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OPENSEQ.org
3G7Z
Genes: A B A+B
Length: 72 101 170
Sequences: 319 293 251
Seq/Len: 4.43 2.9 1.48
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 1.45
2 0.00 0.00 1.45
5 0.00 0.00 1.45
10 0.01 0.00 1.45
20 0.01 0.01 1.45
100 0.02 0.02 1.43
∞ 0.04 0.03 1.43
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
64_S 70_S 1.89 0.97 0.85
69_N 72_P 1.87 0.96 0.84
56_A 29_G 1.45 0.83 0.55
55_V 66_T 1.38 0.79 0.47
45_K 26_D 1.38 0.79 0.47
12_D 3_F 1.28 0.71 0.38
24_I 99_W 1.23 0.67 0.33
65_F 2_Q 1.22 0.65 0.32
21_D 66_T 1.19 0.63 0.30
67_D 2_Q 1.16 0.60 0.27
55_V 67_D 1.15 0.59 0.27
6_T 79_E 1.14 0.58 0.25
19_A 77_G 1.12 0.56 0.24
55_V 29_G 1.07 0.51 0.20
55_V 87_E 1.06 0.50 0.20
32_M 16_L 1.05 0.49 0.19
11_S 81_A 1.05 0.49 0.19
11_S 3_F 1.04 0.48 0.18
36_A 29_G 1.04 0.47 0.18
65_F 14_Y 1.02 0.46 0.17
8_T 83_L 1.02 0.46 0.17
40_R 25_I 1.02 0.46 0.17
43_R 20_V 1.02 0.46 0.17
30_T 94_I 1.01 0.45 0.17
9_V 16_L 1.01 0.45 0.16
58_F 61_W 1.00 0.44 0.16
67_D 8_Y 0.99 0.43 0.15
56_A 28_P 0.99 0.43 0.15
51_G 47_S 0.98 0.42 0.14
39_L 3_F 0.95 0.39 0.13
14_Y 62_R 0.95 0.38 0.13
38_R 55_H 0.94 0.38 0.12
66_A 70_S 0.92 0.36 0.11
26_G 98_F 0.92 0.36 0.11
25_S 52_P 0.92 0.36 0.11
31_T 100_G 0.92 0.35 0.11
60_E 59_E 0.91 0.35 0.11
53_A 5_V 0.91 0.35 0.11
65_F 8_Y 0.90 0.34 0.10
27_L 22_S 0.90 0.34 0.10
11_S 16_L 0.89 0.33 0.10
69_N 71_V 0.89 0.33 0.10
69_N 70_S 0.88 0.32 0.09
54_E 13_R 0.88 0.32 0.09
18_K 32_M 0.88 0.32 0.09
65_F 70_S 0.87 0.32 0.09
34_N 94_I 0.86 0.30 0.09
18_K 16_L 0.85 0.30 0.08
19_A 3_F 0.85 0.29 0.08
47_E 68_M 0.85 0.29 0.08
47_E 38_S 0.84 0.29 0.08
18_K 89_D 0.84 0.29 0.08
68_E 39_A 0.84 0.29 0.08
15_Q 58_D 0.84 0.29 0.08
29_S 66_T 0.84 0.28 0.08
71_D 70_S 0.83 0.28 0.08
9_V 98_F 0.83 0.28 0.08
44_W 100_G 0.83 0.28 0.08
53_A 57_G 0.83 0.28 0.08
31_T 2_Q 0.82 0.27 0.07
26_G 14_Y 0.82 0.27 0.07
35_E 34_I 0.82 0.27 0.07
21_D 68_M 0.82 0.27 0.07
43_R 13_R 0.81 0.27 0.07
23_N 52_P 0.81 0.27 0.07
28_V 2_Q 0.81 0.27 0.07
2_K 16_L 0.81 0.26 0.07
14_Y 47_S 0.81 0.26 0.07
5_I 99_W 0.81 0.26 0.07
32_M 95_N 0.81 0.26 0.07
32_M 15_R 0.81 0.26 0.07
28_V 64_M 0.81 0.26 0.07
66_A 2_Q 0.80 0.26 0.07
40_R 92_N 0.80 0.25 0.07
14_Y 8_Y 0.80 0.25 0.07
29_S 10_R 0.80 0.25 0.07
13_S 99_W 0.79 0.24 0.06
26_G 4_K 0.78 0.24 0.06
54_E 74_S 0.78 0.24 0.06
46_A 57_G 0.77 0.23 0.06
25_S 6_Y 0.77 0.23 0.06
18_K 49_E 0.77 0.23 0.06
56_A 15_R 0.77 0.23 0.06
44_W 25_I 0.77 0.23 0.06
5_I 26_D 0.77 0.23 0.06
22_V 27_T 0.77 0.23 0.06
35_E 20_V 0.76 0.23 0.06
22_V 100_G 0.76 0.23 0.06
59_I 66_T 0.76 0.23 0.06
51_G 46_V 0.76 0.23 0.06
6_T 21_Q 0.76 0.22 0.05
37_R 100_G 0.75 0.22 0.05
8_T 97_M 0.75 0.22 0.05
58_F 46_V 0.75 0.22 0.05
59_I 67_D 0.75 0.22 0.05
29_S 95_N 0.75 0.22 0.05
65_F 67_D 0.75 0.22 0.05
28_V 30_R 0.74 0.21 0.05
47_E 48_R 0.74 0.21 0.05
66_A 69_A 0.74 0.21 0.05
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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