoc2 - PFAM28P - GREMLIN Contacts

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Thoc2 - Transcription- and export-related complex subunit

PFAM:	PF11732	Sequences: LAKLAHSNPLIVFDVILNQIESYDNLIEPVVEALKYLTPLGYDVLTYCLLEALSNPGRSRLKEDGTNISQWLQSLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (76)
Sequences:	529 (380)
Seq/√Len:	43.6
META:	0.554

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_E	58_R	4.489	1.00
17_L	48_C	4.156	1.00
21_E	52_A	3.469	1.00
60_R	72_L	2.721	1.00
9_P	44_V	2.618	1.00
10_L	33_A	2.155	1.00
45_L	50_L	2.147	1.00
47_Y	51_E	2.095	0.99
64_D	67_N	1.994	0.99
62_K	67_N	1.906	0.99
1_L	37_L	1.785	0.98
21_E	29_P	1.568	0.96
55_N	58_R	1.516	0.95
37_L	42_Y	1.455	0.94
67_N	70_Q	1.430	0.93
13_F	25_N	1.389	0.92
33_A	47_Y	1.382	0.92
2_A	8_N	1.379	0.92
17_L	28_E	1.366	0.92
62_K	66_T	1.332	0.91
13_F	45_L	1.313	0.90
29_P	38_T	1.262	0.88
56_P	59_S	1.235	0.87
71_W	75_L	1.180	0.84
62_K	70_Q	1.172	0.84
25_N	72_L	1.150	0.83
31_V	50_L	1.121	0.81
27_I	53_L	1.092	0.79
23_Y	76_A	1.029	0.75
69_S	72_L	1.020	0.75
34_L	42_Y	1.018	0.74
5_A	41_G	1.006	0.74
52_A	61_L	0.984	0.72
37_L	41_G	0.983	0.72
6_H	38_T	0.969	0.71
40_L	48_C	0.948	0.69
52_A	58_R	0.940	0.68
32_E	55_N	0.936	0.68
2_A	10_L	0.930	0.68
15_V	18_N	0.922	0.67
65_G	71_W	0.910	0.66
12_V	27_I	0.880	0.63
20_I	27_I	0.855	0.61
6_H	47_Y	0.852	0.61
50_L	54_S	0.850	0.61
63_E	68_I	0.836	0.59
14_D	29_P	0.833	0.59
16_I	32_E	0.832	0.59
20_I	67_N	0.830	0.59
26_L	55_N	0.822	0.58
28_E	49_L	0.810	0.57
4_L	12_V	0.800	0.56
35_K	69_S	0.782	0.54
57_G	61_L	0.777	0.54
2_A	34_L	0.777	0.54
24_D	47_Y	0.776	0.54
5_A	8_N	0.774	0.53
18_N	24_D	0.766	0.53
23_Y	65_G	0.760	0.52
6_H	37_L	0.756	0.52
31_V	56_P	0.756	0.52
47_Y	59_S	0.755	0.52
56_P	61_L	0.752	0.51
56_P	70_Q	0.749	0.51
46_T	57_G	0.738	0.50
70_Q	73_Q	0.732	0.49
25_N	74_S	0.726	0.49
3_K	15_V	0.720	0.48
70_Q	76_A	0.715	0.48
72_L	76_A	0.713	0.48
14_D	18_N	0.708	0.47
61_L	68_I	0.703	0.47
30_V	44_V	0.700	0.46
26_L	42_Y	0.698	0.46
15_V	19_Q	0.691	0.45
24_D	74_S	0.691	0.45
52_A	72_L	0.688	0.45
68_I	75_L	0.688	0.45
27_I	41_G	0.683	0.45
9_P	36_Y	0.681	0.45
31_V	74_S	0.675	0.44
51_E	74_S	0.672	0.44
35_K	64_D	0.671	0.44
14_D	50_L	0.661	0.43
21_E	32_E	0.659	0.42
14_D	73_Q	0.632	0.40
22_S	25_N	0.618	0.39
27_I	40_L	0.611	0.38
17_L	46_T	0.610	0.38
11_I	44_V	0.609	0.38
34_L	37_L	0.608	0.38
61_L	66_T	0.607	0.38
59_S	70_Q	0.598	0.37
68_I	74_S	0.593	0.36
33_A	49_L	0.589	0.36
69_S	75_L	0.589	0.36
13_F	39_P	0.585	0.36
2_A	5_A	0.583	0.36
51_E	54_S	0.583	0.36
14_D	26_L	0.583	0.36
25_N	33_A	0.577	0.35
10_L	44_V	0.569	0.34
63_E	66_T	0.566	0.34
11_I	31_V	0.563	0.34
59_S	76_A	0.552	0.33
19_Q	26_L	0.543	0.32
12_V	46_T	0.540	0.32
7_S	36_Y	0.533	0.31
20_I	39_P	0.532	0.31
44_V	49_L	0.529	0.31
41_G	62_K	0.511	0.30
8_N	61_L	0.510	0.29
67_N	74_S	0.508	0.29
4_L	39_P	0.500	0.29

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
3nftA	2	0.3816	24.9	0.885	Contact Map
2j0oA	1	0.3289	21.4	0.888	Contact Map
3ohwB	1	0.6447	15.6	0.895	Contact Map
3l6xA	1	0.8947	13.5	0.898	Contact Map
3osjA	1	0.6447	13.4	0.898	Contact Map
2ky4A	1	0.7895	8.2	0.907	Contact Map
3nphB	1	0.6447	7.3	0.909	Contact Map
3pruC	1	0.8026	6.9	0.91	Contact Map
4wisA	2	0.6974	6.8	0.911	Contact Map
3b40A	1	0.2632	6.1	0.913	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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