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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 386
Sequences: 2698 2773 1329
Seq/Len: 11.01 17.44 3.44
MirrorTree (Pazo et al. 2001) 0.88
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 1.02
2 0.00 0.00 3.29
5 0.00 0.00 3.62
10 0.00 0.00 3.85
20 0.00 0.00 3.86
100 0.00 0.00 3.93
∞ 0.02 0.03 4.50
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 2.56 1.00 1.00
46_A 137_P 1.52 0.97 0.91
83_V 12_A 1.28 0.90 0.80
167_V 39_T 1.18 0.85 0.72
49_Q 107_Q 1.16 0.83 0.69
118_M 107_Q 1.16 0.83 0.69
65_I 36_L 1.10 0.79 0.64
48_Y 107_Q 1.03 0.72 0.56
87_K 5_R 1.02 0.71 0.55
124_V 36_L 1.01 0.69 0.53
83_V 9_L 0.95 0.63 0.46
172_I 96_E 0.93 0.61 0.44
14_L 121_I 0.92 0.59 0.42
91_L 42_E 0.91 0.58 0.41
48_Y 109_V 0.89 0.56 0.39
48_Y 135_T 0.89 0.56 0.39
136_L 15_V 0.88 0.54 0.37
154_L 15_V 0.88 0.54 0.37
90_N 107_Q 0.87 0.53 0.36
48_Y 104_R 0.87 0.53 0.36
185_Q 130_H 0.87 0.53 0.36
36_G 139_V 0.86 0.52 0.35
4_T 112_Q 0.84 0.50 0.33
195_D 139_V 0.84 0.49 0.33
25_L 69_G 0.84 0.49 0.32
195_D 59_R 0.81 0.46 0.29
136_L 70_S 0.81 0.45 0.29
168_V 19_L 0.80 0.44 0.28
65_I 35_D 0.79 0.43 0.27
64_A 104_R 0.79 0.42 0.27
86_M 5_R 0.79 0.42 0.27
67_S 95_Y 0.79 0.42 0.27
133_L 123_A 0.78 0.42 0.26
181_N 19_L 0.78 0.41 0.26
79_F 16_L 0.78 0.41 0.26
207_F 16_L 0.77 0.41 0.25
31_V 76_N 0.77 0.40 0.25
110_T 127_L 0.77 0.40 0.25
121_T 127_L 0.77 0.40 0.25
34_T 118_G 0.76 0.39 0.23
217_T 110_V 0.75 0.38 0.23
236_S 68_P 0.75 0.38 0.23
9_A 3_I 0.74 0.37 0.22
234_W 5_R 0.74 0.37 0.22
170_L 16_L 0.74 0.37 0.22
164_L 116_E 0.74 0.37 0.22
84_W 107_Q 0.73 0.35 0.21
50_Q 126_V 0.73 0.35 0.21
195_D 62_V 0.72 0.35 0.20
143_I 117_K 0.72 0.35 0.20
8_L 110_V 0.72 0.35 0.20
134_V 71_V 0.72 0.35 0.20
170_L 76_N 0.71 0.33 0.19
178_E 32_S 0.71 0.33 0.19
63_A 28_Y 0.71 0.33 0.19
185_Q 131_D 0.71 0.33 0.19
43_F 83_T 0.70 0.32 0.18
156_G 36_L 0.70 0.32 0.18
10_I 5_R 0.70 0.32 0.18
173_I 65_M 0.70 0.32 0.18
59_L 83_T 0.70 0.32 0.18
6_H 8_R 0.70 0.32 0.18
34_T 145_A 0.70 0.32 0.18
116_K 129_K 0.70 0.32 0.18
13_R 94_S 0.69 0.30 0.17
15_Y 13_C 0.69 0.30 0.17
48_Y 39_T 0.69 0.30 0.17
211_L 109_V 0.68 0.29 0.16
168_V 93_V 0.68 0.29 0.16
182_T 41_G 0.68 0.29 0.16
71_Y 125_E 0.68 0.29 0.16
167_V 42_E 0.67 0.29 0.16
168_V 62_V 0.67 0.29 0.16
6_H 9_L 0.67 0.28 0.16
103_F 62_V 0.67 0.28 0.15
173_I 105_E 0.67 0.28 0.15
44_A 137_P 0.66 0.28 0.15
141_G 20_A 0.66 0.28 0.15
79_F 12_A 0.66 0.28 0.15
129_L 104_R 0.66 0.28 0.15
68_M 62_V 0.66 0.28 0.15
122_W 142_A 0.66 0.28 0.15
93_V 58_Q 0.66 0.27 0.15
185_Q 63_G 0.66 0.27 0.15
70_I 133_N 0.66 0.27 0.15
229_E 5_R 0.65 0.27 0.14
215_T 14_A 0.65 0.27 0.14
175_Y 107_Q 0.65 0.26 0.14
211_L 88_E 0.65 0.26 0.14
182_T 71_V 0.65 0.26 0.14
33_L 78_L 0.65 0.26 0.14
236_S 122_L 0.65 0.26 0.14
35_V 25_L 0.65 0.26 0.14
25_L 71_V 0.65 0.26 0.14
179_W 63_G 0.64 0.26 0.14
136_L 89_G 0.64 0.26 0.14
165_I 43_I 0.64 0.26 0.14
57_I 112_Q 0.64 0.26 0.14
117_P 102_L 0.64 0.26 0.14
170_L 104_R 0.64 0.25 0.13
78_A 109_V 0.64 0.25 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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