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OPENSEQ.org
3G7Z_Jackhmmer
Genes: A B A+B
Length: 72 101 170
Sequences: 223 199 165
Seq/Len: 3.1 1.97 0.97
MirrorTree (Pazo et al. 2001) 0.68
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 0.95
2 0.00 0.00 0.95
5 0.00 0.00 0.95
10 0.00 0.00 0.95
20 0.00 0.00 0.95
100 0.00 0.00 0.95
∞ 0.01 0.01 0.95
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
69_N 72_P 2.35 0.99 0.95
64_S 70_S 1.81 0.91 0.78
65_F 2_Q 1.54 0.79 0.57
67_D 2_Q 1.54 0.79 0.57
26_G 98_F 1.42 0.70 0.45
9_V 42_L 1.37 0.66 0.41
21_D 68_M 1.37 0.66 0.40
24_I 99_W 1.35 0.65 0.39
2_K 34_I 1.29 0.59 0.32
8_T 83_L 1.28 0.59 0.32
12_D 3_F 1.27 0.58 0.31
9_V 16_L 1.25 0.56 0.29
56_A 28_P 1.24 0.54 0.28
31_T 100_G 1.15 0.46 0.21
58_F 46_V 1.13 0.45 0.20
9_V 98_F 1.12 0.44 0.19
55_V 66_T 1.11 0.43 0.18
32_M 15_R 1.10 0.42 0.18
34_N 94_I 1.08 0.40 0.16
11_S 16_L 1.08 0.40 0.16
21_D 26_D 1.08 0.40 0.16
59_I 66_T 1.07 0.40 0.16
56_A 15_R 1.05 0.37 0.14
66_A 2_Q 1.04 0.36 0.14
55_V 29_G 1.03 0.36 0.14
40_R 25_I 1.02 0.35 0.13
51_G 46_V 1.02 0.35 0.13
40_R 56_I 1.01 0.34 0.12
43_R 94_I 1.00 0.34 0.12
14_Y 62_R 1.00 0.34 0.12
6_T 79_E 1.00 0.34 0.12
13_S 30_R 1.00 0.34 0.12
65_F 70_S 0.99 0.33 0.12
48_N 19_D 0.99 0.32 0.11
31_T 4_K 0.98 0.32 0.11
12_D 18_V 0.97 0.31 0.10
44_W 19_D 0.97 0.31 0.10
70_R 19_D 0.96 0.30 0.10
2_K 5_V 0.96 0.30 0.10
3_Q 26_D 0.95 0.30 0.10
22_V 100_G 0.95 0.30 0.10
22_V 28_P 0.95 0.30 0.10
50_E 89_D 0.95 0.29 0.10
6_T 21_Q 0.94 0.28 0.09
22_V 16_L 0.94 0.28 0.09
3_Q 28_P 0.94 0.28 0.09
32_M 16_L 0.93 0.28 0.09
18_K 16_L 0.92 0.27 0.08
22_V 98_F 0.91 0.27 0.08
56_A 29_G 0.91 0.26 0.08
58_F 61_W 0.91 0.26 0.08
55_V 87_E 0.91 0.26 0.08
44_W 25_I 0.91 0.26 0.08
52_M 76_I 0.91 0.26 0.08
26_G 82_D 0.90 0.26 0.08
45_K 60_S 0.89 0.25 0.07
26_G 68_M 0.89 0.25 0.07
22_V 96_L 0.89 0.25 0.07
31_T 2_Q 0.89 0.25 0.07
64_S 97_M 0.89 0.25 0.07
57_R 18_V 0.89 0.25 0.07
51_G 19_D 0.89 0.25 0.07
69_N 71_V 0.88 0.25 0.07
6_T 72_P 0.88 0.24 0.07
37_R 96_L 0.87 0.24 0.07
19_A 77_G 0.87 0.24 0.07
67_D 8_Y 0.87 0.23 0.07
23_N 65_T 0.86 0.23 0.06
29_S 10_R 0.85 0.22 0.06
7_V 77_G 0.85 0.22 0.06
2_K 62_R 0.85 0.22 0.06
53_A 56_I 0.84 0.22 0.06
52_M 96_L 0.84 0.21 0.06
23_N 6_Y 0.83 0.21 0.06
44_W 100_G 0.83 0.21 0.06
47_E 68_M 0.83 0.21 0.06
11_S 3_F 0.82 0.21 0.05
65_F 14_Y 0.82 0.21 0.05
36_A 76_I 0.82 0.20 0.05
18_K 89_D 0.82 0.20 0.05
55_V 67_D 0.82 0.20 0.05
53_A 27_T 0.82 0.20 0.05
34_N 48_R 0.82 0.20 0.05
66_A 33_V 0.81 0.20 0.05
50_E 91_K 0.81 0.20 0.05
31_T 14_Y 0.81 0.20 0.05
18_K 86_R 0.81 0.20 0.05
67_D 75_V 0.80 0.20 0.05
45_K 26_D 0.80 0.20 0.05
40_R 34_I 0.80 0.19 0.05
24_I 2_Q 0.80 0.19 0.05
29_S 54_V 0.80 0.19 0.05
69_N 70_S 0.80 0.19 0.05
13_S 49_E 0.80 0.19 0.05
29_S 66_T 0.79 0.19 0.04
6_T 47_S 0.79 0.19 0.04
66_A 69_A 0.79 0.19 0.04
59_I 83_L 0.79 0.19 0.04
47_E 5_V 0.79 0.19 0.04
29_S 25_I 0.79 0.18 0.04
36_A 97_M 0.79 0.18 0.04
25_S 52_P 0.78 0.18 0.04
30_T 94_I 0.78 0.18 0.04
71_D 70_S 0.78 0.18 0.04
62_N 86_R 0.78 0.18 0.04
66_A 70_S 0.77 0.18 0.04
38_R 57_G 0.77 0.18 0.04
38_R 82_D 0.77 0.17 0.04
24_I 67_D 0.77 0.17 0.04
15_Q 79_E 0.77 0.17 0.04
30_T 39_A 0.76 0.17 0.04
51_G 66_T 0.76 0.17 0.04
35_E 20_V 0.76 0.17 0.04
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
4822 1.48 3G7Z Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
2742 1.26 CcdA_CcdB Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.96 Done
0729 0.97 3G7Z_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.95 Done
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