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OPENSEQ.org
CCMC_CCMD
Genes: A B A+B
Length: 245 69 305
Sequences: 692 360 272
Seq/Len: 2.82 5.22 0.89
MirrorTree (Pazo et al. 2001) 0.77
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 0.00 0.00 0.86
5 0.00 0.00 0.86
10 0.00 0.00 0.86
20 0.00 0.00 0.86
100 0.00 0.00 0.86
∞ 0.01 0.00 0.87
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 2.73 1.00 0.99
102_V 31_P 1.80 0.89 0.79
122_W 20_F 1.70 0.85 0.73
239_I 47_L 1.63 0.81 0.67
52_N 17_Y 1.43 0.68 0.48
42_G 3_P 1.43 0.68 0.48
113_A 23_L 1.38 0.64 0.43
57_I 3_P 1.31 0.58 0.36
134_V 18_A 1.31 0.58 0.36
129_L 15_G 1.30 0.58 0.36
59_L 44_R 1.28 0.56 0.34
39_W 5_F 1.23 0.52 0.29
30_V 12_F 1.22 0.50 0.28
150_D 4_A 1.19 0.47 0.25
43_F 5_F 1.15 0.44 0.22
201_P 5_F 1.15 0.44 0.22
200_S 25_V 1.14 0.43 0.21
219_M 39_S 1.13 0.43 0.21
136_L 25_V 1.13 0.42 0.20
236_S 57_E 1.13 0.42 0.20
41_F 25_V 1.11 0.41 0.19
217_T 18_A 1.11 0.41 0.19
198_M 14_M 1.10 0.40 0.18
102_V 35_L 1.09 0.39 0.18
44_A 15_G 1.08 0.38 0.17
113_A 27_M 1.08 0.38 0.17
143_I 32_L 1.04 0.35 0.15
236_S 54_R 1.03 0.34 0.14
99_I 35_L 1.01 0.32 0.13
223_N 46_I 1.01 0.32 0.13
59_L 25_V 1.00 0.32 0.12
138_L 22_W 1.00 0.31 0.12
215_T 26_V 1.00 0.31 0.12
29_S 24_A 0.99 0.31 0.12
35_V 20_F 0.98 0.30 0.11
157_R 51_A 0.98 0.30 0.11
210_L 17_Y 0.96 0.29 0.10
129_L 11_F 0.96 0.28 0.10
105_F 30_I 0.95 0.28 0.10
137_F 22_W 0.95 0.28 0.10
38_I 5_F 0.95 0.28 0.10
3_K 23_L 0.94 0.27 0.10
157_R 52_Q 0.94 0.27 0.09
229_E 21_V 0.93 0.26 0.09
212_L 36_V 0.92 0.25 0.09
69_G 17_Y 0.92 0.25 0.09
121_T 10_E 0.92 0.25 0.09
189_R 50_V 0.91 0.25 0.08
167_V 59_R 0.91 0.25 0.08
143_I 4_A 0.91 0.25 0.08
37_W 52_Q 0.91 0.25 0.08
9_A 24_A 0.90 0.24 0.08
168_V 24_A 0.90 0.24 0.08
155_A 63_A 0.90 0.24 0.08
175_Y 9_N 0.90 0.24 0.08
164_L 26_V 0.90 0.24 0.08
212_L 25_V 0.89 0.24 0.08
212_L 35_L 0.89 0.24 0.08
42_G 5_F 0.89 0.24 0.08
161_I 53_Q 0.89 0.23 0.07
155_A 19_F 0.88 0.23 0.07
30_V 45_A 0.88 0.23 0.07
161_I 49_G 0.88 0.23 0.07
65_I 5_F 0.87 0.22 0.07
109_V 27_M 0.87 0.22 0.07
163_V 22_W 0.86 0.22 0.07
103_F 25_V 0.86 0.22 0.07
230_K 58_A 0.86 0.22 0.07
182_T 13_A 0.86 0.22 0.07
44_A 20_F 0.86 0.22 0.06
33_L 28_T 0.86 0.21 0.06
157_R 44_R 0.85 0.21 0.06
236_S 50_V 0.85 0.21 0.06
85_Q 35_L 0.85 0.21 0.06
208_G 18_A 0.85 0.21 0.06
34_T 45_A 0.85 0.21 0.06
28_A 44_R 0.85 0.21 0.06
27_I 27_M 0.85 0.21 0.06
140_V 12_F 0.85 0.21 0.06
66_W 17_Y 0.85 0.21 0.06
172_I 44_R 0.84 0.20 0.06
207_F 11_F 0.84 0.20 0.06
73_S 50_V 0.84 0.20 0.06
55_R 22_W 0.83 0.20 0.06
201_P 35_L 0.83 0.20 0.06
23_P 20_F 0.83 0.20 0.06
42_G 18_A 0.83 0.20 0.06
231_R 24_A 0.83 0.20 0.06
222_R 61_R 0.82 0.20 0.05
161_I 54_R 0.82 0.20 0.05
132_E 17_Y 0.82 0.19 0.05
54_Y 53_Q 0.81 0.19 0.05
7_Q 26_V 0.81 0.19 0.05
83_V 50_V 0.81 0.19 0.05
122_W 14_M 0.81 0.19 0.05
136_L 20_F 0.81 0.19 0.05
49_Q 15_G 0.80 0.18 0.05
63_A 39_S 0.80 0.18 0.05
22_I 43_H 0.80 0.18 0.05
29_S 31_P 0.80 0.18 0.05
24_W 44_R 0.79 0.18 0.05
157_R 24_A 0.79 0.18 0.05
66_W 12_F 0.79 0.18 0.04
189_R 48_R 0.79 0.17 0.04
240_L 24_A 0.78 0.17 0.04
3_K 31_P 0.78 0.17 0.04
188_T 53_Q 0.78 0.17 0.04
20_W 18_A 0.78 0.17 0.04
163_V 12_F 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)
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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