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OPENSEQ.org
CCMC_CCMD
Genes: A B A+B
Length: 245 69 306
Sequences: 1466 360 278
Seq/Len: 5.98 5.22 0.91
MirrorTree (Pazo et al. 2001) 0.41
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 0.86
2 0.01 0.00 0.89
5 0.42 0.00 0.89
10 0.42 0.00 0.89
20 0.42 0.00 0.89
100 0.43 0.00 0.89
∞ 0.47 0.00 0.89
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
118_M 17_Y 2.31 0.98 0.94
102_V 31_P 1.92 0.93 0.81
122_W 20_F 1.67 0.84 0.64
239_I 47_L 1.54 0.77 0.52
113_A 23_L 1.52 0.75 0.50
42_G 3_P 1.42 0.68 0.40
52_N 17_Y 1.35 0.63 0.34
57_I 3_P 1.33 0.61 0.32
143_I 32_L 1.26 0.55 0.26
129_L 15_G 1.25 0.54 0.25
236_S 57_E 1.24 0.53 0.24
134_V 18_A 1.23 0.52 0.24
43_F 5_F 1.22 0.51 0.23
150_D 4_A 1.22 0.51 0.23
219_M 39_S 1.19 0.48 0.20
44_A 15_G 1.16 0.46 0.19
39_W 5_F 1.15 0.45 0.18
200_S 25_V 1.14 0.44 0.17
198_M 14_M 1.13 0.43 0.17
27_I 27_M 1.12 0.42 0.16
37_W 52_Q 1.12 0.42 0.16
136_L 25_V 1.12 0.42 0.16
59_L 44_R 1.09 0.39 0.14
24_W 44_R 1.08 0.39 0.14
113_A 27_M 1.07 0.38 0.14
59_L 25_V 1.07 0.38 0.13
229_E 21_V 1.06 0.37 0.13
156_G 53_Q 1.06 0.37 0.13
217_T 18_A 1.03 0.35 0.12
30_V 12_F 1.03 0.35 0.12
41_F 25_V 1.03 0.34 0.11
231_R 24_A 1.03 0.34 0.11
201_P 5_F 1.01 0.33 0.11
109_V 27_M 1.00 0.32 0.10
22_I 43_H 0.99 0.31 0.10
236_S 50_V 0.99 0.31 0.09
223_N 46_I 0.98 0.30 0.09
121_T 10_E 0.96 0.29 0.09
210_L 17_Y 0.96 0.29 0.09
38_I 5_F 0.95 0.28 0.08
161_I 49_G 0.95 0.28 0.08
189_R 50_V 0.95 0.28 0.08
158_A 15_G 0.94 0.28 0.08
136_L 20_F 0.94 0.27 0.08
138_L 22_W 0.94 0.27 0.07
157_R 51_A 0.93 0.27 0.07
69_G 17_Y 0.93 0.27 0.07
218_L 29_V 0.93 0.26 0.07
236_S 54_R 0.93 0.26 0.07
155_A 63_A 0.91 0.25 0.07
129_L 11_F 0.91 0.25 0.07
20_W 18_A 0.90 0.25 0.07
85_Q 35_L 0.90 0.24 0.06
66_W 12_F 0.89 0.24 0.06
188_T 53_Q 0.89 0.24 0.06
9_A 24_A 0.89 0.24 0.06
22_I 13_A 0.89 0.24 0.06
122_W 14_M 0.89 0.24 0.06
124_V 24_A 0.88 0.24 0.06
155_A 19_F 0.88 0.23 0.06
34_T 45_A 0.88 0.23 0.06
240_L 24_A 0.88 0.23 0.06
137_F 22_W 0.87 0.23 0.06
67_S 30_I 0.87 0.23 0.06
33_L 28_T 0.87 0.22 0.06
29_S 31_P 0.86 0.22 0.05
208_G 18_A 0.86 0.22 0.05
23_P 20_F 0.86 0.22 0.05
150_D 52_Q 0.86 0.22 0.05
189_R 48_R 0.85 0.21 0.05
99_I 35_L 0.85 0.21 0.05
222_R 61_R 0.84 0.21 0.05
212_L 25_V 0.84 0.21 0.05
212_L 36_V 0.84 0.21 0.05
13_R 18_A 0.83 0.20 0.05
216_L 36_V 0.83 0.20 0.05
164_L 26_V 0.83 0.20 0.05
149_F 56_R 0.83 0.20 0.04
42_G 18_A 0.83 0.20 0.04
182_T 13_A 0.83 0.20 0.04
65_I 5_F 0.82 0.20 0.04
163_V 32_L 0.82 0.20 0.04
157_R 52_Q 0.82 0.20 0.04
103_F 25_V 0.82 0.20 0.04
168_V 24_A 0.81 0.19 0.04
49_Q 15_G 0.81 0.19 0.04
9_A 19_F 0.81 0.19 0.04
42_G 5_F 0.81 0.19 0.04
74_M 16_G 0.81 0.19 0.04
203_R 3_P 0.81 0.19 0.04
34_T 48_R 0.81 0.19 0.04
73_S 50_V 0.81 0.19 0.04
168_V 42_Q 0.80 0.19 0.04
3_K 31_P 0.80 0.19 0.04
118_M 19_F 0.80 0.19 0.04
105_F 30_I 0.80 0.18 0.04
212_L 35_L 0.80 0.18 0.04
30_V 45_A 0.80 0.18 0.04
204_W 12_F 0.80 0.18 0.04
54_Y 53_Q 0.79 0.18 0.04
143_I 4_A 0.79 0.18 0.04
175_Y 9_N 0.79 0.18 0.04
35_V 41_M 0.79 0.18 0.04
167_V 59_R 0.79 0.18 0.04
230_K 58_A 0.79 0.18 0.04
193_S 31_P 0.78 0.18 0.04
12_P 21_V 0.78 0.18 0.04
207_F 31_P 0.78 0.18 0.04
41_F 27_M 0.78 0.17 0.04
161_I 53_Q 0.78 0.17 0.04
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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.42 > 0.4) of paralogs.
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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