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OPENSEQ.org
cI_6_60_cI_9_60_tt
Genes: A B A+B
Length: 181 182 305
Sequences: 850 289 170
Seq/Len: 4.7 1.59 0.56
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 0.01 0.00 0.39
20 0.01 0.00 0.40
100 0.02 0.00 0.42
∞ 0.04 0.00 0.47
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 2.37 0.96 0.86
85_S 66_Y 1.72 0.75 0.43
85_S 143_T 1.72 0.75 0.43
21_F 24_V 1.63 0.69 0.35
75_A 74_E 1.49 0.59 0.25
103_K 147_R 1.36 0.48 0.17
27_L 10_L 1.34 0.47 0.16
60_L 8_Q 1.30 0.44 0.14
16_R 17_L 1.30 0.44 0.14
159_R 103_L 1.30 0.44 0.14
100_P 150_A 1.29 0.43 0.13
85_S 139_D 1.28 0.43 0.13
56_A 16_Y 1.27 0.42 0.12
16_R 15_K 1.26 0.41 0.12
56_A 122_A 1.23 0.39 0.11
36_L 107_A 1.22 0.38 0.10
75_A 33_L 1.21 0.37 0.10
21_F 62_A 1.20 0.37 0.10
15_E 62_A 1.18 0.35 0.09
56_A 112_A 1.17 0.34 0.09
65_S 121_M 1.16 0.33 0.08
70_A 21_P 1.15 0.33 0.08
100_P 47_P 1.14 0.32 0.07
14_L 15_K 1.14 0.32 0.07
52_A 121_M 1.14 0.32 0.07
103_K 4_K 1.14 0.32 0.07
85_S 40_R 1.13 0.32 0.07
28_V 48_N 1.13 0.31 0.07
20_L 73_A 1.12 0.31 0.07
26_K 134_E 1.12 0.31 0.07
24_L 138_V 1.11 0.30 0.07
122_A 85_E 1.11 0.30 0.07
19_I 103_L 1.10 0.29 0.06
152_M 24_V 1.10 0.29 0.06
135_V 3_L 1.10 0.29 0.06
70_A 3_L 1.09 0.28 0.06
94_R 11_G 1.08 0.28 0.06
20_L 62_A 1.07 0.28 0.06
55_D 156_P 1.07 0.28 0.06
106_I 123_D 1.07 0.28 0.06
85_S 118_D 1.07 0.27 0.06
19_I 21_P 1.06 0.27 0.06
77_V 15_K 1.04 0.25 0.05
20_L 121_M 1.04 0.25 0.05
106_I 69_Y 1.03 0.25 0.05
119_N 69_Y 1.02 0.24 0.05
150_A 52_K 1.02 0.24 0.04
101_D 5_A 1.01 0.24 0.04
56_A 85_E 1.01 0.24 0.04
26_K 17_L 1.01 0.24 0.04
104_W 5_A 1.00 0.23 0.04
156_K 143_T 1.00 0.23 0.04
77_V 100_F 0.99 0.23 0.04
60_L 130_V 0.99 0.23 0.04
53_S 135_D 0.99 0.23 0.04
150_A 55_G 0.99 0.23 0.04
77_V 73_A 0.98 0.22 0.04
70_A 16_Y 0.97 0.21 0.04
34_N 48_N 0.96 0.21 0.03
104_W 141_V 0.95 0.21 0.03
60_L 105_E 0.95 0.21 0.03
20_L 20_K 0.94 0.20 0.03
77_V 69_Y 0.94 0.20 0.03
26_K 107_A 0.94 0.20 0.03
63_F 128_D 0.94 0.20 0.03
36_L 119_F 0.94 0.20 0.03
62_R 134_E 0.93 0.20 0.03
158_V 21_P 0.93 0.20 0.03
130_V 100_F 0.93 0.20 0.03
34_N 6_L 0.93 0.20 0.03
161_Q 31_V 0.93 0.19 0.03
104_W 100_F 0.92 0.19 0.03
135_V 19_S 0.91 0.19 0.03
77_V 126_Y 0.91 0.19 0.03
77_V 89_K 0.90 0.18 0.03
21_F 72_P 0.90 0.18 0.03
17_E 15_K 0.90 0.18 0.03
22_T 105_E 0.90 0.18 0.03
152_M 143_T 0.90 0.18 0.03
52_A 32_A 0.90 0.18 0.03
22_T 132_G 0.90 0.18 0.03
31_G 21_P 0.90 0.18 0.03
13_E 121_M 0.89 0.18 0.03
151_V 10_L 0.89 0.18 0.03
27_L 69_Y 0.89 0.17 0.03
75_A 15_K 0.89 0.17 0.03
75_A 3_L 0.88 0.17 0.03
148_I 138_V 0.88 0.17 0.02
153_Q 35_P 0.88 0.17 0.02
60_L 126_Y 0.88 0.17 0.02
27_L 61_A 0.88 0.17 0.02
20_L 12_I 0.87 0.17 0.02
135_V 16_Y 0.87 0.17 0.02
56_A 21_P 0.87 0.17 0.02
67_V 142_G 0.87 0.17 0.02
135_V 115_L 0.87 0.17 0.02
26_K 10_L 0.86 0.16 0.02
67_V 22_V 0.86 0.16 0.02
153_Q 105_E 0.86 0.16 0.02
129_S 155_K 0.86 0.16 0.02
32_R 100_F 0.86 0.16 0.02
104_W 127_S 0.86 0.16 0.02
68_F 25_P 0.86 0.16 0.02
38_P 13_T 0.85 0.16 0.02
156_K 126_Y 0.85 0.16 0.02
160_G 124_Y 0.85 0.16 0.02
21_F 154_G 0.84 0.15 0.02
52_A 90_V 0.83 0.15 0.02
26_K 138_V 0.83 0.15 0.02
70_A 28_D 0.83 0.15 0.02
152_M 66_Y 0.83 0.15 0.02
36_L 112_A 0.83 0.15 0.02
159_R 157_V 0.82 0.15 0.02
56_A 14_L 0.82 0.15 0.02
152_M 31_V 0.82 0.15 0.02
18_G 28_D 0.82 0.15 0.02
151_V 155_K 0.82 0.15 0.02
56_A 153_T 0.82 0.15 0.02
165_E 131_Y 0.82 0.15 0.02
159_R 119_F 0.82 0.14 0.02
106_I 127_S 0.82 0.14 0.02
36_L 135_D 0.81 0.14 0.02
153_Q 154_G 0.81 0.14 0.02
20_L 74_E 0.81 0.14 0.02
21_F 112_A 0.81 0.14 0.02
152_M 28_D 0.81 0.14 0.02
144_P 47_P 0.81 0.14 0.02
150_A 144_K 0.80 0.14 0.02
77_V 131_Y 0.80 0.14 0.02
38_P 14_L 0.80 0.14 0.02
152_M 90_V 0.80 0.14 0.02
52_A 11_G 0.80 0.14 0.02
135_V 123_D 0.79 0.14 0.02
67_V 6_L 0.79 0.14 0.02
56_A 156_P 0.79 0.14 0.02
85_S 116_G 0.79 0.14 0.02
24_L 126_Y 0.79 0.13 0.01
37_W 13_T 0.79 0.13 0.01
18_G 126_Y 0.79 0.13 0.01
17_E 10_L 0.79 0.13 0.01
26_K 20_K 0.79 0.13 0.01
148_I 20_K 0.78 0.13 0.01
38_P 6_L 0.78 0.13 0.01
53_S 128_D 0.78 0.13 0.01
150_A 44_T 0.78 0.13 0.01
150_A 46_H 0.78 0.13 0.01
135_V 2_T 0.78 0.13 0.01
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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