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OPENSEQ.org
ccme-ccmc
Genes: A B A+B
Length: 245 159 379
Sequences: 1704 856 655
Seq/Len: 6.96 5.38 1.73
MirrorTree (Pazo et al. 2001) 0.35
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 0.12 0.00 1.18
2 0.12 0.00 1.45
5 0.45 0.00 1.57
10 0.45 0.00 1.60
20 0.45 0.00 1.62
100 0.46 0.00 1.63
∞ 0.48 0.01 1.78
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
46_A 60_L 1.13 0.62 0.00
59_L 125_E 1.12 0.61 0.00
146_W 5_R 1.09 0.58 0.00
216_L 41_G 1.09 0.58 0.00
99_I 111_V 1.09 0.57 0.00
110_T 33_N 1.06 0.55 0.00
206_I 12_A 0.98 0.46 0.00
47_D 73_R 0.97 0.45 0.00
97_A 73_R 0.96 0.43 0.00
106_I 68_P 0.96 0.43 0.00
143_I 148_R 0.94 0.42 0.00
83_V 16_L 0.93 0.41 0.00
134_V 6_K 0.93 0.41 0.00
62_P 66_V 0.92 0.40 0.00
185_Q 130_H 0.92 0.39 0.00
141_G 71_V 0.91 0.39 0.00
122_W 126_V 0.88 0.36 0.00
162_L 101_D 0.86 0.34 0.00
207_F 74_D 0.85 0.33 0.00
183_L 127_L 0.84 0.32 0.00
32_V 19_L 0.84 0.32 0.00
202_L 33_N 0.84 0.32 0.00
102_V 84_I 0.82 0.30 0.00
58_Y 42_E 0.81 0.29 0.00
54_Y 130_H 0.80 0.28 0.00
55_R 62_V 0.79 0.28 0.00
158_A 62_V 0.79 0.27 0.00
184_H 60_L 0.78 0.26 0.00
208_G 29_A 0.78 0.26 0.00
122_W 133_N 0.78 0.26 0.00
188_T 124_K 0.78 0.26 0.00
224_L 109_V 0.77 0.26 0.00
54_Y 132_E 0.77 0.26 0.00
17_I 141_K 0.77 0.26 0.00
83_V 114_E 0.77 0.26 0.00
207_F 120_H 0.77 0.26 0.00
62_P 102_L 0.77 0.25 0.00
179_W 22_T 0.76 0.25 0.00
184_H 121_I 0.76 0.25 0.00
22_I 62_V 0.76 0.25 0.00
192_Q 131_D 0.76 0.25 0.00
85_Q 39_T 0.76 0.24 0.00
49_Q 107_Q 0.76 0.24 0.00
30_V 32_S 0.75 0.24 0.00
168_V 19_L 0.75 0.24 0.00
63_A 42_E 0.74 0.23 0.00
46_A 144_E 0.74 0.23 0.00
214_A 148_R 0.74 0.23 0.00
133_L 125_E 0.74 0.23 0.00
204_W 41_G 0.74 0.23 0.00
34_T 118_G 0.73 0.23 0.00
122_W 138_E 0.73 0.22 0.00
185_Q 131_D 0.73 0.22 0.00
57_I 35_D 0.72 0.22 0.00
204_W 72_Q 0.72 0.22 0.00
203_R 53_M 0.72 0.22 0.00
76_V 5_R 0.72 0.22 0.00
143_I 90_S 0.72 0.22 0.00
57_I 12_A 0.72 0.22 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.45 > 0.4) of paralogs.
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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