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OPENSEQ.org
cI_6_20_cI_9_60_tt
Genes: A B A+B
Length: 181 182 306
Sequences: 1141 289 174
Seq/Len: 6.3 1.59 0.57
MirrorTree (Pazo et al. 2001) 0.62
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 0.01 0.00 0.00
2 0.01 0.00 0.01
5 0.01 0.00 0.03
10 0.02 0.00 0.39
20 0.02 0.00 0.42
100 0.03 0.00 0.42
∞ 0.08 0.00 0.48
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
56_A 22_V 1.85 0.82 0.08
85_S 66_Y 1.68 0.73 0.05
85_S 143_T 1.65 0.71 0.05
21_F 24_V 1.65 0.71 0.05
77_V 126_Y 1.39 0.52 0.02
75_A 74_E 1.39 0.52 0.02
152_M 10_L 1.37 0.50 0.02
122_A 85_E 1.36 0.49 0.02
103_K 147_R 1.32 0.46 0.02
60_L 8_Q 1.28 0.43 0.02
131_V 147_R 1.27 0.42 0.01
85_S 139_D 1.25 0.40 0.01
56_A 112_A 1.25 0.40 0.01
100_P 150_A 1.25 0.40 0.01
52_A 121_M 1.24 0.39 0.01
13_E 121_M 1.23 0.39 0.01
16_R 15_K 1.23 0.39 0.01
21_F 62_A 1.22 0.39 0.01
75_A 33_L 1.20 0.37 0.01
71_S 90_V 1.20 0.36 0.01
106_I 123_D 1.19 0.36 0.01
28_V 48_N 1.16 0.34 0.01
94_R 11_G 1.15 0.33 0.01
77_V 15_K 1.15 0.33 0.01
24_L 138_V 1.14 0.32 0.01
20_L 62_A 1.13 0.32 0.01
85_S 40_R 1.12 0.31 0.01
56_A 85_E 1.12 0.31 0.01
16_R 17_L 1.11 0.30 0.01
104_W 134_E 1.09 0.29 0.01
77_V 89_K 1.09 0.29 0.01
63_F 130_V 1.08 0.28 0.01
103_K 4_K 1.07 0.28 0.01
16_R 155_K 1.07 0.28 0.01
36_L 107_A 1.06 0.27 0.01
26_K 10_L 1.06 0.27 0.01
159_R 157_V 1.05 0.27 0.01
15_E 62_A 1.05 0.27 0.01
100_P 47_P 1.04 0.26 0.01
104_W 5_A 1.04 0.26 0.01
85_S 118_D 1.04 0.26 0.01
65_S 121_M 1.03 0.25 0.01
70_A 21_P 1.03 0.25 0.01
161_Q 31_V 1.03 0.25 0.01
19_I 21_P 1.03 0.25 0.01
56_A 21_P 1.02 0.25 0.01
150_A 55_G 1.02 0.25 0.01
68_F 25_P 1.01 0.24 0.01
70_A 16_Y 1.00 0.23 0.01
106_I 127_S 0.99 0.23 0.01
24_L 126_Y 0.98 0.23 0.01
77_V 100_F 0.98 0.23 0.01
27_L 69_Y 0.98 0.22 0.01
33_S 14_L 0.97 0.22 0.01
40_T 141_V 0.97 0.22 0.01
60_L 15_K 0.96 0.21 0.01
159_R 103_L 0.96 0.21 0.01
26_K 20_K 0.96 0.21 0.01
101_D 5_A 0.96 0.21 0.01
20_L 73_A 0.96 0.21 0.01
70_A 28_D 0.95 0.21 0.01
22_T 105_E 0.95 0.21 0.01
63_F 128_D 0.94 0.20 0.01
52_A 32_A 0.94 0.20 0.01
20_L 12_I 0.94 0.20 0.01
60_L 7_A 0.94 0.20 0.01
27_L 10_L 0.93 0.20 0.01
56_A 122_A 0.93 0.20 0.01
106_I 69_Y 0.93 0.20 0.01
54_T 135_D 0.93 0.20 0.01
47_A 75_N 0.93 0.20 0.01
104_W 127_S 0.92 0.19 0.01
21_F 72_P 0.92 0.19 0.01
164_N 128_D 0.92 0.19 0.01
77_V 69_Y 0.92 0.19 0.01
104_W 100_F 0.91 0.19 0.01
156_K 143_T 0.91 0.19 0.01
130_V 100_F 0.91 0.19 0.00
24_L 20_K 0.91 0.19 0.00
56_A 16_Y 0.90 0.18 0.00
34_N 6_L 0.90 0.18 0.00
153_Q 105_E 0.90 0.18 0.00
20_L 121_M 0.90 0.18 0.00
38_P 6_L 0.88 0.17 0.00
18_G 126_Y 0.88 0.17 0.00
55_D 20_K 0.88 0.17 0.00
153_Q 35_P 0.88 0.17 0.00
62_R 134_E 0.87 0.17 0.00
25_E 155_K 0.87 0.17 0.00
26_K 138_V 0.87 0.17 0.00
28_V 25_P 0.87 0.17 0.00
77_V 124_Y 0.87 0.17 0.00
148_I 138_V 0.86 0.17 0.00
67_V 142_G 0.86 0.17 0.00
155_Q 10_L 0.86 0.16 0.00
60_L 105_E 0.86 0.16 0.00
16_R 130_V 0.86 0.16 0.00
26_K 17_L 0.85 0.16 0.00
21_F 14_L 0.85 0.16 0.00
100_P 25_P 0.85 0.16 0.00
36_L 119_F 0.85 0.16 0.00
8_E 146_Q 0.85 0.16 0.00
47_A 152_R 0.84 0.16 0.00
122_A 100_F 0.84 0.15 0.00
14_L 38_H 0.83 0.15 0.00
53_S 128_D 0.83 0.15 0.00
26_K 134_E 0.83 0.15 0.00
160_G 17_L 0.83 0.15 0.00
135_V 2_T 0.82 0.15 0.00
38_P 13_T 0.82 0.15 0.00
18_G 8_Q 0.82 0.15 0.00
27_L 125_E 0.82 0.15 0.00
153_Q 10_L 0.82 0.15 0.00
70_A 75_N 0.82 0.15 0.00
52_A 90_V 0.82 0.15 0.00
52_A 11_G 0.82 0.15 0.00
67_V 6_L 0.82 0.15 0.00
67_V 22_V 0.81 0.14 0.00
32_R 100_F 0.81 0.14 0.00
129_S 155_K 0.81 0.14 0.00
23_T 154_G 0.81 0.14 0.00
60_L 20_K 0.81 0.14 0.00
55_D 47_P 0.81 0.14 0.00
53_S 32_A 0.81 0.14 0.00
60_L 12_I 0.81 0.14 0.00
150_A 44_T 0.81 0.14 0.00
150_A 46_H 0.81 0.14 0.00
25_E 12_I 0.80 0.14 0.00
77_V 131_Y 0.80 0.14 0.00
101_D 156_P 0.80 0.14 0.00
85_S 127_S 0.80 0.14 0.00
27_L 138_V 0.80 0.14 0.00
20_L 74_E 0.80 0.14 0.00
104_W 15_K 0.80 0.14 0.00
14_L 47_P 0.80 0.14 0.00
37_W 13_T 0.80 0.14 0.00
20_L 149_E 0.79 0.14 0.00
159_R 119_F 0.79 0.14 0.00
156_K 151_K 0.79 0.14 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
4979 0.57 cI_6_20_cI_9_60_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
4978 0.56 cI_6_60_cI_9_60_tt Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4977 0.56 cI_6_40_cI_9_60_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.90 Done - Shared
4976 2.08 cI_6_40_cI_9_20_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.45 Done - Shared
4975 1.47 cI_6_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.64 Done - Shared
4974 1.46 cI_6_20_cI_9_40_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.63 Done - Shared
4972 1.85 cI_6_20_cI_9_10_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.35 Done - Shared
4971 2.05 cI_6_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.59 Done - Shared
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