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OPENSEQ.org
CCMD_CCME
Genes: A B A+B
Length: 69 159 213
Sequences: 1202 2773 858
Seq/Len: 17.42 17.44 4.03
MirrorTree (Pazo et al. 2001) 0.78
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 3.76
2 0.00 0.00 3.76
5 0.00 0.00 3.81
10 0.00 0.00 3.81
20 0.00 0.00 3.81
100 0.00 0.00 3.79
∞ 0.03 0.03 3.91
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
17_Y 62_V 1.39 0.96 0.64
56_R 104_R 1.31 0.94 0.57
53_Q 43_I 1.28 0.92 0.54
35_L 109_V 1.26 0.92 0.53
5_F 35_D 1.23 0.90 0.49
5_F 28_Y 1.19 0.88 0.46
37_V 120_H 1.12 0.84 0.39
18_A 111_V 1.09 0.82 0.36
15_G 104_R 1.09 0.82 0.36
40_V 96_E 1.08 0.81 0.35
52_Q 18_G 1.05 0.79 0.33
44_R 45_Y 1.05 0.79 0.33
36_V 91_V 0.95 0.68 0.24
35_L 28_Y 0.95 0.68 0.24
24_A 95_Y 0.95 0.68 0.24
28_T 39_T 0.91 0.63 0.21
39_S 14_A 0.91 0.63 0.21
37_V 56_V 0.90 0.62 0.20
25_V 135_T 0.89 0.60 0.19
5_F 107_Q 0.89 0.60 0.19
35_L 60_L 0.89 0.60 0.19
17_Y 60_L 0.88 0.59 0.19
10_E 125_E 0.88 0.58 0.18
45_A 13_C 0.86 0.57 0.17
39_S 108_G 0.86 0.57 0.17
42_Q 139_V 0.85 0.56 0.17
5_F 139_V 0.85 0.55 0.17
5_F 60_L 0.85 0.55 0.17
35_L 139_V 0.85 0.55 0.17
4_A 67_M 0.84 0.54 0.16
17_Y 4_R 0.84 0.54 0.16
5_F 78_L 0.84 0.53 0.16
50_V 49_E 0.82 0.51 0.15
5_F 36_L 0.82 0.51 0.14
44_R 109_V 0.81 0.50 0.14
39_S 20_A 0.80 0.49 0.14
37_V 93_V 0.80 0.48 0.14
39_S 87_A 0.80 0.48 0.13
18_A 51_Q 0.80 0.48 0.13
16_G 140_E 0.79 0.47 0.13
31_P 143_M 0.79 0.47 0.13
24_A 22_T 0.78 0.46 0.13
40_V 89_G 0.77 0.45 0.12
27_M 45_Y 0.77 0.44 0.12
24_A 140_E 0.77 0.44 0.12
29_V 6_K 0.76 0.43 0.12
5_F 30_L 0.75 0.42 0.11
30_I 92_D 0.75 0.41 0.11
58_A 133_N 0.74 0.41 0.11
4_A 77_S 0.74 0.41 0.11
13_A 43_I 0.74 0.41 0.10
27_M 62_V 0.74 0.40 0.10
35_L 18_G 0.73 0.40 0.10
21_V 111_V 0.73 0.39 0.10
55_A 20_A 0.73 0.39 0.10
15_G 112_Q 0.72 0.39 0.10
24_A 79_K 0.72 0.38 0.10
30_I 81_T 0.71 0.37 0.09
7_S 11_I 0.71 0.37 0.09
30_I 90_S 0.71 0.37 0.09
30_I 119_N 0.71 0.36 0.09
42_Q 45_Y 0.71 0.36 0.09
56_R 71_V 0.70 0.36 0.09
20_F 136_P 0.70 0.36 0.09
25_V 85_Y 0.70 0.36 0.09
46_I 8_R 0.70 0.36 0.09
12_F 122_L 0.70 0.36 0.09
48_R 109_V 0.70 0.35 0.09
61_R 85_Y 0.70 0.35 0.09
18_A 104_R 0.70 0.35 0.09
60_L 121_I 0.69 0.35 0.09
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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