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OPENSEQ.org
CcdA_CcdB
Genes: A B A+B
Length: 72 101 170
Sequences: 261 278 214
Seq/Len: 3.62 2.75 1.26
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 1.24
2 0.00 0.00 1.24
5 0.01 0.00 1.24
10 0.01 0.00 1.24
20 0.01 0.01 1.24
100 0.02 0.01 1.24
∞ 0.03 0.03 1.24
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 2.27 0.99 0.96
69_N 72_P 2.09 0.98 0.94
45_K 26_D 1.38 0.75 0.53
55_V 67_D 1.35 0.72 0.50
55_V 66_T 1.27 0.65 0.41
31_T 2_Q 1.26 0.65 0.41
40_R 25_I 1.24 0.63 0.39
65_F 2_Q 1.20 0.59 0.35
25_S 52_P 1.20 0.59 0.34
67_D 2_Q 1.17 0.56 0.32
24_I 99_W 1.16 0.55 0.31
26_G 98_F 1.15 0.54 0.30
55_V 29_G 1.12 0.51 0.27
11_S 81_A 1.10 0.49 0.25
58_F 61_W 1.08 0.48 0.24
53_A 57_G 1.05 0.45 0.21
30_T 94_I 1.03 0.43 0.20
21_D 68_M 1.03 0.43 0.20
5_I 26_D 1.02 0.41 0.19
27_L 22_S 1.02 0.41 0.19
32_M 16_L 1.01 0.41 0.18
54_E 74_S 1.01 0.41 0.18
29_S 66_T 1.00 0.40 0.18
23_N 52_P 0.98 0.38 0.16
19_A 77_G 0.98 0.38 0.16
8_T 97_M 0.98 0.38 0.16
12_D 3_F 0.95 0.35 0.15
51_G 47_S 0.95 0.35 0.15
65_F 14_Y 0.95 0.35 0.15
65_F 70_S 0.94 0.34 0.14
24_I 87_E 0.94 0.34 0.14
26_G 82_D 0.94 0.34 0.14
12_D 89_D 0.92 0.33 0.13
52_M 45_K 0.92 0.33 0.13
32_M 11_E 0.92 0.32 0.13
68_E 39_A 0.92 0.32 0.12
15_Q 89_D 0.91 0.31 0.12
64_S 72_P 0.91 0.31 0.12
5_I 99_W 0.90 0.30 0.11
67_D 75_V 0.89 0.29 0.11
22_V 27_T 0.88 0.29 0.11
26_G 45_K 0.88 0.29 0.11
13_S 30_R 0.88 0.29 0.10
60_E 59_E 0.88 0.29 0.10
11_S 16_L 0.87 0.28 0.10
15_Q 78_E 0.86 0.27 0.10
28_V 2_Q 0.86 0.27 0.10
67_D 17_F 0.85 0.27 0.09
21_D 66_T 0.85 0.27 0.09
32_M 64_M 0.85 0.26 0.09
43_R 20_V 0.85 0.26 0.09
38_R 82_D 0.84 0.26 0.09
59_I 66_T 0.84 0.26 0.09
53_A 5_V 0.84 0.26 0.09
68_E 11_E 0.83 0.25 0.09
66_A 70_S 0.83 0.25 0.09
8_T 83_L 0.83 0.25 0.09
2_K 2_Q 0.83 0.25 0.08
8_T 91_K 0.83 0.25 0.08
7_V 77_G 0.83 0.25 0.08
12_D 39_A 0.82 0.24 0.08
2_K 62_R 0.82 0.24 0.08
64_S 97_M 0.82 0.24 0.08
10_D 49_E 0.81 0.24 0.08
56_A 29_G 0.81 0.24 0.08
55_V 15_R 0.81 0.24 0.08
41_A 96_L 0.81 0.24 0.08
24_I 44_D 0.81 0.24 0.08
47_E 68_M 0.81 0.23 0.07
13_S 28_P 0.81 0.23 0.07
59_I 83_L 0.81 0.23 0.07
11_S 3_F 0.80 0.23 0.07
16_L 77_G 0.80 0.23 0.07
4_R 74_S 0.80 0.23 0.07
65_F 8_Y 0.80 0.23 0.07
26_G 14_Y 0.80 0.23 0.07
14_Y 62_R 0.80 0.23 0.07
56_A 28_P 0.79 0.22 0.07
24_I 98_F 0.79 0.22 0.07
17_L 97_M 0.79 0.22 0.07
61_M 10_R 0.79 0.22 0.07
50_E 75_V 0.79 0.22 0.07
55_V 87_E 0.79 0.22 0.07
47_E 54_V 0.78 0.22 0.07
46_A 4_K 0.78 0.22 0.07
19_A 32_M 0.78 0.21 0.07
6_T 79_E 0.78 0.21 0.07
11_S 32_M 0.78 0.21 0.06
38_R 55_H 0.77 0.21 0.06
69_N 31_R 0.77 0.21 0.06
42_E 61_W 0.77 0.21 0.06
35_E 20_V 0.76 0.20 0.06
15_Q 84_S 0.76 0.20 0.06
10_D 24_I 0.76 0.20 0.06
19_A 3_F 0.76 0.20 0.06
40_R 56_I 0.76 0.20 0.06
36_A 29_G 0.76 0.20 0.06
13_S 95_N 0.76 0.20 0.06
6_T 3_F 0.76 0.20 0.06
16_L 25_I 0.76 0.20 0.06
30_T 43_S 0.75 0.20 0.06
13_S 37_A 0.75 0.20 0.06
58_F 67_D 0.75 0.20 0.06
40_R 20_V 0.75 0.20 0.06
40_R 63_M 0.75 0.20 0.06
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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