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OPENSEQ.org
CCMD_CCME
Genes: A B A+B
Length: 69 159 219
Sequences: 360 664 275
Seq/Len: 5.22 4.18 1.26
MirrorTree (Pazo et al. 2001) 0.76
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 1.22
2 0.00 0.00 1.21
5 0.00 0.00 1.21
10 0.00 0.00 1.21
20 0.00 0.00 1.21
100 0.00 0.00 1.21
∞ 0.00 0.01 1.29
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
15_G 104_R 1.70 0.91 0.41
31_P 143_M 1.59 0.87 0.33
53_Q 43_I 1.50 0.82 0.26
24_A 22_T 1.47 0.80 0.24
35_L 60_L 1.41 0.76 0.21
25_V 135_T 1.37 0.74 0.19
5_F 28_Y 1.35 0.72 0.18
26_V 109_V 1.31 0.69 0.16
5_F 35_D 1.29 0.67 0.15
20_F 18_G 1.27 0.66 0.14
5_F 60_L 1.26 0.64 0.14
24_A 30_L 1.26 0.64 0.13
27_M 125_E 1.22 0.61 0.12
56_R 104_R 1.22 0.61 0.12
39_S 74_D 1.21 0.59 0.11
5_F 36_L 1.20 0.59 0.11
35_L 139_V 1.20 0.58 0.11
12_F 141_K 1.19 0.58 0.11
28_T 39_T 1.17 0.56 0.10
17_Y 60_L 1.15 0.54 0.09
48_R 109_V 1.11 0.50 0.08
52_Q 144_E 1.11 0.50 0.08
56_R 78_L 1.10 0.49 0.08
5_F 78_L 1.10 0.49 0.08
26_V 19_L 1.10 0.49 0.08
17_Y 62_V 1.10 0.49 0.08
5_F 139_V 1.08 0.47 0.07
5_F 30_L 1.08 0.47 0.07
15_G 39_T 1.07 0.46 0.07
20_F 21_L 1.07 0.46 0.07
10_E 12_A 1.06 0.46 0.07
59_R 4_R 1.05 0.44 0.07
37_V 120_H 1.04 0.44 0.06
25_V 81_T 1.04 0.44 0.06
54_R 42_E 1.04 0.43 0.06
55_A 146_N 1.03 0.42 0.06
23_L 87_A 1.00 0.39 0.05
53_Q 142_A 0.99 0.39 0.05
66_Q 50_T 0.98 0.37 0.05
54_R 77_S 0.97 0.37 0.05
37_V 21_L 0.96 0.35 0.05
65_Q 50_T 0.95 0.35 0.04
44_R 92_D 0.95 0.35 0.04
17_Y 4_R 0.95 0.34 0.04
8_W 65_M 0.94 0.34 0.04
24_A 21_L 0.93 0.34 0.04
33_V 11_I 0.93 0.33 0.04
58_A 41_G 0.92 0.33 0.04
59_R 27_L 0.92 0.32 0.04
63_A 121_I 0.92 0.32 0.04
28_T 90_S 0.92 0.32 0.04
63_A 124_K 0.92 0.32 0.04
66_Q 49_E 0.90 0.31 0.04
11_F 138_E 0.90 0.30 0.04
41_M 23_I 0.90 0.30 0.04
30_I 62_V 0.89 0.30 0.04
23_L 93_V 0.89 0.29 0.03
52_Q 13_C 0.89 0.29 0.03
51_A 109_V 0.88 0.29 0.03
51_A 27_L 0.87 0.28 0.03
44_R 45_Y 0.86 0.28 0.03
16_G 4_R 0.86 0.27 0.03
3_P 135_T 0.86 0.27 0.03
15_G 18_G 0.86 0.27 0.03
57_E 36_L 0.85 0.27 0.03
48_R 26_V 0.85 0.26 0.03
18_A 32_S 0.83 0.25 0.03
49_G 18_G 0.83 0.25 0.03
28_T 137_P 0.83 0.25 0.03
11_F 107_Q 0.83 0.25 0.03
54_R 93_V 0.83 0.25 0.03
46_I 96_E 0.82 0.25 0.03
60_L 133_N 0.82 0.25 0.03
47_L 46_G 0.82 0.24 0.03
9_N 23_I 0.82 0.24 0.03
36_V 70_S 0.82 0.24 0.03
27_M 20_A 0.82 0.24 0.03
15_G 2_N 0.82 0.24 0.03
47_L 5_R 0.81 0.24 0.03
2_T 139_V 0.81 0.23 0.03
59_R 57_G 0.81 0.23 0.03
28_T 12_A 0.81 0.23 0.02
66_Q 52_Q 0.80 0.23 0.02
62_A 15_V 0.80 0.23 0.02
17_Y 55_E 0.80 0.23 0.02
33_V 15_V 0.80 0.23 0.02
56_R 6_K 0.79 0.22 0.02
23_L 107_Q 0.79 0.22 0.02
40_V 116_E 0.79 0.22 0.02
37_V 12_A 0.79 0.22 0.02
39_S 87_A 0.79 0.22 0.02
31_P 7_N 0.79 0.22 0.02
63_A 23_I 0.78 0.22 0.02
34_V 51_Q 0.78 0.21 0.02
17_Y 39_T 0.77 0.21 0.02
29_V 75_P 0.77 0.21 0.02
8_W 135_T 0.77 0.21 0.02
9_N 151_A 0.77 0.21 0.02
64_Q 48_R 0.77 0.21 0.02
3_P 48_R 0.77 0.21 0.02
11_F 126_V 0.77 0.20 0.02
60_L 121_I 0.76 0.20 0.02
57_E 142_A 0.76 0.20 0.02
24_A 106_G 0.76 0.20 0.02
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
8060 1.77 ccmDE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.71 Done - Shared
7038 4.03 CCMD_CCME Δgene:(1, 1) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.64 Done
1096 1.26 CCMD_CCME Δgene:(1, 5) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.41 Done
1095 0.4 CCMD_CCME Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed
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