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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 384
Sequences: 2698 2773 1819
Seq/Len: 11.01 17.44 4.74
MirrorTree (Pazo et al. 2001) 0.90
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 3.30
5 0.00 0.00 3.63
10 0.00 0.00 3.84
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 2.30 1.00 0.99
124_V 36_L 1.51 0.98 0.92
46_A 137_P 1.36 0.96 0.87
121_T 127_L 1.34 0.96 0.86
185_Q 130_H 1.18 0.90 0.75
49_Q 107_Q 1.09 0.85 0.67
91_L 42_E 1.03 0.80 0.60
83_V 12_A 1.03 0.80 0.60
185_Q 131_D 1.00 0.77 0.56
87_K 5_R 0.99 0.77 0.56
188_T 130_H 0.94 0.71 0.49
117_P 102_L 0.94 0.71 0.49
185_Q 132_E 0.93 0.70 0.48
48_Y 107_Q 0.91 0.67 0.45
181_N 42_E 0.90 0.66 0.44
133_L 123_A 0.83 0.58 0.36
183_L 127_L 0.81 0.54 0.33
58_Y 148_R 0.81 0.54 0.33
185_Q 40_P 0.78 0.50 0.29
168_V 93_V 0.78 0.50 0.29
183_L 63_G 0.76 0.47 0.27
83_V 9_L 0.76 0.47 0.27
185_Q 108_G 0.76 0.47 0.27
172_I 96_E 0.74 0.45 0.25
170_L 104_R 0.73 0.43 0.24
62_P 63_G 0.73 0.43 0.24
14_L 121_I 0.72 0.42 0.23
96_M 71_V 0.72 0.42 0.23
131_S 128_A 0.72 0.42 0.23
9_A 3_I 0.72 0.41 0.23
48_Y 135_T 0.71 0.41 0.23
195_D 139_V 0.71 0.40 0.22
118_M 107_Q 0.70 0.39 0.21
56_I 128_A 0.70 0.39 0.21
94_A 75_P 0.70 0.39 0.21
4_T 112_Q 0.69 0.38 0.21
165_I 45_Y 0.69 0.38 0.20
120_G 99_L 0.69 0.38 0.20
48_Y 104_R 0.69 0.38 0.20
170_L 16_L 0.69 0.37 0.20
65_I 36_L 0.69 0.37 0.20
236_S 68_P 0.68 0.37 0.19
108_L 109_V 0.68 0.37 0.19
58_Y 42_E 0.68 0.36 0.19
185_Q 63_G 0.68 0.36 0.19
57_I 130_H 0.68 0.36 0.19
49_Q 109_V 0.67 0.35 0.18
90_N 26_V 0.67 0.35 0.18
117_P 63_G 0.66 0.34 0.18
136_L 130_H 0.66 0.34 0.17
118_M 105_E 0.66 0.34 0.17
79_F 12_A 0.66 0.34 0.17
10_I 5_R 0.65 0.33 0.17
118_M 130_H 0.65 0.33 0.17
156_G 109_V 0.65 0.33 0.17
27_I 72_Q 0.65 0.33 0.17
55_R 110_V 0.65 0.32 0.16
120_G 128_A 0.65 0.32 0.16
133_L 99_L 0.65 0.32 0.16
168_V 10_W 0.64 0.32 0.16
208_G 24_G 0.64 0.32 0.16
35_V 25_L 0.64 0.32 0.16
84_W 9_L 0.64 0.31 0.16
9_A 101_D 0.64 0.31 0.15
48_Y 109_V 0.64 0.31 0.15
44_A 137_P 0.63 0.31 0.15
136_L 15_V 0.63 0.31 0.15
136_L 132_E 0.63 0.30 0.15
133_L 101_D 0.63 0.30 0.15
130_T 61_R 0.62 0.30 0.14
7_Q 67_M 0.62 0.29 0.14
141_G 20_A 0.62 0.29 0.14
90_N 107_Q 0.62 0.29 0.14
124_V 125_E 0.61 0.29 0.14
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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