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OPENSEQ.org
ccmDE
Genes: A B A+B
Length: 69 159 198
Sequences: 433 933 351
Seq/Len: 6.28 5.87 1.77
MirrorTree (Pazo et al. 2001) 0.71
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.11 1.52
2 0.00 0.11 1.53
5 0.00 0.11 1.54
10 0.00 0.11 1.54
20 0.01 0.11 1.54
100 0.01 0.11 1.54
∞ 0.01 0.12 1.55
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
53_Q 43_I 1.69 0.95 0.71
15_G 104_R 1.40 0.84 0.47
17_Y 62_V 1.34 0.80 0.41
17_Y 60_L 1.32 0.79 0.40
17_Y 4_R 1.29 0.77 0.37
24_A 22_T 1.27 0.75 0.35
51_A 27_L 1.25 0.73 0.33
27_M 125_E 1.24 0.73 0.33
5_F 28_Y 1.21 0.70 0.30
25_V 135_T 1.21 0.70 0.30
40_V 8_R 1.20 0.69 0.29
10_E 17_A 1.14 0.64 0.25
5_F 60_L 1.14 0.63 0.24
6_A 12_A 1.12 0.61 0.23
35_L 28_Y 1.09 0.58 0.21
5_F 35_D 1.07 0.56 0.19
35_L 60_L 1.05 0.54 0.18
37_V 12_A 1.05 0.54 0.18
20_F 70_S 1.02 0.51 0.17
11_F 69_G 1.02 0.50 0.16
26_V 19_L 1.01 0.50 0.16
26_V 109_V 1.01 0.50 0.16
28_T 12_A 1.00 0.49 0.15
39_S 74_D 0.99 0.47 0.14
44_R 9_L 0.98 0.47 0.14
19_F 34_I 0.97 0.46 0.14
25_V 60_L 0.97 0.45 0.13
5_F 36_L 0.94 0.42 0.12
50_V 49_E 0.93 0.41 0.12
43_H 41_G 0.92 0.40 0.11
48_R 20_A 0.91 0.39 0.11
46_I 70_S 0.91 0.39 0.11
52_Q 88_E 0.90 0.39 0.10
32_L 90_S 0.90 0.38 0.10
27_M 45_Y 0.89 0.37 0.10
30_I 62_V 0.89 0.37 0.10
54_R 34_I 0.88 0.36 0.09
59_R 4_R 0.86 0.34 0.09
16_G 93_V 0.85 0.33 0.08
39_S 4_R 0.84 0.32 0.08
34_V 125_E 0.84 0.32 0.08
23_L 87_A 0.83 0.32 0.08
3_P 42_E 0.83 0.31 0.07
52_Q 13_C 0.83 0.31 0.07
17_Y 87_A 0.83 0.31 0.07
18_A 72_Q 0.82 0.31 0.07
44_R 45_Y 0.82 0.30 0.07
24_A 21_L 0.82 0.30 0.07
3_P 108_G 0.82 0.30 0.07
34_V 17_A 0.81 0.30 0.07
28_T 118_G 0.81 0.30 0.07
56_R 30_L 0.81 0.29 0.07
11_F 88_E 0.81 0.29 0.07
41_M 68_P 0.80 0.29 0.07
37_V 11_I 0.79 0.28 0.06
48_R 109_V 0.79 0.28 0.06
25_V 133_N 0.79 0.28 0.06
11_F 138_E 0.78 0.27 0.06
46_I 79_K 0.78 0.27 0.06
18_A 117_K 0.78 0.27 0.06
56_R 3_I 0.77 0.26 0.06
27_M 34_I 0.77 0.26 0.06
24_A 121_I 0.77 0.26 0.06
5_F 78_L 0.77 0.26 0.06
5_F 3_I 0.77 0.26 0.06
26_V 11_I 0.77 0.26 0.06
4_A 135_T 0.76 0.26 0.06
25_V 81_T 0.76 0.25 0.06
32_L 29_A 0.76 0.25 0.06
13_A 43_I 0.76 0.25 0.06
29_V 124_K 0.76 0.25 0.05
17_Y 39_T 0.75 0.24 0.05
49_G 13_C 0.75 0.24 0.05
12_F 42_E 0.75 0.24 0.05
34_V 16_L 0.75 0.24 0.05
56_R 5_R 0.75 0.24 0.05
36_V 111_V 0.74 0.24 0.05
46_I 111_V 0.74 0.24 0.05
58_A 20_A 0.73 0.23 0.05
50_V 39_T 0.73 0.23 0.05
56_R 78_L 0.73 0.23 0.05
23_L 93_V 0.72 0.22 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
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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