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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 387
Sequences: 692 664 540
Seq/Len: 2.82 4.18 1.4
MirrorTree (Pazo et al. 2001) 0.91
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 0.15
2 0.00 0.00 0.91
5 0.00 0.00 1.03
10 0.00 0.00 1.09
20 0.00 0.00 1.09
100 0.00 0.00 1.12
∞ 0.01 0.01 1.34
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 2.43 1.00 0.98
49_Q 107_Q 1.63 0.91 0.81
185_Q 130_H 1.53 0.86 0.74
121_T 127_L 1.41 0.80 0.64
134_V 6_K 1.33 0.74 0.56
58_Y 148_R 1.31 0.72 0.54
185_Q 132_E 1.28 0.69 0.50
99_I 110_V 1.25 0.67 0.47
185_Q 131_D 1.23 0.65 0.45
87_K 5_R 1.23 0.65 0.45
55_R 110_V 1.22 0.64 0.43
9_A 4_R 1.18 0.60 0.40
182_T 27_L 1.17 0.59 0.39
183_L 63_G 1.16 0.58 0.37
188_T 130_H 1.14 0.57 0.36
236_S 68_P 1.13 0.56 0.35
185_Q 40_P 1.13 0.55 0.34
124_V 36_L 1.12 0.55 0.34
48_Y 104_R 1.10 0.53 0.32
185_Q 102_L 1.10 0.52 0.32
52_N 92_D 1.08 0.50 0.29
185_Q 63_G 1.08 0.50 0.29
65_I 36_L 1.05 0.47 0.27
8_L 95_Y 1.05 0.47 0.27
161_I 35_D 1.03 0.46 0.25
107_A 41_G 1.02 0.44 0.24
183_L 127_L 1.02 0.44 0.24
164_L 19_L 1.01 0.44 0.23
194_I 5_R 1.01 0.43 0.23
177_V 63_G 1.01 0.43 0.23
90_N 147_H 1.01 0.43 0.23
120_G 99_L 1.00 0.43 0.23
94_A 84_I 1.00 0.43 0.23
84_W 98_I 1.00 0.42 0.22
65_I 121_I 1.00 0.42 0.22
146_W 42_E 1.00 0.42 0.22
193_S 133_N 0.99 0.41 0.21
163_V 109_V 0.99 0.41 0.21
136_L 130_H 0.99 0.41 0.21
93_V 38_Y 0.98 0.40 0.21
195_D 139_V 0.98 0.40 0.21
174_H 104_R 0.98 0.40 0.21
112_S 88_E 0.98 0.40 0.20
79_F 19_L 0.96 0.38 0.19
128_R 103_F 0.95 0.37 0.18
166_G 127_L 0.95 0.37 0.18
54_Y 5_R 0.95 0.37 0.18
48_Y 107_Q 0.94 0.36 0.18
108_L 100_P 0.94 0.36 0.18
185_Q 135_T 0.92 0.35 0.16
133_L 123_A 0.92 0.34 0.16
188_T 40_P 0.91 0.34 0.16
131_S 128_A 0.91 0.33 0.15
57_I 130_H 0.90 0.33 0.15
103_F 118_G 0.90 0.33 0.15
27_I 75_P 0.90 0.33 0.15
116_K 77_S 0.90 0.33 0.15
129_L 19_L 0.90 0.33 0.15
170_L 67_M 0.89 0.32 0.14
69_G 60_L 0.88 0.31 0.14
107_A 80_V 0.88 0.31 0.13
208_G 59_R 0.88 0.31 0.13
96_M 72_Q 0.88 0.30 0.13
106_I 145_A 0.87 0.30 0.13
185_Q 108_G 0.87 0.30 0.13
13_R 71_V 0.87 0.30 0.13
47_D 63_G 0.86 0.29 0.13
62_P 80_V 0.86 0.29 0.12
91_L 42_E 0.85 0.28 0.12
177_V 130_H 0.84 0.28 0.12
80_I 115_L 0.84 0.28 0.11
25_L 81_T 0.84 0.28 0.11
136_L 70_S 0.84 0.27 0.11
211_L 17_A 0.84 0.27 0.11
113_A 36_L 0.84 0.27 0.11
142_V 121_I 0.83 0.27 0.11
121_T 29_A 0.83 0.27 0.11
89_A 22_T 0.83 0.27 0.11
188_T 132_E 0.83 0.27 0.11
92_A 121_I 0.83 0.27 0.11
219_M 12_A 0.82 0.26 0.10
9_A 3_I 0.82 0.26 0.10
154_L 112_Q 0.82 0.26 0.10
229_E 5_R 0.82 0.26 0.10
192_Q 27_L 0.81 0.26 0.10
94_A 75_P 0.81 0.26 0.10
129_L 104_R 0.81 0.26 0.10
50_Q 63_G 0.81 0.26 0.10
54_Y 132_E 0.81 0.25 0.10
35_V 20_A 0.81 0.25 0.10
157_R 98_I 0.81 0.25 0.10
112_S 117_K 0.81 0.25 0.10
63_A 133_N 0.80 0.25 0.10
183_L 131_D 0.80 0.25 0.09
157_R 56_V 0.80 0.24 0.09
198_M 142_A 0.80 0.24 0.09
122_W 75_P 0.80 0.24 0.09
220_R 124_K 0.80 0.24 0.09
219_M 89_G 0.80 0.24 0.09
168_V 90_S 0.80 0.24 0.09
96_M 71_V 0.80 0.24 0.09
83_V 118_G 0.80 0.24 0.09
83_V 9_L 0.80 0.24 0.09
78_A 44_L 0.79 0.24 0.09
227_L 92_D 0.79 0.24 0.09
55_R 136_P 0.79 0.24 0.09
188_T 131_D 0.79 0.24 0.09
118_M 107_Q 0.79 0.24 0.09
230_K 98_I 0.79 0.23 0.09
9_A 62_V 0.79 0.23 0.09
117_P 108_G 0.78 0.23 0.09
90_N 149_R 0.78 0.23 0.09
189_R 141_K 0.78 0.23 0.09
136_L 84_I 0.78 0.23 0.08
178_E 109_V 0.78 0.23 0.08
30_V 94_S 0.78 0.23 0.08
8_L 72_Q 0.77 0.23 0.08
14_L 121_I 0.77 0.22 0.08
204_W 111_V 0.77 0.22 0.08
118_M 130_H 0.77 0.22 0.08
181_N 42_E 0.77 0.22 0.08
5_L 87_A 0.76 0.22 0.08
106_I 114_E 0.76 0.22 0.08
35_V 119_N 0.76 0.22 0.08
153_R 111_V 0.76 0.22 0.08
34_T 41_G 0.76 0.22 0.08
164_L 120_H 0.76 0.22 0.08
133_L 99_L 0.76 0.22 0.08
182_T 126_V 0.76 0.22 0.08
10_I 4_R 0.76 0.21 0.07
12_P 4_R 0.75 0.21 0.07
47_D 102_L 0.75 0.21 0.07
168_V 93_V 0.75 0.21 0.07
31_V 44_L 0.75 0.21 0.07
68_M 57_G 0.74 0.21 0.07
137_F 76_N 0.74 0.21 0.07
168_V 20_A 0.74 0.20 0.07
62_P 63_G 0.74 0.20 0.07
229_E 73_R 0.74 0.20 0.07
137_F 131_D 0.74 0.20 0.07
38_I 28_Y 0.74 0.20 0.07
168_V 10_W 0.74 0.20 0.07
15_Y 5_R 0.73 0.20 0.07
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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