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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 393
Sequences: 692 664 367
Seq/Len: 2.82 4.18 0.93
MirrorTree (Pazo et al. 2001) 0.89
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 0.15
2 0.00 0.00 0.91
5 0.00 0.00 1.03
10 0.00 0.00 1.09
20 0.00 0.00 1.09
100 0.00 0.00 1.12
∞ 0.01 0.01 1.34
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
49_Q 104_R 2.30 0.98 0.94
49_Q 107_Q 1.51 0.75 0.50
195_D 139_V 1.49 0.74 0.48
48_Y 104_R 1.43 0.70 0.42
9_A 4_R 1.36 0.64 0.36
129_L 104_R 1.35 0.64 0.35
87_K 5_R 1.31 0.60 0.32
65_I 36_L 1.30 0.59 0.30
107_A 115_L 1.25 0.55 0.27
93_V 38_Y 1.25 0.54 0.26
116_K 77_S 1.24 0.54 0.26
78_A 44_L 1.23 0.53 0.24
182_T 27_L 1.20 0.49 0.22
69_G 60_L 1.19 0.49 0.21
173_I 27_L 1.18 0.48 0.20
91_L 26_V 1.13 0.43 0.17
129_L 19_L 1.11 0.42 0.16
29_S 43_I 1.10 0.41 0.16
153_R 60_L 1.10 0.41 0.16
77_A 84_I 1.09 0.40 0.15
34_T 118_G 1.08 0.39 0.14
146_W 42_E 1.08 0.39 0.14
8_L 95_Y 1.07 0.38 0.14
164_L 7_N 1.07 0.38 0.14
164_L 19_L 1.06 0.38 0.14
173_I 105_E 1.06 0.37 0.13
112_S 88_E 1.05 0.37 0.13
71_Y 125_E 1.03 0.35 0.12
59_L 144_E 1.02 0.34 0.12
172_I 69_G 1.02 0.34 0.12
199_R 135_T 1.02 0.34 0.12
84_W 107_Q 1.01 0.33 0.11
187_S 17_A 1.01 0.33 0.11
25_L 45_Y 1.00 0.33 0.11
31_V 145_A 1.00 0.32 0.10
162_L 18_G 1.00 0.32 0.10
68_M 57_G 1.00 0.32 0.10
138_L 29_A 0.99 0.32 0.10
143_I 26_V 0.99 0.31 0.10
206_I 42_E 0.98 0.31 0.10
161_I 57_G 0.98 0.31 0.10
198_M 142_A 0.98 0.30 0.09
178_E 18_G 0.97 0.30 0.09
166_G 86_D 0.97 0.30 0.09
106_I 111_V 0.97 0.30 0.09
175_Y 43_I 0.97 0.30 0.09
208_G 59_R 0.96 0.30 0.09
10_I 4_R 0.96 0.30 0.09
70_I 133_N 0.96 0.30 0.09
172_I 95_Y 0.96 0.29 0.09
118_M 107_Q 0.96 0.29 0.09
79_F 85_Y 0.95 0.29 0.09
121_T 125_E 0.95 0.29 0.08
68_M 29_A 0.95 0.29 0.08
147_H 38_Y 0.94 0.28 0.08
187_S 71_V 0.94 0.28 0.08
91_L 16_L 0.94 0.28 0.08
74_M 69_G 0.94 0.28 0.08
234_W 73_R 0.92 0.27 0.07
234_W 5_R 0.92 0.27 0.07
46_A 137_P 0.92 0.27 0.07
174_H 104_R 0.92 0.27 0.07
124_V 105_E 0.92 0.26 0.07
206_I 13_C 0.92 0.26 0.07
136_L 148_R 0.92 0.26 0.07
133_L 128_A 0.92 0.26 0.07
92_A 121_I 0.92 0.26 0.07
14_L 85_Y 0.92 0.26 0.07
182_T 41_G 0.91 0.26 0.07
192_Q 32_S 0.91 0.26 0.07
15_Y 5_R 0.91 0.25 0.07
54_Y 5_R 0.90 0.25 0.07
219_M 57_G 0.90 0.25 0.07
193_S 23_I 0.90 0.25 0.07
113_A 87_A 0.90 0.25 0.07
14_L 49_E 0.90 0.25 0.07
192_Q 27_L 0.90 0.25 0.07
21_F 65_M 0.90 0.25 0.07
44_A 5_R 0.90 0.25 0.07
141_G 4_R 0.90 0.25 0.07
108_L 100_P 0.90 0.25 0.07
25_L 122_L 0.89 0.24 0.07
122_W 29_A 0.89 0.24 0.07
38_I 30_L 0.89 0.24 0.07
129_L 107_Q 0.89 0.24 0.07
75_A 22_T 0.89 0.24 0.06
236_S 68_P 0.89 0.24 0.06
130_T 100_P 0.89 0.24 0.06
158_A 126_V 0.88 0.23 0.06
235_V 138_E 0.87 0.23 0.06
189_R 65_M 0.87 0.23 0.06
194_I 5_R 0.87 0.23 0.06
79_F 19_L 0.87 0.23 0.06
188_T 43_I 0.87 0.23 0.06
121_T 122_L 0.87 0.23 0.06
221_M 34_I 0.86 0.23 0.06
170_L 67_M 0.86 0.23 0.06
189_R 140_E 0.86 0.23 0.06
161_I 87_A 0.86 0.23 0.06
157_R 94_S 0.86 0.23 0.06
96_M 72_Q 0.86 0.22 0.06
42_G 148_R 0.86 0.22 0.06
21_F 56_V 0.86 0.22 0.06
232_R 55_E 0.86 0.22 0.06
10_I 5_R 0.86 0.22 0.06
155_A 22_T 0.86 0.22 0.06
48_Y 107_Q 0.86 0.22 0.06
153_R 23_I 0.85 0.22 0.05
107_A 5_R 0.85 0.22 0.05
146_W 111_V 0.85 0.22 0.05
127_A 125_E 0.85 0.22 0.05
35_V 119_N 0.85 0.21 0.05
65_I 121_I 0.84 0.21 0.05
152_R 30_L 0.84 0.21 0.05
93_V 93_V 0.84 0.21 0.05
127_A 126_V 0.84 0.21 0.05
116_K 78_L 0.84 0.21 0.05
13_R 94_S 0.84 0.21 0.05
98_P 99_L 0.84 0.21 0.05
227_L 117_K 0.84 0.21 0.05
116_K 125_E 0.84 0.21 0.05
57_I 135_T 0.84 0.21 0.05
178_E 139_V 0.83 0.21 0.05
234_W 46_G 0.83 0.21 0.05
162_L 139_V 0.83 0.20 0.05
85_Q 112_Q 0.83 0.20 0.05
148_A 139_V 0.83 0.20 0.05
52_N 77_S 0.83 0.20 0.05
56_I 100_P 0.83 0.20 0.05
214_A 124_K 0.83 0.20 0.05
81_G 60_L 0.83 0.20 0.05
235_V 46_G 0.82 0.20 0.05
167_V 110_V 0.82 0.20 0.05
65_I 62_V 0.82 0.20 0.05
108_L 127_L 0.82 0.20 0.05
157_R 91_V 0.82 0.20 0.05
209_F 133_N 0.82 0.20 0.05
175_Y 109_V 0.82 0.20 0.05
75_A 110_V 0.82 0.20 0.05
144_A 37_F 0.82 0.20 0.04
163_V 109_V 0.82 0.20 0.04
236_S 41_G 0.82 0.20 0.04
8_L 72_Q 0.82 0.20 0.04
186_G 138_E 0.82 0.20 0.04
167_V 20_A 0.81 0.20 0.04
79_F 60_L 0.81 0.20 0.04
217_T 77_S 0.81 0.20 0.04
94_A 81_T 0.81 0.19 0.04
116_K 129_K 0.81 0.19 0.04
18_C 121_I 0.81 0.19 0.04
9_A 62_V 0.81 0.19 0.04
58_Y 107_Q 0.81 0.19 0.04
65_I 35_D 0.80 0.19 0.04
238_L 111_V 0.80 0.19 0.04
173_I 37_F 0.80 0.19 0.04
59_L 138_E 0.80 0.19 0.04
205_S 16_L 0.80 0.19 0.04
204_W 72_Q 0.80 0.19 0.04
116_K 21_L 0.80 0.19 0.04
115_G 8_R 0.80 0.18 0.04
58_Y 139_V 0.79 0.18 0.04
37_W 65_M 0.79 0.18 0.04
31_V 69_G 0.79 0.18 0.04
209_F 141_K 0.79 0.18 0.04
226_L 46_G 0.79 0.18 0.04
105_F 87_A 0.79 0.18 0.04
167_V 30_L 0.79 0.18 0.04
181_N 19_L 0.79 0.18 0.04
94_A 75_P 0.79 0.18 0.04
135_L 127_L 0.79 0.18 0.04
127_A 142_A 0.79 0.18 0.04
89_A 123_A 0.79 0.18 0.04
156_G 42_E 0.78 0.18 0.04
173_I 73_R 0.78 0.18 0.04
200_S 94_S 0.78 0.18 0.04
127_A 136_P 0.78 0.18 0.04
136_L 58_Q 0.78 0.18 0.04
17_I 28_Y 0.78 0.18 0.04
201_P 139_V 0.78 0.18 0.04
34_T 148_R 0.78 0.18 0.04
150_D 42_E 0.78 0.18 0.04
159_A 83_T 0.78 0.17 0.04
38_I 28_Y 0.78 0.17 0.04
162_L 78_L 0.77 0.17 0.04
121_T 127_L 0.77 0.17 0.04
90_N 4_R 0.77 0.17 0.04
83_V 9_L 0.77 0.17 0.04
98_P 126_V 0.77 0.17 0.04
68_M 62_V 0.77 0.17 0.04
134_V 6_K 0.77 0.17 0.04
10_I 58_Q 0.77 0.17 0.04
108_L 123_A 0.77 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
8059 1.57 cCmCE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.95 Done - Shared
7373 1.66 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-40, 2) msa: Jackhmmer (r132) 0.98 Done
7372 2.68 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-40, 4) msa: Jackhmmer (r132) 1.00 Done
7371 2.77 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 1.00 Done
7370 0.47 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (r132) 0.70 Done
7369 0.06 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (r132) Killed
7351 3.08 CCMC_CCME Δgene:(1, 2) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 1.00 Done
7347 0.47 CCMC_CCME Δgene:(1, 2) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (r132) 0.61 Done
7037 4.74 CCMC_CCME Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.99 Done
7034 3.44 CCMC_CCME Δgene:(1, 2) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done
6982 5.17 ccmc_ccme Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.20 Done - Shared
2431 1.73 ccme-ccmc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1105 0.93 CCMC_CCME Δgene:(1, 2) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.94 Done
1099 1.4 CCMC_CCME Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.98 Done
1097 0.15 CCMC_CCME Δgene:(1, 1) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed
1094 1.28 CCMC_CCME Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done
1049 1.51 CCMC_CCME Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done
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