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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 387
Sequences: 1339 1985 1038
Seq/Len: 5.47 12.48 2.68
MirrorTree (Pazo et al. 2001) 0.81
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 0.63
2 0.00 0.00 2.57
5 0.00 0.00 2.58
10 0.00 0.00 2.60
20 0.00 0.00 2.60
100 0.00 0.00 2.62
∞ 0.03 0.03 2.90
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 2.77 1.00 1.00
83_V 12_A 1.46 0.94 0.87
49_Q 107_Q 1.44 0.93 0.86
46_A 137_P 1.42 0.92 0.84
83_V 9_L 1.33 0.89 0.79
48_Y 107_Q 1.28 0.86 0.76
164_L 116_E 1.20 0.80 0.68
118_M 107_Q 1.12 0.74 0.61
87_K 5_R 1.12 0.74 0.60
48_Y 104_R 1.10 0.72 0.58
136_L 70_S 1.08 0.70 0.56
172_I 96_E 1.08 0.70 0.56
48_Y 135_T 1.06 0.68 0.53
14_L 121_I 1.06 0.68 0.53
188_T 43_I 1.03 0.64 0.49
134_V 71_V 0.97 0.58 0.43
167_V 39_T 0.96 0.56 0.41
64_A 104_R 0.94 0.54 0.38
6_H 8_R 0.93 0.53 0.37
113_A 30_L 0.92 0.51 0.36
86_M 5_R 0.91 0.51 0.35
65_I 36_L 0.91 0.51 0.35
68_M 62_V 0.89 0.48 0.33
67_S 95_Y 0.89 0.48 0.33
234_W 5_R 0.88 0.47 0.32
192_Q 27_L 0.87 0.46 0.31
148_A 24_G 0.87 0.46 0.30
118_M 78_L 0.86 0.45 0.30
90_N 107_Q 0.85 0.43 0.29
201_P 107_Q 0.84 0.43 0.28
65_I 35_D 0.83 0.41 0.26
10_I 5_R 0.83 0.41 0.26
91_L 42_E 0.83 0.41 0.26
170_L 16_L 0.83 0.41 0.26
187_S 36_L 0.82 0.39 0.25
70_I 133_N 0.82 0.39 0.25
4_T 112_Q 0.81 0.39 0.24
172_I 81_T 0.81 0.38 0.24
78_A 109_V 0.81 0.38 0.24
168_V 19_L 0.81 0.38 0.24
80_I 69_G 0.80 0.38 0.23
101_A 142_A 0.80 0.38 0.23
160_G 114_E 0.80 0.37 0.23
116_K 129_K 0.80 0.37 0.23
182_T 27_L 0.79 0.36 0.22
67_S 24_G 0.78 0.35 0.22
107_A 37_F 0.78 0.35 0.22
178_E 109_V 0.78 0.35 0.21
28_A 95_Y 0.77 0.35 0.21
118_M 12_A 0.77 0.35 0.21
84_W 107_Q 0.77 0.35 0.21
181_N 32_S 0.77 0.34 0.21
106_I 18_G 0.77 0.34 0.20
168_V 95_Y 0.77 0.34 0.20
210_L 62_V 0.77 0.34 0.20
238_L 111_V 0.76 0.33 0.20
48_Y 109_V 0.76 0.33 0.20
91_L 26_V 0.76 0.33 0.20
236_S 122_L 0.76 0.33 0.20
181_N 19_L 0.76 0.33 0.19
129_L 104_R 0.75 0.33 0.19
43_F 67_M 0.75 0.32 0.19
36_G 139_V 0.75 0.32 0.19
218_L 60_L 0.74 0.32 0.18
229_E 5_R 0.74 0.31 0.18
175_Y 107_Q 0.74 0.31 0.18
182_T 71_V 0.74 0.31 0.18
194_I 84_I 0.74 0.31 0.18
69_G 60_L 0.74 0.31 0.18
34_T 118_G 0.73 0.30 0.17
113_A 20_A 0.73 0.30 0.17
215_T 14_A 0.73 0.30 0.17
195_D 139_V 0.73 0.30 0.17
44_A 43_I 0.73 0.30 0.17
168_V 93_V 0.72 0.29 0.17
9_A 3_I 0.72 0.29 0.16
160_G 49_E 0.72 0.29 0.16
27_I 72_Q 0.72 0.29 0.16
67_S 133_N 0.71 0.28 0.16
124_V 133_N 0.71 0.28 0.16
211_L 109_V 0.71 0.28 0.16
25_L 45_Y 0.71 0.28 0.16
24_W 148_R 0.71 0.28 0.15
64_A 143_M 0.71 0.28 0.15
79_F 12_A 0.70 0.27 0.15
192_Q 109_V 0.70 0.27 0.15
4_T 38_Y 0.70 0.27 0.15
141_G 106_G 0.70 0.27 0.15
88_M 95_Y 0.69 0.27 0.14
174_H 107_Q 0.69 0.27 0.14
6_H 9_L 0.69 0.27 0.14
136_L 15_V 0.69 0.26 0.14
188_T 23_I 0.69 0.26 0.14
104_T 111_V 0.69 0.26 0.14
36_G 140_E 0.69 0.26 0.14
36_G 104_R 0.68 0.26 0.14
193_S 115_L 0.68 0.25 0.14
71_Y 111_V 0.68 0.25 0.14
90_N 18_G 0.68 0.25 0.14
134_V 36_L 0.68 0.25 0.13
164_L 19_L 0.68 0.25 0.13
188_T 42_E 0.67 0.25 0.13
68_M 67_M 0.67 0.25 0.13
162_L 139_V 0.67 0.24 0.13
122_W 29_A 0.67 0.24 0.13
175_Y 104_R 0.67 0.24 0.13
122_W 71_V 0.67 0.24 0.12
103_F 62_V 0.67 0.24 0.12
33_L 92_D 0.67 0.24 0.12
157_R 67_M 0.67 0.24 0.12
59_L 87_A 0.67 0.24 0.12
174_H 104_R 0.66 0.24 0.12
222_R 75_P 0.66 0.24 0.12
209_F 6_K 0.66 0.23 0.12
79_F 16_L 0.66 0.23 0.12
35_V 90_S 0.66 0.23 0.12
121_T 60_L 0.66 0.23 0.12
170_L 6_K 0.66 0.23 0.12
172_I 111_V 0.66 0.23 0.12
83_V 6_K 0.66 0.23 0.12
17_I 23_I 0.65 0.23 0.12
68_M 108_G 0.65 0.23 0.12
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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