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OPENSEQ.org
CCMC_CCMD
Genes: A B A+B
Length: 245 69 301
Sequences: 5196 1202 824
Seq/Len: 21.21 17.42 2.74
MirrorTree (Pazo et al. 2001) 0.43
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 2.44
2 0.02 0.00 2.62
5 0.50 0.00 2.63
10 0.51 0.00 2.63
20 0.51 0.00 2.63
100 0.51 0.00 2.63
∞ 0.53 0.03 2.65
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
102_V 31_P 2.86 1.00 1.00
52_N 17_Y 2.44 1.00 0.99
118_M 17_Y 2.23 1.00 0.99
113_A 23_L 1.98 0.99 0.98
59_L 28_T 1.89 0.99 0.97
109_V 27_M 1.84 0.99 0.97
113_A 27_M 1.79 0.99 0.96
239_I 47_L 1.74 0.98 0.95
102_V 35_L 1.66 0.97 0.94
236_S 57_E 1.62 0.97 0.93
209_F 28_T 1.45 0.94 0.86
223_N 46_I 1.45 0.93 0.86
122_W 20_F 1.31 0.88 0.78
59_L 25_V 1.25 0.84 0.73
63_A 28_T 1.17 0.79 0.66
110_T 24_A 1.16 0.78 0.65
219_M 39_S 1.13 0.75 0.62
129_L 15_G 1.04 0.66 0.51
217_T 18_A 1.03 0.65 0.50
118_M 18_A 1.03 0.65 0.50
105_F 27_M 0.97 0.58 0.43
58_Y 27_M 0.97 0.58 0.43
122_W 17_Y 0.96 0.58 0.42
207_F 64_Q 0.96 0.57 0.42
39_W 5_F 0.93 0.54 0.39
42_G 5_F 0.93 0.54 0.38
43_F 5_F 0.90 0.50 0.35
157_R 44_R 0.90 0.50 0.34
216_L 36_V 0.89 0.48 0.33
64_A 25_V 0.89 0.48 0.33
227_L 42_Q 0.88 0.48 0.33
30_V 45_A 0.88 0.48 0.33
22_I 37_V 0.87 0.46 0.31
221_M 46_I 0.87 0.46 0.31
168_V 45_A 0.86 0.45 0.30
6_H 20_F 0.85 0.45 0.30
216_L 35_L 0.85 0.44 0.29
137_F 22_W 0.85 0.44 0.29
143_I 32_L 0.81 0.40 0.25
134_V 9_N 0.81 0.39 0.25
188_T 26_V 0.80 0.38 0.24
223_N 45_A 0.80 0.38 0.24
205_S 50_V 0.78 0.36 0.22
142_V 56_R 0.78 0.36 0.22
65_I 5_F 0.78 0.36 0.22
161_I 34_V 0.78 0.36 0.22
190_M 17_Y 0.77 0.35 0.21
44_A 15_G 0.77 0.35 0.21
41_F 25_V 0.77 0.35 0.21
220_R 39_S 0.76 0.34 0.20
201_P 5_F 0.76 0.33 0.20
203_R 12_F 0.75 0.33 0.19
225_I 20_F 0.75 0.32 0.19
189_R 24_A 0.75 0.32 0.19
161_I 8_W 0.74 0.31 0.18
219_M 40_V 0.73 0.31 0.18
92_A 24_A 0.73 0.30 0.17
200_S 30_I 0.73 0.30 0.17
163_V 22_W 0.73 0.30 0.17
227_L 46_I 0.73 0.30 0.17
40_G 58_A 0.72 0.29 0.17
216_L 39_S 0.72 0.29 0.17
89_A 25_V 0.72 0.29 0.17
104_T 28_T 0.72 0.29 0.17
122_W 19_F 0.72 0.29 0.16
134_V 16_G 0.72 0.29 0.16
44_A 20_F 0.71 0.29 0.16
105_F 31_P 0.71 0.29 0.16
150_D 24_A 0.71 0.29 0.16
187_S 6_A 0.71 0.28 0.16
207_F 47_L 0.70 0.28 0.15
65_I 4_A 0.70 0.27 0.15
38_I 5_F 0.69 0.27 0.15
212_L 32_L 0.69 0.27 0.15
188_T 53_Q 0.69 0.27 0.15
68_M 48_R 0.69 0.26 0.14
122_W 21_V 0.69 0.26 0.14
238_L 16_G 0.69 0.26 0.14
76_V 51_A 0.69 0.26 0.14
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
8058 1.12 checkback Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
7036 2.54 CCMC_CCMD Δgene:(1, 1) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 1.00 Done
7035 2.74 CCMC_CCMD Δgene:(1, 2) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 1.00 Done
1101 0.89 CCMC_CCMD Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.99 Done
1052 0.89 CCMC_CCMD Δgene:(1, 5) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2014_03) 0.98 Done
1050 0.91 CCMC_CCMD Δgene:(1, 5) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.94 Done
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