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OPENSEQ.org
cI_6_40_cI_9_60_tt
Genes: A B A+B
Length: 181 182 305
Sequences: 1163 289 170
Seq/Len: 6.43 1.59 0.56
MirrorTree (Pazo et al. 2001) 0.52
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 0.40
100 0.03 0.00 0.42
∞ 0.08 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 2.44 0.97 0.90
85_S 66_Y 1.72 0.75 0.47
28_V 48_N 1.62 0.68 0.38
85_S 143_T 1.61 0.68 0.37
103_K 147_R 1.57 0.65 0.34
16_R 17_L 1.46 0.56 0.25
21_F 62_A 1.45 0.56 0.25
75_A 33_L 1.40 0.52 0.21
21_F 24_V 1.34 0.47 0.18
159_R 103_L 1.30 0.44 0.15
27_L 10_L 1.29 0.43 0.15
100_P 150_A 1.27 0.42 0.14
75_A 74_E 1.26 0.41 0.13
52_A 121_M 1.25 0.40 0.13
122_A 85_E 1.20 0.36 0.10
85_S 139_D 1.19 0.36 0.10
100_P 47_P 1.18 0.35 0.10
60_L 8_Q 1.18 0.35 0.10
85_S 40_R 1.15 0.33 0.09
65_S 121_M 1.14 0.32 0.09
22_T 130_V 1.13 0.32 0.08
94_R 11_G 1.13 0.31 0.08
26_K 17_L 1.12 0.31 0.08
151_V 10_L 1.11 0.30 0.07
20_L 73_A 1.11 0.30 0.07
106_I 123_D 1.11 0.30 0.07
16_R 15_K 1.09 0.29 0.07
150_A 52_K 1.08 0.28 0.07
56_A 16_Y 1.08 0.28 0.07
56_A 122_A 1.07 0.28 0.06
131_V 147_R 1.06 0.27 0.06
19_I 103_L 1.06 0.27 0.06
130_V 100_F 1.05 0.26 0.06
150_A 55_G 1.05 0.26 0.06
24_L 138_V 1.04 0.26 0.06
20_L 121_M 1.04 0.25 0.06
104_W 134_E 1.03 0.25 0.05
67_V 142_G 1.01 0.24 0.05
161_Q 31_V 1.01 0.24 0.05
36_L 119_F 1.01 0.24 0.05
148_I 138_V 1.00 0.23 0.05
77_V 126_Y 1.00 0.23 0.05
63_F 128_D 1.00 0.23 0.05
85_S 118_D 1.00 0.23 0.05
13_E 121_M 0.99 0.23 0.04
70_A 3_L 0.99 0.23 0.04
21_F 72_P 0.99 0.23 0.04
105_V 106_E 0.98 0.22 0.04
153_Q 154_G 0.98 0.22 0.04
68_F 25_P 0.98 0.22 0.04
20_L 20_K 0.97 0.22 0.04
19_I 21_P 0.97 0.22 0.04
77_V 89_K 0.95 0.21 0.04
104_W 5_A 0.95 0.21 0.04
26_K 138_V 0.95 0.20 0.04
52_A 32_A 0.95 0.20 0.04
103_K 4_K 0.95 0.20 0.04
77_V 100_F 0.94 0.20 0.04
153_Q 35_P 0.94 0.20 0.04
70_A 21_P 0.94 0.20 0.04
21_F 154_G 0.93 0.20 0.03
33_S 126_Y 0.93 0.20 0.03
122_A 100_F 0.93 0.19 0.03
27_L 61_A 0.93 0.19 0.03
70_A 28_D 0.93 0.19 0.03
156_K 126_Y 0.91 0.19 0.03
56_A 85_E 0.91 0.19 0.03
77_V 15_K 0.91 0.19 0.03
63_F 105_E 0.91 0.19 0.03
22_T 19_S 0.91 0.18 0.03
56_A 112_A 0.91 0.18 0.03
106_I 69_Y 0.90 0.18 0.03
28_V 32_A 0.90 0.18 0.03
62_R 134_E 0.89 0.18 0.03
144_P 47_P 0.89 0.18 0.03
26_K 107_A 0.88 0.17 0.03
28_V 132_G 0.88 0.17 0.03
77_V 131_Y 0.86 0.16 0.03
164_N 131_Y 0.86 0.16 0.02
106_I 127_S 0.86 0.16 0.02
77_V 69_Y 0.86 0.16 0.02
14_L 38_H 0.85 0.16 0.02
150_A 144_K 0.85 0.16 0.02
70_A 75_N 0.85 0.16 0.02
47_A 75_N 0.85 0.16 0.02
15_E 62_A 0.85 0.16 0.02
36_L 107_A 0.84 0.16 0.02
135_V 76_D 0.84 0.16 0.02
17_E 15_K 0.84 0.16 0.02
150_A 44_T 0.84 0.15 0.02
150_A 46_H 0.84 0.15 0.02
160_G 134_E 0.84 0.15 0.02
34_N 6_L 0.83 0.15 0.02
106_I 76_D 0.83 0.15 0.02
55_D 156_P 0.83 0.15 0.02
135_V 115_L 0.83 0.15 0.02
32_R 100_F 0.83 0.15 0.02
104_W 100_F 0.83 0.15 0.02
129_S 155_K 0.83 0.15 0.02
53_S 130_V 0.82 0.15 0.02
23_T 35_P 0.82 0.15 0.02
60_L 126_Y 0.82 0.14 0.02
22_T 33_L 0.81 0.14 0.02
77_V 73_A 0.81 0.14 0.02
26_K 134_E 0.81 0.14 0.02
160_G 17_L 0.81 0.14 0.02
159_R 90_V 0.81 0.14 0.02
101_D 5_A 0.81 0.14 0.02
60_L 105_E 0.81 0.14 0.02
61_A 96_L 0.81 0.14 0.02
22_T 105_E 0.80 0.14 0.02
153_Q 105_E 0.80 0.14 0.02
17_E 10_L 0.80 0.14 0.02
38_P 14_L 0.80 0.14 0.02
60_L 130_V 0.80 0.14 0.02
67_V 6_L 0.80 0.14 0.02
135_V 28_D 0.80 0.14 0.02
135_V 16_Y 0.80 0.14 0.02
14_L 15_K 0.80 0.14 0.02
135_V 121_M 0.79 0.14 0.02
75_A 3_L 0.79 0.14 0.02
63_F 48_N 0.79 0.14 0.02
53_S 33_L 0.79 0.13 0.02
160_G 124_Y 0.79 0.13 0.02
67_V 22_V 0.79 0.13 0.02
103_K 112_A 0.79 0.13 0.02
70_A 16_Y 0.79 0.13 0.02
37_W 14_L 0.78 0.13 0.02
159_R 119_F 0.78 0.13 0.02
38_P 6_L 0.78 0.13 0.02
20_L 62_A 0.78 0.13 0.02
104_W 127_S 0.78 0.13 0.02
18_G 146_Q 0.77 0.13 0.02
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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