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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 385
Sequences: 1895 2171 1185
Seq/Len: 7.73 13.65 3.08
MirrorTree (Pazo et al. 2001) 0.84
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 0.79
2 0.00 0.00 2.93
5 0.00 0.00 2.97
10 0.00 0.00 2.98
20 0.00 0.00 2.99
100 0.00 0.00 3.04
∞ 0.02 0.03 3.51
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 2.75 1.00 1.00
46_A 137_P 1.59 0.97 0.93
83_V 12_A 1.48 0.95 0.89
49_Q 107_Q 1.27 0.88 0.77
48_Y 107_Q 1.22 0.85 0.73
167_V 39_T 1.20 0.84 0.72
118_M 107_Q 1.19 0.83 0.70
83_V 9_L 1.17 0.82 0.69
181_N 19_L 1.13 0.79 0.65
36_G 139_V 1.09 0.75 0.60
87_K 5_R 1.09 0.75 0.60
172_I 96_E 1.08 0.74 0.60
170_L 16_L 1.08 0.74 0.59
134_V 71_V 1.02 0.68 0.53
65_I 36_L 0.99 0.64 0.49
64_A 104_R 0.98 0.63 0.47
86_M 5_R 0.98 0.63 0.47
48_Y 104_R 0.98 0.63 0.47
90_N 107_Q 0.98 0.63 0.47
136_L 70_S 0.96 0.61 0.45
14_L 121_I 0.95 0.60 0.44
164_L 116_E 0.93 0.57 0.41
48_Y 135_T 0.93 0.57 0.41
6_H 8_R 0.88 0.51 0.35
36_G 140_E 0.88 0.51 0.35
129_L 104_R 0.88 0.50 0.35
65_I 35_D 0.85 0.48 0.32
48_Y 39_T 0.85 0.47 0.31
195_D 139_V 0.84 0.46 0.30
84_W 107_Q 0.83 0.44 0.29
201_P 107_Q 0.82 0.44 0.28
118_M 78_L 0.82 0.43 0.28
67_S 95_Y 0.81 0.42 0.27
78_A 109_V 0.80 0.41 0.27
59_L 21_L 0.79 0.40 0.25
229_E 5_R 0.78 0.39 0.24
211_L 109_V 0.78 0.38 0.24
113_A 30_L 0.78 0.38 0.24
116_K 129_K 0.78 0.38 0.24
68_M 62_V 0.78 0.38 0.24
160_G 49_E 0.77 0.37 0.23
79_F 12_A 0.77 0.37 0.23
175_Y 35_D 0.76 0.36 0.22
136_L 15_V 0.75 0.35 0.22
124_V 36_L 0.75 0.35 0.22
188_T 43_I 0.75 0.35 0.21
160_G 114_E 0.75 0.35 0.21
210_L 62_V 0.74 0.34 0.20
6_H 9_L 0.74 0.34 0.20
4_T 112_Q 0.73 0.33 0.20
122_W 71_V 0.73 0.33 0.20
91_L 42_E 0.73 0.33 0.19
182_T 27_L 0.73 0.33 0.19
107_A 37_F 0.73 0.32 0.19
148_A 24_G 0.72 0.32 0.19
187_S 36_L 0.72 0.32 0.19
59_L 83_T 0.72 0.32 0.18
234_W 5_R 0.72 0.31 0.18
194_I 84_I 0.71 0.31 0.17
9_A 101_D 0.71 0.30 0.17
182_T 71_V 0.71 0.30 0.17
192_Q 109_V 0.70 0.30 0.17
174_H 107_Q 0.70 0.30 0.17
59_L 87_A 0.70 0.30 0.17
165_I 43_I 0.70 0.30 0.17
168_V 93_V 0.70 0.29 0.17
57_I 112_Q 0.69 0.29 0.16
134_V 36_L 0.69 0.29 0.16
226_L 38_Y 0.69 0.29 0.16
192_Q 27_L 0.69 0.28 0.16
31_V 76_N 0.69 0.28 0.16
236_S 122_L 0.69 0.28 0.16
80_I 69_G 0.68 0.28 0.15
182_T 41_G 0.68 0.28 0.15
68_M 67_M 0.68 0.27 0.15
70_I 133_N 0.68 0.27 0.15
63_A 122_L 0.67 0.27 0.15
73_S 119_N 0.67 0.27 0.15
4_T 38_Y 0.67 0.27 0.14
8_L 110_V 0.67 0.27 0.14
164_L 19_L 0.67 0.27 0.14
213_S 42_E 0.67 0.26 0.14
32_V 17_A 0.67 0.26 0.14
211_L 88_E 0.67 0.26 0.14
68_M 6_K 0.66 0.26 0.14
64_A 22_T 0.66 0.26 0.14
159_A 44_L 0.66 0.26 0.14
168_V 19_L 0.66 0.26 0.14
215_T 14_A 0.66 0.25 0.13
168_V 10_W 0.65 0.25 0.13
15_Y 13_C 0.65 0.25 0.13
76_V 13_C 0.65 0.25 0.13
35_V 20_A 0.65 0.25 0.13
136_L 29_A 0.65 0.25 0.13
63_A 28_Y 0.65 0.25 0.13
65_I 37_F 0.65 0.24 0.13
127_A 142_A 0.65 0.24 0.13
188_T 6_K 0.65 0.24 0.13
79_F 16_L 0.65 0.24 0.13
175_Y 107_Q 0.64 0.24 0.13
34_T 75_P 0.64 0.24 0.13
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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