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OPENSEQ.org
MORNDT2
Genes: A B A+B
Length: 74 89 142
Sequences: 33541 11229 82
Seq/Len: 453.26 126.17 0.58
MirrorTree (Pazo et al. 2001) 0.47
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.08 0.02 0.24
2 0.09 0.02 0.33
5 0.11 0.04 0.39
10 0.13 0.05 0.43
20 0.16 0.07 0.50
100 0.23 0.12 0.79
∞ 0.28 0.20 0.96
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
59_V 9_L 1.66 0.72 0.01
34_S 5_V 1.54 0.64 0.01
8_L 26_K 1.39 0.52 0.00
26_M 65_L 1.33 0.47 0.00
33_L 62_S 1.32 0.46 0.00
58_P 9_L 1.26 0.41 0.00
33_L 48_N 1.22 0.39 0.00
12_I 44_S 1.20 0.37 0.00
23_A 62_S 1.17 0.35 0.00
55_L 49_D 1.16 0.34 0.00
59_V 14_K 1.16 0.34 0.00
58_P 71_W 1.14 0.33 0.00
47_E 10_K 1.12 0.32 0.00
25_A 68_G 1.08 0.29 0.00
18_T 19_K 1.07 0.28 0.00
39_G 17_N 1.06 0.28 0.00
51_A 61_L 1.06 0.28 0.00
28_L 61_L 1.05 0.27 0.00
14_E 15_I 1.03 0.26 0.00
32_S 19_K 1.01 0.24 0.00
29_S 39_S 0.98 0.23 0.00
37_L 44_S 0.98 0.23 0.00
52_I 19_K 0.97 0.22 0.00
38_N 72_L 0.97 0.22 0.00
19_Q 67_V 0.96 0.22 0.00
26_M 43_L 0.96 0.21 0.00
48_I 43_L 0.95 0.21 0.00
25_A 77_V 0.95 0.21 0.00
21_N 17_N 0.95 0.21 0.00
47_E 39_S 0.93 0.20 0.00
55_L 8_R 0.93 0.20 0.00
68_K 47_I 0.93 0.20 0.00
42_G 24_I 0.92 0.20 0.00
18_T 56_D 0.92 0.20 0.00
25_A 65_L 0.92 0.19 0.00
21_N 20_Q 0.91 0.19 0.00
65_Y 65_L 0.91 0.19 0.00
23_A 82_V 0.89 0.18 0.00
50_K 9_L 0.89 0.18 0.00
45_D 48_N 0.89 0.18 0.00
39_G 80_Y 0.89 0.18 0.00
20_Y 6_S 0.88 0.17 0.00
24_I 22_D 0.88 0.17 0.00
41_V 18_L 0.88 0.17 0.00
37_L 77_V 0.88 0.17 0.00
38_N 76_D 0.88 0.17 0.00
48_I 67_V 0.87 0.17 0.00
34_S 40_K 0.86 0.17 0.00
70_K 13_M 0.86 0.17 0.00
33_L 82_V 0.86 0.17 0.00
16_Y 62_S 0.85 0.16 0.00
11_K 72_L 0.85 0.16 0.00
8_L 81_R 0.84 0.16 0.00
33_L 74_G 0.84 0.16 0.00
66_F 67_V 0.84 0.16 0.00
31_R 61_L 0.84 0.16 0.00
36_K 67_V 0.84 0.15 0.00
18_T 46_Y 0.83 0.15 0.00
61_K 12_I 0.83 0.15 0.00
50_K 63_K 0.83 0.15 0.00
64_L 27_S 0.83 0.15 0.00
42_G 25_N 0.83 0.15 0.00
8_L 9_L 0.82 0.15 0.00
33_L 18_L 0.82 0.15 0.00
47_E 69_E 0.82 0.15 0.00
43_W 27_S 0.81 0.14 0.00
49_W 19_K 0.81 0.14 0.00
24_I 14_K 0.81 0.14 0.00
12_I 23_I 0.81 0.14 0.00
43_W 64_T 0.80 0.14 0.00
18_T 59_Y 0.79 0.14 0.00
19_Q 21_V 0.79 0.14 0.00
18_T 52_S 0.79 0.14 0.00
50_K 38_L 0.79 0.14 0.00
5_Y 73_M 0.78 0.13 0.00
40_K 45_Q 0.78 0.13 0.00
40_K 64_T 0.78 0.13 0.00
53_Q 11_H 0.78 0.13 0.00
22_F 47_I 0.77 0.13 0.00
56_D 52_S 0.77 0.13 0.00
11_K 65_L 0.77 0.13 0.00
8_L 61_L 0.76 0.13 0.00
41_V 19_K 0.76 0.13 0.00
50_K 74_G 0.76 0.13 0.00
14_E 8_R 0.76 0.12 0.00
30_E 26_K 0.75 0.12 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
9344 0.58 MORNDT2 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.01 Done - Shared
9341 0.66 MORNDT2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done - Shared
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