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OPENSEQ.org
CCMC_CCMD
Genes: A B A+B
Length: 245 69 306
Sequences: 1466 360 273
Seq/Len: 5.98 5.22 0.89
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 0.85
2 0.01 0.00 0.87
5 0.42 0.00 0.87
10 0.42 0.00 0.87
20 0.42 0.00 0.87
100 0.43 0.00 0.87
∞ 0.47 0.00 0.88
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 2.67 0.99 0.98
102_V 31_P 1.94 0.93 0.86
239_I 47_L 1.70 0.85 0.72
113_A 23_L 1.59 0.79 0.63
52_N 17_Y 1.51 0.74 0.56
122_W 20_F 1.45 0.70 0.50
134_V 18_A 1.39 0.65 0.44
121_T 10_E 1.31 0.58 0.35
24_W 44_R 1.27 0.55 0.32
41_F 25_V 1.24 0.52 0.29
109_V 27_M 1.24 0.52 0.29
156_G 53_Q 1.22 0.50 0.27
43_F 5_F 1.22 0.50 0.27
44_A 15_G 1.21 0.50 0.27
129_L 15_G 1.21 0.49 0.26
150_D 4_A 1.20 0.49 0.26
59_L 25_V 1.18 0.47 0.24
231_R 24_A 1.16 0.45 0.22
217_T 18_A 1.13 0.42 0.20
236_S 57_E 1.10 0.40 0.18
200_S 25_V 1.09 0.39 0.17
54_Y 53_Q 1.06 0.37 0.16
22_I 43_H 1.06 0.36 0.15
219_M 39_S 1.05 0.36 0.15
216_L 36_V 1.05 0.36 0.15
189_R 48_R 1.05 0.35 0.15
201_P 5_F 1.04 0.34 0.14
143_I 32_L 1.02 0.33 0.13
229_E 21_V 1.01 0.32 0.12
210_L 17_Y 1.00 0.31 0.12
28_A 44_R 1.00 0.31 0.12
34_T 45_A 0.98 0.30 0.11
136_L 20_F 0.97 0.29 0.11
212_L 35_L 0.97 0.29 0.11
236_S 54_R 0.97 0.29 0.11
74_M 16_G 0.97 0.29 0.11
34_T 48_R 0.96 0.29 0.10
136_L 25_V 0.96 0.28 0.10
138_L 22_W 0.95 0.28 0.10
113_A 27_M 0.95 0.28 0.10
38_I 5_F 0.94 0.27 0.09
175_Y 9_N 0.93 0.27 0.09
157_R 51_A 0.93 0.26 0.09
103_F 25_V 0.93 0.26 0.09
122_W 14_M 0.93 0.26 0.09
163_V 32_L 0.93 0.26 0.09
208_G 18_A 0.92 0.26 0.09
65_I 5_F 0.90 0.24 0.08
240_L 24_A 0.90 0.24 0.08
30_V 12_F 0.90 0.24 0.08
212_L 36_V 0.90 0.24 0.08
155_A 19_F 0.90 0.24 0.07
39_W 5_F 0.89 0.24 0.07
42_G 5_F 0.89 0.24 0.07
69_G 17_Y 0.89 0.24 0.07
236_S 50_V 0.89 0.24 0.07
67_S 30_I 0.88 0.23 0.07
9_A 24_A 0.88 0.23 0.07
70_I 17_Y 0.87 0.23 0.07
129_L 11_F 0.87 0.22 0.07
66_W 12_F 0.86 0.22 0.06
198_M 14_M 0.86 0.22 0.06
193_S 57_E 0.86 0.22 0.06
137_F 22_W 0.86 0.22 0.06
79_F 32_L 0.85 0.21 0.06
194_I 54_R 0.85 0.21 0.06
212_L 32_L 0.85 0.21 0.06
37_W 52_Q 0.85 0.21 0.06
29_S 31_P 0.85 0.21 0.06
229_E 54_R 0.84 0.20 0.06
3_K 31_P 0.84 0.20 0.06
158_A 15_G 0.84 0.20 0.06
5_L 17_Y 0.83 0.20 0.06
161_I 37_V 0.83 0.20 0.06
191_Q 25_V 0.83 0.20 0.06
182_T 13_A 0.83 0.20 0.06
89_A 31_P 0.83 0.20 0.06
112_S 7_S 0.83 0.20 0.06
63_A 30_I 0.83 0.20 0.06
167_V 59_R 0.83 0.20 0.05
85_Q 35_L 0.83 0.20 0.05
22_I 13_A 0.83 0.20 0.05
110_T 24_A 0.82 0.20 0.05
143_I 4_A 0.82 0.20 0.05
212_L 25_V 0.82 0.19 0.05
99_I 35_L 0.82 0.19 0.05
27_I 27_M 0.82 0.19 0.05
42_G 18_A 0.82 0.19 0.05
157_R 44_R 0.82 0.19 0.05
215_T 36_V 0.81 0.19 0.05
189_R 50_V 0.81 0.19 0.05
157_R 54_R 0.81 0.19 0.05
14_L 25_V 0.81 0.19 0.05
46_A 28_T 0.80 0.18 0.05
33_L 28_T 0.80 0.18 0.05
30_V 33_V 0.80 0.18 0.05
225_I 60_L 0.80 0.18 0.05
218_L 29_V 0.80 0.18 0.05
236_S 27_M 0.80 0.18 0.05
12_P 39_S 0.80 0.18 0.05
105_F 47_L 0.80 0.18 0.05
116_K 32_L 0.79 0.18 0.05
208_G 52_Q 0.79 0.18 0.04
22_I 45_A 0.79 0.18 0.04
93_V 18_A 0.78 0.17 0.04
208_G 36_V 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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