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OPENSEQ.org
bolagrxd
Genes: A B A+B
Length: 105 115 210
Sequences: 1004 1516 383
Seq/Len: 9.56 13.18 1.82
MirrorTree (Pazo et al. 2001) 0.65
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 0.02
10 0.00 0.00 0.02
20 0.00 0.00 0.04
100 0.00 0.00 0.16
∞ 0.00 0.01 1.74
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 1.25 0.74 0.02
62_S 67_N 1.01 0.51 0.01
37_S 36_A 0.92 0.40 0.01
49_T 76_V 0.86 0.35 0.01
61_Y 37_V 0.85 0.34 0.01
71_T 45_E 0.85 0.34 0.01
30_N 17_I 0.84 0.33 0.01
32_P 45_E 0.83 0.32 0.01
62_S 25_P 0.82 0.31 0.01
49_T 65_Y 0.82 0.31 0.01
89_Q 81_V 0.81 0.30 0.01
94_A 40_L 0.81 0.30 0.01
22_V 44_G 0.81 0.30 0.01
53_F 37_V 0.80 0.29 0.01
53_F 65_Y 0.80 0.29 0.01
77_L 34_A 0.78 0.28 0.01
83_K 99_L 0.78 0.28 0.01
13_A 98_Q 0.78 0.27 0.01
52_R 60_A 0.77 0.26 0.01
28_R 41_A 0.77 0.26 0.01
34_G 36_A 0.77 0.26 0.01
11_L 91_Y 0.76 0.26 0.01
58_R 12_I 0.75 0.25 0.01
54_L 7_K 0.75 0.24 0.01
53_F 89_E 0.74 0.24 0.01
90_D 10_R 0.73 0.23 0.01
71_T 34_A 0.73 0.23 0.01
40_K 97_Q 0.72 0.23 0.01
35_S 51_D 0.72 0.23 0.01
37_S 109_S 0.72 0.23 0.00
10_K 18_L 0.71 0.22 0.00
36_E 43_C 0.71 0.22 0.00
59_M 39_A 0.71 0.22 0.00
57_H 42_A 0.71 0.22 0.00
50_G 44_G 0.71 0.21 0.00
14_A 89_E 0.70 0.21 0.00
78_H 47_F 0.70 0.21 0.00
32_P 46_R 0.70 0.21 0.00
70_T 92_Q 0.70 0.21 0.00
81_T 51_D 0.69 0.21 0.00
11_L 104_A 0.69 0.20 0.00
6_R 52_I 0.68 0.19 0.00
57_H 34_A 0.67 0.19 0.00
52_R 27_L 0.67 0.19 0.00
65_A 81_V 0.66 0.18 0.00
55_N 60_A 0.66 0.18 0.00
15_F 6_E 0.66 0.18 0.00
54_L 15_N 0.66 0.18 0.00
45_S 14_E 0.66 0.18 0.00
37_S 11_Q 0.66 0.18 0.00
39_F 71_F 0.66 0.18 0.00
69_S 92_Q 0.66 0.18 0.00
102_G 65_Y 0.66 0.18 0.00
14_A 102_E 0.66 0.18 0.00
60_I 40_L 0.66 0.18 0.00
80_Y 58_I 0.65 0.18 0.00
61_Y 25_P 0.65 0.17 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
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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