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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 359
Sequences: 1466 664 458
Seq/Len: 5.98 4.18 1.28
MirrorTree (Pazo et al. 2001) 0.38
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 1.13
2 0.01 0.00 1.28
5 0.42 0.00 1.39
10 0.42 0.00 1.41
20 0.42 0.00 1.41
100 0.43 0.00 1.42
∞ 0.47 0.01 1.49
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
139_Y 91_V 1.10 0.49 0.00
63_A 42_E 1.03 0.43 0.00
146_W 5_R 0.99 0.39 0.00
202_L 58_Q 0.94 0.35 0.00
47_D 73_R 0.94 0.34 0.00
55_R 62_V 0.92 0.33 0.00
110_T 33_N 0.92 0.32 0.00
83_V 38_Y 0.90 0.31 0.00
28_A 6_K 0.86 0.28 0.00
63_A 142_A 0.86 0.28 0.00
194_I 27_L 0.86 0.27 0.00
204_W 16_L 0.85 0.27 0.00
224_L 109_V 0.84 0.26 0.00
158_A 62_V 0.84 0.26 0.00
83_V 16_L 0.83 0.25 0.00
211_L 30_L 0.83 0.25 0.00
59_L 19_L 0.82 0.25 0.00
90_N 37_F 0.81 0.24 0.00
66_W 5_R 0.81 0.24 0.00
59_L 87_A 0.80 0.23 0.00
33_L 145_A 0.80 0.23 0.00
158_A 46_G 0.80 0.23 0.00
99_I 26_V 0.79 0.22 0.00
36_G 14_A 0.78 0.22 0.00
55_R 17_A 0.78 0.22 0.00
45_P 13_C 0.78 0.21 0.00
138_L 31_R 0.78 0.21 0.00
183_L 98_I 0.77 0.21 0.00
133_L 21_L 0.77 0.21 0.00
99_I 111_V 0.76 0.21 0.00
100_G 91_V 0.76 0.20 0.00
47_D 98_I 0.75 0.20 0.00
113_A 17_A 0.75 0.20 0.00
183_L 17_A 0.75 0.20 0.00
56_I 61_R 0.75 0.20 0.00
79_F 84_I 0.75 0.20 0.00
85_Q 6_K 0.74 0.19 0.00
33_L 68_P 0.74 0.19 0.00
110_T 3_I 0.74 0.19 0.00
212_L 118_G 0.74 0.19 0.00
198_M 20_A 0.74 0.19 0.00
149_F 5_R 0.73 0.19 0.00
74_M 142_A 0.73 0.19 0.00
158_A 5_R 0.73 0.19 0.00
197_A 133_N 0.73 0.18 0.00
206_I 12_A 0.73 0.18 0.00
141_G 71_V 0.73 0.18 0.00
133_L 31_R 0.72 0.18 0.00
209_F 58_Q 0.71 0.17 0.00
206_I 54_P 0.71 0.17 0.00
99_I 94_S 0.70 0.17 0.00
59_L 44_L 0.70 0.17 0.00
120_G 64_G 0.70 0.17 0.00
186_G 70_S 0.69 0.17 0.00
169_N 112_Q 0.69 0.16 0.00
54_Y 132_E 0.69 0.16 0.00
100_G 124_K 0.69 0.16 0.00
209_F 59_R 0.69 0.16 0.00
79_F 81_T 0.68 0.16 0.00
98_P 144_E 0.68 0.16 0.00
191_Q 80_V 0.68 0.16 0.00
173_I 135_T 0.68 0.16 0.00
133_L 125_E 0.68 0.16 0.00
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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