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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 394
Sequences: 1339 811 656
Seq/Len: 5.47 5.1 1.66
MirrorTree (Pazo et al. 2001) 0.80
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 0.19
2 0.00 0.00 1.62
5 0.00 0.00 1.62
10 0.00 0.00 1.63
20 0.00 0.00 1.63
100 0.00 0.00 1.63
∞ 0.03 0.03 1.68
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 2.32 1.00 0.98
195_D 139_V 1.46 0.86 0.74
48_Y 107_Q 1.34 0.79 0.64
188_T 43_I 1.26 0.73 0.56
6_H 8_R 1.20 0.67 0.48
19_G 112_Q 1.17 0.65 0.46
69_G 60_L 1.16 0.64 0.45
107_A 37_F 1.15 0.63 0.44
175_Y 109_V 1.10 0.57 0.38
43_F 67_M 1.10 0.57 0.38
48_Y 104_R 1.07 0.55 0.35
143_I 33_N 1.06 0.53 0.33
68_M 62_V 1.03 0.50 0.31
201_P 107_Q 1.03 0.50 0.30
208_G 24_G 1.01 0.48 0.29
129_L 104_R 1.01 0.48 0.28
187_S 91_V 0.99 0.46 0.27
192_Q 27_L 0.99 0.46 0.27
136_L 70_S 0.99 0.46 0.27
17_I 23_I 0.98 0.45 0.26
49_Q 107_Q 0.98 0.45 0.26
167_V 39_T 0.98 0.45 0.26
178_E 109_V 0.98 0.45 0.26
148_A 24_G 0.97 0.44 0.25
164_L 116_E 0.97 0.43 0.24
90_N 18_G 0.97 0.43 0.24
53_S 138_E 0.96 0.43 0.24
143_I 31_R 0.96 0.43 0.24
174_H 104_R 0.95 0.41 0.23
35_V 75_P 0.95 0.41 0.23
118_M 120_H 0.95 0.41 0.23
124_V 125_E 0.94 0.40 0.22
66_W 42_E 0.94 0.40 0.22
121_T 20_A 0.93 0.40 0.21
64_A 104_R 0.93 0.39 0.21
175_Y 107_Q 0.93 0.39 0.21
118_M 78_L 0.92 0.39 0.21
210_L 62_V 0.92 0.39 0.21
71_Y 111_V 0.92 0.39 0.20
235_V 138_E 0.92 0.38 0.20
168_V 93_V 0.92 0.38 0.20
174_H 107_Q 0.92 0.38 0.20
157_R 67_M 0.91 0.38 0.20
48_Y 109_V 0.91 0.38 0.20
28_A 117_K 0.91 0.37 0.19
161_I 22_T 0.90 0.37 0.19
235_V 24_G 0.90 0.37 0.19
202_L 107_Q 0.90 0.37 0.19
72_A 39_T 0.90 0.37 0.19
58_Y 84_I 0.90 0.36 0.19
59_L 83_T 0.90 0.36 0.19
65_I 36_L 0.88 0.35 0.18
144_A 71_V 0.88 0.35 0.17
87_K 5_R 0.88 0.34 0.17
29_S 20_A 0.87 0.34 0.17
67_S 62_V 0.86 0.33 0.16
231_R 121_I 0.86 0.33 0.16
118_M 62_V 0.86 0.33 0.16
161_I 83_T 0.86 0.32 0.16
149_F 28_Y 0.86 0.32 0.16
31_V 13_C 0.85 0.32 0.16
85_Q 8_R 0.85 0.32 0.15
193_S 90_S 0.85 0.32 0.15
181_N 19_L 0.84 0.31 0.15
70_I 133_N 0.84 0.31 0.14
42_G 124_K 0.84 0.30 0.14
25_L 57_G 0.83 0.30 0.14
78_A 20_A 0.83 0.30 0.14
103_F 18_G 0.83 0.30 0.14
239_I 38_Y 0.83 0.30 0.14
38_I 36_L 0.83 0.30 0.14
188_T 12_A 0.83 0.30 0.14
211_L 96_E 0.83 0.30 0.14
107_A 38_Y 0.83 0.30 0.14
4_T 38_Y 0.83 0.30 0.14
232_R 57_G 0.82 0.29 0.14
10_I 48_R 0.82 0.29 0.14
234_W 5_R 0.82 0.29 0.13
215_T 14_A 0.82 0.29 0.13
104_T 140_E 0.82 0.29 0.13
68_M 112_Q 0.82 0.29 0.13
57_I 67_M 0.82 0.29 0.13
65_I 35_D 0.81 0.29 0.13
93_V 38_Y 0.81 0.28 0.13
148_A 65_M 0.81 0.28 0.13
134_V 81_T 0.81 0.28 0.13
58_Y 117_K 0.81 0.28 0.12
146_W 111_V 0.81 0.28 0.12
39_W 110_V 0.81 0.28 0.12
172_I 111_V 0.80 0.28 0.12
20_W 65_M 0.80 0.28 0.12
121_T 22_T 0.80 0.27 0.12
221_M 145_A 0.80 0.27 0.12
64_A 143_M 0.80 0.27 0.12
106_I 121_I 0.80 0.27 0.12
189_R 62_V 0.80 0.27 0.12
52_N 65_M 0.80 0.27 0.12
110_T 111_V 0.80 0.27 0.12
96_M 16_L 0.79 0.27 0.12
152_R 19_L 0.79 0.27 0.12
31_V 92_D 0.79 0.27 0.12
142_V 121_I 0.79 0.26 0.11
88_M 148_R 0.79 0.26 0.11
207_F 16_L 0.79 0.26 0.11
63_A 21_L 0.78 0.26 0.11
129_L 143_M 0.78 0.26 0.11
29_S 65_M 0.78 0.26 0.11
157_R 89_G 0.78 0.26 0.11
5_L 58_Q 0.78 0.26 0.11
89_A 143_M 0.78 0.26 0.11
99_I 69_G 0.78 0.26 0.11
217_T 13_C 0.78 0.26 0.11
159_A 44_L 0.78 0.25 0.11
41_F 67_M 0.77 0.25 0.10
157_R 26_V 0.77 0.25 0.10
161_I 118_G 0.77 0.24 0.10
28_A 96_E 0.76 0.24 0.10
4_T 112_Q 0.76 0.24 0.10
210_L 35_D 0.75 0.24 0.10
7_Q 31_R 0.75 0.23 0.10
58_Y 107_Q 0.75 0.23 0.10
34_T 76_N 0.75 0.23 0.10
196_P 109_V 0.75 0.23 0.10
22_I 34_I 0.75 0.23 0.10
18_C 60_L 0.75 0.23 0.09
107_A 33_N 0.74 0.23 0.09
192_Q 109_V 0.74 0.23 0.09
73_S 114_E 0.74 0.23 0.09
156_G 109_V 0.74 0.23 0.09
136_L 73_R 0.74 0.23 0.09
88_M 93_V 0.74 0.23 0.09
84_W 107_Q 0.74 0.23 0.09
65_I 30_L 0.74 0.23 0.09
91_L 76_N 0.74 0.23 0.09
10_I 54_P 0.74 0.23 0.09
129_L 39_T 0.74 0.23 0.09
232_R 106_G 0.74 0.22 0.09
142_V 12_A 0.74 0.22 0.09
101_A 142_A 0.74 0.22 0.09
232_R 116_E 0.73 0.22 0.09
8_L 7_N 0.73 0.22 0.09
63_A 14_A 0.73 0.22 0.09
218_L 110_V 0.73 0.22 0.09
38_I 60_L 0.73 0.22 0.09
39_W 36_L 0.72 0.21 0.08
15_Y 13_C 0.72 0.21 0.08
129_L 107_Q 0.72 0.21 0.08
157_R 114_E 0.72 0.21 0.08
83_V 9_L 0.72 0.21 0.08
124_V 133_N 0.72 0.21 0.08
22_I 24_G 0.72 0.21 0.08
104_T 37_F 0.72 0.21 0.08
168_V 10_W 0.72 0.21 0.08
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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