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OPENSEQ.org
CCMC_CCMD
Genes: A B A+B
Length: 245 69 301
Sequences: 2698 1202 764
Seq/Len: 11.01 17.42 2.54
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 2.43
2 0.00 0.00 2.44
5 0.00 0.00 2.45
10 0.00 0.00 2.45
20 0.00 0.00 2.45
100 0.00 0.00 2.45
∞ 0.02 0.03 2.43
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 2.68 1.00 1.00
52_N 17_Y 2.44 1.00 0.99
118_M 17_Y 2.17 1.00 0.99
109_V 27_M 2.05 0.99 0.98
59_L 28_T 1.97 0.99 0.97
113_A 23_L 1.93 0.99 0.97
113_A 27_M 1.78 0.98 0.95
102_V 35_L 1.73 0.98 0.94
236_S 57_E 1.69 0.97 0.94
239_I 47_L 1.65 0.97 0.93
223_N 46_I 1.59 0.96 0.91
59_L 25_V 1.49 0.94 0.87
209_F 28_T 1.47 0.93 0.86
219_M 39_S 1.23 0.81 0.69
122_W 20_F 1.19 0.79 0.66
110_T 24_A 1.18 0.78 0.65
63_A 28_T 1.15 0.75 0.62
122_W 17_Y 1.11 0.71 0.57
42_G 5_F 1.10 0.70 0.56
129_L 15_G 1.09 0.70 0.55
118_M 18_A 1.09 0.70 0.55
157_R 44_R 1.09 0.70 0.55
217_T 18_A 1.04 0.64 0.49
30_V 45_A 1.02 0.62 0.46
207_F 64_Q 1.01 0.60 0.45
39_W 5_F 1.00 0.60 0.45
216_L 35_L 1.00 0.59 0.44
58_Y 27_M 0.99 0.58 0.43
59_L 17_Y 0.97 0.56 0.40
216_L 36_V 0.96 0.55 0.39
221_M 46_I 0.95 0.54 0.39
43_F 5_F 0.93 0.51 0.36
105_F 27_M 0.92 0.50 0.34
201_P 5_F 0.91 0.49 0.34
44_A 20_F 0.91 0.49 0.34
227_L 42_Q 0.91 0.49 0.34
225_I 20_F 0.89 0.47 0.31
64_A 25_V 0.88 0.45 0.30
44_A 15_G 0.88 0.45 0.30
205_S 50_V 0.87 0.45 0.29
22_I 37_V 0.86 0.43 0.28
168_V 45_A 0.86 0.43 0.28
188_T 26_V 0.84 0.41 0.26
106_I 28_T 0.83 0.40 0.25
27_I 27_M 0.83 0.40 0.25
113_A 24_A 0.82 0.39 0.24
41_F 25_V 0.82 0.39 0.24
216_L 39_S 0.82 0.39 0.24
208_G 37_V 0.82 0.39 0.24
134_V 9_N 0.82 0.39 0.24
66_W 23_L 0.81 0.38 0.23
206_I 50_V 0.80 0.37 0.22
122_W 19_F 0.80 0.36 0.22
190_M 17_Y 0.80 0.36 0.22
143_I 32_L 0.80 0.36 0.22
65_I 5_F 0.78 0.34 0.20
225_I 27_M 0.78 0.34 0.20
38_I 5_F 0.78 0.34 0.20
198_M 14_M 0.77 0.33 0.19
83_V 55_A 0.77 0.33 0.19
207_F 58_A 0.77 0.33 0.19
85_Q 29_V 0.76 0.32 0.19
167_V 59_R 0.76 0.32 0.18
76_V 51_A 0.75 0.31 0.18
161_I 8_W 0.75 0.31 0.18
227_L 46_I 0.75 0.31 0.17
99_I 27_M 0.75 0.31 0.17
89_A 25_V 0.74 0.30 0.17
36_G 10_E 0.74 0.30 0.17
142_V 56_R 0.74 0.30 0.17
76_V 13_A 0.73 0.29 0.16
200_S 25_V 0.73 0.29 0.16
193_S 30_I 0.73 0.29 0.16
55_R 22_W 0.73 0.29 0.16
157_R 24_A 0.73 0.29 0.16
212_L 32_L 0.73 0.29 0.16
21_F 12_F 0.73 0.29 0.16
137_F 22_W 0.73 0.29 0.16
134_V 16_G 0.72 0.28 0.16
189_R 24_A 0.72 0.28 0.15
201_P 35_L 0.72 0.28 0.15
163_V 22_W 0.72 0.28 0.15
220_R 39_S 0.71 0.28 0.15
66_W 17_Y 0.71 0.27 0.15
204_W 48_R 0.71 0.27 0.14
167_V 12_F 0.71 0.27 0.14
104_T 28_T 0.71 0.27 0.14
14_L 29_V 0.70 0.27 0.14
193_S 25_V 0.70 0.26 0.14
54_Y 53_Q 0.70 0.26 0.14
112_S 33_V 0.70 0.26 0.14
35_V 50_V 0.70 0.26 0.14
161_I 34_V 0.69 0.25 0.13
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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