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OPENSEQ.org
MORNTD
Genes: A B A+B
Length: 74 80 150
Sequences: 100 77 66
Seq/Len: 1.35 0.96 0.44
MirrorTree (Pazo et al. 2001) 0.34
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.42
2 0.00 0.00 0.43
5 0.00 0.00 0.43
10 0.00 0.00 0.43
20 0.00 0.00 0.43
100 0.00 0.00 0.43
∞ 0.00 0.00 0.43
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
5_Y 28_I 1.53 0.54 0.00
63_D 24_L 1.52 0.54 0.00
41_D 30_F 1.38 0.43 0.00
7_Y 55_Q 1.38 0.43 0.00
18_C 5_T 1.31 0.39 0.00
54_V 11_Q 1.25 0.34 0.00
59_L 75_F 1.24 0.34 0.00
52_K 30_F 1.19 0.30 0.00
51_L 68_S 1.13 0.27 0.00
22_Y 59_Y 1.12 0.26 0.00
58_E 12_I 1.11 0.26 0.00
5_Y 25_N 1.11 0.26 0.00
59_L 17_N 1.10 0.25 0.00
47_D 64_T 1.10 0.25 0.00
70_N 34_F 1.10 0.25 0.00
17_K 19_K 1.09 0.24 0.00
49_E 54_D 1.05 0.23 0.00
25_A 35_G 1.04 0.22 0.00
29_G 37_K 1.04 0.22 0.00
72_K 30_F 1.01 0.21 0.00
58_E 17_N 1.01 0.20 0.00
21_Q 29_P 1.00 0.20 0.00
13_K 33_K 1.00 0.20 0.00
70_N 39_S 0.99 0.19 0.00
70_N 48_N 0.98 0.19 0.00
37_L 10_K 0.98 0.19 0.00
33_R 10_K 0.97 0.18 0.00
41_D 56_N 0.97 0.18 0.00
25_A 68_S 0.96 0.18 0.00
59_L 55_Q 0.96 0.18 0.00
72_K 40_K 0.96 0.18 0.00
29_G 42_T 0.95 0.18 0.00
5_Y 50_V 0.95 0.18 0.00
61_P 38_L 0.95 0.17 0.00
57_L 46_Y 0.95 0.17 0.00
20_T 16_R 0.94 0.17 0.00
26_I 39_S 0.93 0.17 0.00
22_Y 57_R 0.93 0.17 0.00
61_P 50_V 0.93 0.17 0.00
66_K 36_I 0.93 0.17 0.00
4_S 19_K 0.93 0.17 0.00
9_S 39_S 0.92 0.16 0.00
29_G 29_P 0.91 0.16 0.00
47_D 48_N 0.91 0.16 0.00
37_L 55_Q 0.90 0.16 0.00
46_K 43_L 0.90 0.16 0.00
4_S 58_I 0.90 0.15 0.00
8_S 23_I 0.90 0.15 0.00
35_V 47_V 0.90 0.15 0.00
20_T 41_S 0.88 0.15 0.00
54_V 5_T 0.88 0.15 0.00
66_K 12_I 0.87 0.14 0.00
18_C 48_N 0.87 0.14 0.00
65_P 68_S 0.86 0.14 0.00
35_V 15_E 0.85 0.14 0.00
26_I 56_N 0.84 0.14 0.00
63_D 47_V 0.83 0.13 0.00
43_V 51_Q 0.83 0.13 0.00
34_T 73_M 0.83 0.13 0.00
33_R 70_A 0.83 0.13 0.00
65_P 17_N 0.82 0.13 0.00
9_S 48_N 0.82 0.13 0.00
23_N 11_Q 0.81 0.12 0.00
58_E 66_G 0.81 0.12 0.00
5_Y 55_Q 0.81 0.12 0.00
27_A 69_E 0.81 0.12 0.00
50_I 38_L 0.81 0.12 0.00
18_C 17_N 0.81 0.12 0.00
70_N 73_M 0.81 0.12 0.00
4_S 62_A 0.80 0.12 0.00
45_W 43_L 0.80 0.12 0.00
22_Y 39_S 0.80 0.12 0.00
28_M 56_N 0.79 0.12 0.00
42_K 33_K 0.79 0.12 0.00
20_T 21_V 0.78 0.11 0.00
53_A 23_I 0.78 0.11 0.00
27_A 77_V 0.78 0.11 0.00
64_I 22_D 0.78 0.11 0.00
52_K 4_D 0.77 0.11 0.00
71_A 42_T 0.77 0.11 0.00
59_L 28_I 0.77 0.11 0.00
53_A 13_M 0.77 0.11 0.00
51_L 25_N 0.77 0.11 0.00
63_D 14_A 0.77 0.11 0.00
20_T 38_L 0.76 0.11 0.00
44_T 75_F 0.76 0.11 0.00
14_I 72_L 0.76 0.11 0.00
62_Q 36_I 0.76 0.11 0.00
63_D 73_M 0.75 0.11 0.00
13_K 51_Q 0.75 0.11 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
10711 0.44 MORNTD Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9376 0.87 MORNTD Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.47 Done - Shared
9348 0.43 MORNTD Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9347 0.83 MORNTD Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.11 Done - Shared
9346 0.24 MORNTD Δgene:(1, 1) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
9345 1.05 MORNTD Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9343 0.42 MORNTD Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.59 Done - Shared
9338 0.91 MORNTD Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.07 Done - Shared
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