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OPENSEQ.org
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Genes: A B A+B
Length: 245 69 273
Sequences: 883 433 306
Seq/Len: 3.6 6.28 1.12
MirrorTree (Pazo et al. 2001) 0.76
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 0.00 0.97
2 0.00 0.00 0.97
5 0.00 0.00 0.97
10 0.00 0.00 0.97
20 0.01 0.01 0.97
100 0.01 0.01 0.97
∞ 0.02 0.01 0.97
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
118_M 17_Y 3.00 1.00 1.00
52_N 17_Y 2.27 0.99 0.97
42_G 3_P 1.84 0.94 0.88
102_V 31_P 1.75 0.91 0.84
59_L 28_T 1.52 0.81 0.68
102_V 35_L 1.48 0.79 0.65
41_F 25_V 1.44 0.76 0.61
132_E 17_Y 1.43 0.75 0.59
54_Y 53_Q 1.37 0.70 0.53
105_F 27_M 1.33 0.68 0.50
200_S 25_V 1.32 0.67 0.49
113_A 23_L 1.31 0.65 0.47
129_L 15_G 1.28 0.63 0.44
210_L 17_Y 1.27 0.62 0.43
136_L 53_Q 1.22 0.57 0.38
112_S 3_P 1.22 0.57 0.38
122_W 20_F 1.21 0.56 0.37
109_V 27_M 1.18 0.53 0.33
223_N 46_I 1.15 0.51 0.31
236_S 57_E 1.14 0.50 0.30
113_A 27_M 1.14 0.49 0.29
78_A 27_M 1.10 0.46 0.26
24_W 44_R 1.09 0.45 0.26
216_L 36_V 1.05 0.42 0.22
142_V 56_R 1.05 0.42 0.22
78_A 32_L 1.05 0.41 0.22
34_T 45_A 1.04 0.40 0.21
39_W 5_F 1.03 0.39 0.20
221_M 46_I 1.01 0.38 0.19
216_L 32_L 1.01 0.38 0.19
167_V 59_R 0.99 0.36 0.17
110_T 24_A 0.97 0.34 0.16
74_M 16_G 0.96 0.34 0.15
67_S 17_Y 0.95 0.33 0.15
211_L 57_E 0.94 0.31 0.14
219_M 39_S 0.93 0.31 0.14
34_T 18_A 0.93 0.31 0.14
122_W 19_F 0.93 0.31 0.13
199_R 17_Y 0.93 0.31 0.13
43_F 5_F 0.92 0.30 0.13
149_F 35_L 0.92 0.29 0.13
53_S 7_S 0.92 0.29 0.12
134_V 37_V 0.91 0.29 0.12
87_K 12_F 0.91 0.29 0.12
31_V 30_I 0.91 0.29 0.12
187_S 6_A 0.90 0.28 0.12
105_F 47_L 0.90 0.28 0.12
143_I 32_L 0.90 0.28 0.12
201_P 5_F 0.89 0.27 0.11
208_G 18_A 0.88 0.27 0.11
215_T 18_A 0.88 0.27 0.11
63_A 39_S 0.88 0.26 0.10
121_T 52_Q 0.87 0.26 0.10
38_I 5_F 0.87 0.26 0.10
31_V 36_V 0.86 0.25 0.10
170_L 58_A 0.86 0.25 0.10
59_L 25_V 0.86 0.25 0.10
187_S 3_P 0.86 0.25 0.10
33_L 56_R 0.85 0.25 0.09
159_A 15_G 0.85 0.24 0.09
122_W 52_Q 0.85 0.24 0.09
109_V 29_V 0.85 0.24 0.09
96_M 31_P 0.84 0.24 0.09
201_P 35_L 0.84 0.24 0.09
26_A 37_V 0.84 0.24 0.09
94_A 19_F 0.84 0.24 0.09
85_Q 35_L 0.84 0.24 0.09
30_V 38_H 0.84 0.24 0.09
112_S 58_A 0.83 0.23 0.09
161_I 49_G 0.83 0.23 0.08
91_L 50_V 0.82 0.23 0.08
150_D 24_A 0.82 0.23 0.08
30_V 52_Q 0.82 0.22 0.08
161_I 8_W 0.82 0.22 0.08
88_M 25_V 0.82 0.22 0.08
163_V 4_A 0.82 0.22 0.08
73_S 50_V 0.82 0.22 0.08
103_F 25_V 0.81 0.22 0.08
42_G 18_A 0.81 0.22 0.08
112_S 36_V 0.81 0.22 0.08
65_I 5_F 0.81 0.22 0.07
161_I 54_R 0.81 0.22 0.07
104_T 32_L 0.81 0.22 0.07
78_A 17_Y 0.81 0.22 0.07
43_F 29_V 0.81 0.21 0.07
106_I 19_F 0.80 0.21 0.07
177_V 14_M 0.80 0.21 0.07
57_I 3_P 0.80 0.21 0.07
200_S 44_R 0.80 0.21 0.07
81_G 52_Q 0.80 0.21 0.07
204_W 12_F 0.79 0.21 0.07
127_A 14_M 0.79 0.21 0.07
65_I 23_L 0.79 0.20 0.07
44_A 15_G 0.79 0.20 0.07
134_V 51_A 0.79 0.20 0.07
44_A 20_F 0.78 0.20 0.07
59_L 26_V 0.78 0.20 0.07
49_Q 17_Y 0.78 0.20 0.07
143_I 27_M 0.78 0.20 0.07
27_I 48_R 0.78 0.20 0.07
118_M 16_G 0.78 0.20 0.07
99_I 35_L 0.78 0.20 0.07
34_T 40_V 0.77 0.19 0.06
49_Q 15_G 0.77 0.19 0.06
212_L 5_F 0.76 0.19 0.06
29_S 31_P 0.76 0.19 0.06
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
8058 1.12 checkback Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
7036 2.54 CCMC_CCMD Δgene:(1, 1) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 1.00 Done
7035 2.74 CCMC_CCMD Δgene:(1, 2) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 1.00 Done
1101 0.89 CCMC_CCMD Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.99 Done
1052 0.89 CCMC_CCMD Δgene:(1, 5) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2014_03) 0.98 Done
1050 0.91 CCMC_CCMD Δgene:(1, 5) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.94 Done
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