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OPENSEQ.org
bolagrxd
Genes: A B A+B
Length: 105 115 209
Sequences: 779 1200 325
Seq/Len: 7.42 10.43 1.56
MirrorTree (Pazo et al. 2001) 0.66
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 0.02
2 0.00 0.00 0.02
5 0.00 0.00 0.03
10 0.00 0.00 0.04
20 0.00 0.00 0.05
100 0.00 0.00 0.13
∞ 0.00 0.01 1.48
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
45_S 81_V 1.49 0.87 0.19
37_S 36_A 1.10 0.56 0.06
40_K 51_D 1.03 0.49 0.05
77_L 76_V 0.94 0.39 0.03
41_V 57_D 0.90 0.35 0.03
61_Y 37_V 0.90 0.35 0.03
49_T 76_V 0.88 0.34 0.03
54_L 15_N 0.88 0.33 0.03
52_R 60_A 0.87 0.33 0.03
9_E 56_P 0.86 0.31 0.02
22_V 44_G 0.86 0.31 0.02
72_V 100_I 0.86 0.31 0.02
49_T 65_Y 0.85 0.31 0.02
39_F 67_N 0.84 0.30 0.02
50_G 44_G 0.84 0.29 0.02
77_L 99_L 0.84 0.29 0.02
59_M 39_A 0.83 0.29 0.02
23_V 46_R 0.82 0.28 0.02
35_S 50_V 0.82 0.28 0.02
40_K 47_F 0.78 0.25 0.02
19_F 10_R 0.78 0.25 0.02
61_Y 100_I 0.78 0.25 0.02
13_A 58_I 0.78 0.25 0.02
77_L 84_C 0.78 0.24 0.02
62_S 25_P 0.78 0.24 0.02
101_A 103_T 0.77 0.24 0.02
28_R 41_A 0.77 0.24 0.02
53_F 89_E 0.76 0.23 0.02
50_G 20_Y 0.76 0.23 0.02
61_Y 67_N 0.75 0.23 0.01
61_Y 34_A 0.74 0.22 0.01
72_V 36_A 0.74 0.22 0.01
25_E 56_P 0.74 0.22 0.01
71_T 34_A 0.74 0.21 0.01
42_V 47_F 0.74 0.21 0.01
94_A 40_L 0.73 0.21 0.01
2_M 65_Y 0.72 0.21 0.01
37_S 11_Q 0.72 0.20 0.01
24_D 99_L 0.72 0.20 0.01
78_H 47_F 0.71 0.20 0.01
58_R 54_Q 0.71 0.20 0.01
5_E 98_Q 0.71 0.20 0.01
15_F 6_E 0.71 0.20 0.01
4_R 102_E 0.71 0.20 0.01
4_R 41_A 0.71 0.20 0.01
49_T 81_V 0.71 0.19 0.01
58_R 40_L 0.70 0.19 0.01
46_D 48_A 0.70 0.19 0.01
34_G 36_A 0.70 0.19 0.01
65_A 102_E 0.70 0.19 0.01
69_S 17_I 0.69 0.19 0.01
80_Y 63_P 0.69 0.18 0.01
39_F 71_F 0.69 0.18 0.01
16_Q 51_D 0.69 0.18 0.01
31_V 46_R 0.69 0.18 0.01
53_F 77_D 0.68 0.18 0.01
32_P 45_E 0.68 0.18 0.01
81_T 51_D 0.68 0.18 0.01
55_N 14_E 0.68 0.18 0.01
85_W 15_N 0.68 0.18 0.01
20_L 81_V 0.68 0.18 0.01
25_E 11_Q 0.68 0.18 0.01
22_V 24_S 0.68 0.18 0.01
10_K 91_Y 0.68 0.17 0.01
93_F 40_L 0.68 0.17 0.01
53_F 37_V 0.67 0.17 0.01
79_T 34_A 0.67 0.17 0.01
6_R 52_I 0.67 0.17 0.01
46_D 105_A 0.67 0.17 0.01
57_H 34_A 0.67 0.17 0.01
9_E 65_Y 0.67 0.17 0.01
27_Y 84_C 0.67 0.17 0.01
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
2050 2.83 bolagrxd Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.02 Done - Shared
2037 1.82 bolagrxd Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.02 Done - Shared
2036 0.11 bolagrx Δgene:(1, 5) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2015_03) Killed - Shared
1470 1.56 bolagrxd Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.19 Done - Shared
1469 0.03 bolagrxd Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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