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OPENSEQ.org
cCmCE
Genes: A B A+B
Length: 245 159 354
Sequences: 883 933 557
Seq/Len: 3.6 5.87 1.57
MirrorTree (Pazo et al. 2001) 0.93
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.11 0.21
2 0.00 0.11 1.20
5 0.00 0.11 1.30
10 0.00 0.11 1.37
20 0.01 0.11 1.38
100 0.01 0.11 1.42
∞ 0.02 0.12 1.68
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 2.08 0.99 0.95
185_Q 130_H 1.46 0.85 0.67
49_Q 107_Q 1.42 0.83 0.64
34_T 12_A 1.27 0.72 0.49
185_Q 131_D 1.23 0.69 0.45
93_V 38_Y 1.21 0.67 0.43
183_L 127_L 1.18 0.64 0.40
87_K 5_R 1.18 0.63 0.39
65_I 36_L 1.15 0.61 0.36
133_L 123_A 1.14 0.60 0.36
153_R 60_L 1.14 0.59 0.35
110_T 26_V 1.14 0.59 0.35
116_K 15_V 1.13 0.59 0.34
118_M 107_Q 1.11 0.57 0.33
185_Q 132_E 1.11 0.57 0.32
121_T 127_L 1.09 0.54 0.30
129_L 19_L 1.07 0.53 0.29
78_A 21_L 1.04 0.50 0.26
109_V 41_G 1.04 0.50 0.26
160_G 114_E 1.03 0.48 0.25
164_L 7_N 1.02 0.47 0.24
78_A 44_L 1.02 0.47 0.24
129_L 104_R 1.01 0.47 0.23
79_F 12_A 1.01 0.47 0.23
65_I 35_D 1.01 0.47 0.23
188_T 130_H 1.00 0.45 0.23
35_V 25_L 0.98 0.43 0.20
214_A 62_V 0.98 0.43 0.20
54_Y 5_R 0.97 0.42 0.20
194_I 81_T 0.97 0.42 0.20
35_V 119_N 0.96 0.41 0.19
59_L 111_V 0.96 0.41 0.19
93_V 93_V 0.95 0.41 0.19
107_A 115_L 0.95 0.40 0.19
236_S 21_L 0.94 0.39 0.18
70_I 133_N 0.94 0.39 0.18
121_T 29_A 0.94 0.39 0.18
91_L 26_V 0.94 0.39 0.18
142_V 3_I 0.93 0.39 0.17
72_A 39_T 0.93 0.38 0.17
35_V 20_A 0.93 0.38 0.17
94_A 84_I 0.93 0.38 0.17
62_P 80_V 0.92 0.37 0.16
211_L 120_H 0.91 0.37 0.16
107_A 80_V 0.91 0.37 0.16
101_A 127_L 0.91 0.36 0.16
154_L 19_L 0.91 0.36 0.16
79_F 60_L 0.91 0.36 0.15
157_R 91_V 0.91 0.36 0.15
57_I 22_T 0.90 0.36 0.15
156_G 68_P 0.90 0.35 0.15
229_E 5_R 0.89 0.35 0.15
38_I 30_L 0.89 0.34 0.14
90_N 18_G 0.89 0.34 0.14
138_L 99_L 0.89 0.34 0.14
214_A 116_E 0.88 0.33 0.14
90_N 83_T 0.88 0.33 0.14
146_W 42_E 0.87 0.32 0.13
151_D 84_I 0.86 0.32 0.13
173_I 105_E 0.86 0.32 0.13
163_V 109_V 0.86 0.32 0.13
183_L 63_G 0.86 0.32 0.13
157_R 94_S 0.86 0.31 0.13
167_V 20_A 0.86 0.31 0.13
210_L 62_V 0.86 0.31 0.12
227_L 74_D 0.85 0.31 0.12
128_R 103_F 0.85 0.31 0.12
163_V 133_N 0.85 0.31 0.12
175_Y 43_I 0.85 0.31 0.12
223_N 122_L 0.85 0.31 0.12
76_V 124_K 0.85 0.30 0.12
189_R 30_L 0.85 0.30 0.12
73_S 6_K 0.85 0.30 0.12
221_M 34_I 0.85 0.30 0.12
69_G 60_L 0.84 0.30 0.12
67_S 133_N 0.84 0.30 0.12
223_N 74_D 0.84 0.30 0.12
96_M 71_V 0.84 0.30 0.12
96_M 72_Q 0.84 0.30 0.12
71_Y 125_E 0.84 0.30 0.12
189_R 39_T 0.84 0.30 0.12
154_L 112_Q 0.84 0.29 0.11
104_T 37_F 0.83 0.29 0.11
185_Q 102_L 0.83 0.29 0.11
107_A 37_F 0.83 0.29 0.11
157_R 93_V 0.82 0.28 0.11
185_Q 63_G 0.82 0.28 0.11
215_T 84_I 0.82 0.28 0.11
153_R 14_A 0.82 0.28 0.11
212_L 41_G 0.82 0.28 0.10
213_S 18_G 0.82 0.28 0.10
106_I 114_E 0.82 0.28 0.10
99_I 110_V 0.81 0.28 0.10
226_L 21_L 0.81 0.27 0.10
182_T 27_L 0.81 0.27 0.10
124_V 36_L 0.81 0.27 0.10
167_V 42_E 0.81 0.27 0.10
164_L 17_A 0.81 0.27 0.10
76_V 118_G 0.81 0.27 0.10
162_L 99_L 0.80 0.27 0.10
159_A 67_M 0.80 0.27 0.10
92_A 88_E 0.80 0.27 0.10
193_S 34_I 0.80 0.26 0.10
52_N 65_M 0.80 0.26 0.10
31_V 45_Y 0.80 0.26 0.10
86_M 15_V 0.80 0.26 0.10
144_A 37_F 0.80 0.26 0.09
177_V 130_H 0.80 0.26 0.09
190_M 37_F 0.80 0.26 0.09
47_D 102_L 0.79 0.26 0.09
169_N 132_E 0.79 0.26 0.09
120_G 135_T 0.79 0.26 0.09
75_A 22_T 0.79 0.26 0.09
176_S 66_V 0.79 0.25 0.09
40_G 42_E 0.79 0.25 0.09
170_L 67_M 0.79 0.25 0.09
166_G 43_I 0.79 0.25 0.09
236_S 65_M 0.79 0.25 0.09
90_N 4_R 0.78 0.25 0.09
94_A 109_V 0.78 0.25 0.09
210_L 48_R 0.78 0.25 0.09
116_K 83_T 0.78 0.25 0.09
84_W 111_V 0.78 0.25 0.09
170_L 71_V 0.78 0.25 0.09
136_L 130_H 0.78 0.25 0.09
47_D 63_G 0.78 0.24 0.09
236_S 111_V 0.77 0.24 0.09
162_L 18_G 0.77 0.24 0.08
116_K 12_A 0.77 0.24 0.08
131_S 128_A 0.77 0.24 0.08
125_W 97_G 0.77 0.24 0.08
185_Q 108_G 0.77 0.24 0.08
154_L 35_D 0.77 0.24 0.08
161_I 83_T 0.77 0.24 0.08
211_L 31_R 0.77 0.24 0.08
53_S 16_L 0.77 0.24 0.08
134_V 27_L 0.77 0.24 0.08
229_E 73_R 0.77 0.24 0.08
188_T 37_F 0.77 0.24 0.08
65_I 121_I 0.77 0.24 0.08
164_L 19_L 0.77 0.24 0.08
168_V 42_E 0.77 0.24 0.08
28_A 88_E 0.76 0.24 0.08
133_L 101_D 0.76 0.23 0.08
129_L 107_Q 0.76 0.23 0.08
85_Q 112_Q 0.76 0.23 0.08
112_S 12_A 0.76 0.23 0.08
133_L 128_A 0.76 0.23 0.08
159_A 60_L 0.76 0.23 0.08
161_I 57_G 0.76 0.23 0.08
177_V 63_G 0.76 0.23 0.08
140_V 44_L 0.75 0.23 0.08
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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