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OPENSEQ.org
TA
Genes: A B A+B
Length: 154 111 252
Sequences: 141 92 89
Seq/Len: 0.92 0.83 0.35
MirrorTree (Pazo et al. 2001) 0.82
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 0.00 0.00 0.34
2 0.00 0.00 0.34
5 0.01 0.00 0.34
10 0.01 0.00 0.34
20 0.01 0.01 0.34
100 0.02 0.01 0.34
∞ 0.03 0.01 0.34
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
92_R 107_I 2.19 0.85 0.34
107_I 66_M 1.96 0.75 0.21
119_T 20_R 1.69 0.59 0.10
119_T 107_I 1.64 0.56 0.09
92_R 20_R 1.55 0.49 0.07
69_F 16_K 1.46 0.43 0.05
5_Q 86_P 1.45 0.42 0.05
80_N 29_V 1.42 0.41 0.05
89_G 107_I 1.42 0.40 0.05
91_G 107_I 1.39 0.38 0.04
62_V 46_I 1.36 0.36 0.04
103_E 78_Q 1.34 0.35 0.04
150_T 25_I 1.33 0.34 0.03
67_P 101_V 1.31 0.33 0.03
32_L 14_E 1.28 0.31 0.03
57_E 16_K 1.26 0.30 0.03
114_E 46_I 1.26 0.30 0.03
57_E 41_S 1.23 0.28 0.02
119_T 17_V 1.22 0.28 0.02
78_G 87_F 1.22 0.28 0.02
68_A 41_S 1.21 0.27 0.02
117_L 17_V 1.18 0.26 0.02
69_F 73_L 1.18 0.26 0.02
12_L 51_Q 1.16 0.25 0.02
142_D 101_V 1.15 0.24 0.02
91_G 40_D 1.15 0.24 0.02
122_K 25_I 1.14 0.23 0.02
142_D 93_K 1.14 0.23 0.02
7_V 65_T 1.13 0.23 0.02
77_S 105_D 1.13 0.23 0.02
33_K 34_K 1.13 0.23 0.02
93_Y 40_D 1.13 0.23 0.02
52_V 107_I 1.12 0.23 0.02
13_Y 84_T 1.12 0.22 0.02
91_G 20_R 1.12 0.22 0.02
80_N 80_N 1.12 0.22 0.02
107_I 99_M 1.11 0.22 0.02
143_W 56_R 1.11 0.22 0.01
124_T 31_E 1.10 0.22 0.01
56_I 25_I 1.10 0.22 0.01
43_K 20_R 1.09 0.21 0.01
48_L 19_I 1.09 0.21 0.01
128_T 14_E 1.09 0.21 0.01
144_E 100_D 1.08 0.21 0.01
79_K 99_M 1.08 0.20 0.01
80_N 109_D 1.06 0.20 0.01
89_G 21_G 1.05 0.20 0.01
84_S 105_D 1.05 0.19 0.01
89_G 37_P 1.03 0.18 0.01
44_A 107_I 1.03 0.18 0.01
35_K 32_A 1.03 0.18 0.01
33_K 60_E 1.02 0.18 0.01
12_L 78_Q 1.02 0.18 0.01
40_Y 109_D 1.02 0.18 0.01
149_E 94_K 1.00 0.17 0.01
4_P 96_V 1.00 0.17 0.01
102_K 48_P 1.00 0.17 0.01
8_N 54_M 0.99 0.17 0.01
59_H 56_R 0.99 0.17 0.01
105_V 25_I 0.99 0.17 0.01
23_D 91_Q 0.98 0.17 0.01
46_T 97_A 0.98 0.17 0.01
48_L 107_I 0.98 0.16 0.01
104_K 104_D 0.98 0.16 0.01
36_D 79_N 0.98 0.16 0.01
74_S 64_H 0.98 0.16 0.01
93_Y 17_V 0.97 0.16 0.01
117_L 41_S 0.97 0.16 0.01
48_L 108_G 0.97 0.16 0.01
99_Y 43_H 0.96 0.16 0.01
46_T 16_K 0.96 0.16 0.01
107_I 110_D 0.96 0.16 0.01
40_Y 56_R 0.96 0.16 0.01
149_E 89_I 0.96 0.16 0.01
8_N 27_A 0.96 0.16 0.01
121_G 38_G 0.96 0.16 0.01
132_K 97_A 0.96 0.15 0.01
56_I 53_F 0.95 0.15 0.01
34_G 89_I 0.95 0.15 0.01
128_T 100_D 0.95 0.15 0.01
119_T 19_I 0.94 0.15 0.01
93_Y 20_R 0.94 0.15 0.01
101_E 55_C 0.94 0.15 0.01
17_C 37_P 0.94 0.15 0.01
42_R 101_V 0.94 0.15 0.01
128_T 53_F 0.94 0.15 0.01
48_L 21_G 0.93 0.15 0.01
80_N 47_L 0.93 0.15 0.01
92_R 106_E 0.93 0.15 0.01
27_A 83_K 0.93 0.14 0.01
128_T 93_K 0.93 0.14 0.01
22_Y 110_D 0.93 0.14 0.01
52_V 37_P 0.93 0.14 0.01
41_Q 29_V 0.92 0.14 0.01
54_K 110_D 0.92 0.14 0.01
101_E 31_E 0.92 0.14 0.01
38_E 110_D 0.92 0.14 0.01
138_H 56_R 0.92 0.14 0.01
91_G 106_E 0.92 0.14 0.01
38_E 86_P 0.91 0.14 0.01
105_V 36_K 0.91 0.14 0.01
108_L 91_Q 0.91 0.14 0.01
43_K 44_Y 0.91 0.14 0.01
12_L 45_E 0.91 0.14 0.01
69_F 54_M 0.91 0.14 0.01
46_T 72_F 0.91 0.14 0.01
115_N 105_D 0.91 0.14 0.01
81_K 67_N 0.91 0.14 0.01
23_D 77_I 0.91 0.14 0.01
93_Y 37_P 0.91 0.14 0.01
46_T 60_E 0.90 0.14 0.01
129_V 73_L 0.90 0.14 0.01
28_E 17_V 0.90 0.13 0.01
105_V 40_D 0.90 0.13 0.01
48_L 40_D 0.90 0.13 0.01
52_V 44_Y 0.90 0.13 0.01
141_A 75_A 0.89 0.13 0.01
108_L 108_G 0.89 0.13 0.01
34_G 86_P 0.89 0.13 0.01
42_R 71_R 0.89 0.13 0.01
31_T 82_Q 0.89 0.13 0.01
67_P 29_V 0.89 0.13 0.01
48_L 44_Y 0.89 0.13 0.01
89_G 41_S 0.88 0.13 0.01
100_S 14_E 0.88 0.13 0.01
89_G 40_D 0.88 0.13 0.01
69_F 45_E 0.88 0.13 0.01
23_D 86_P 0.88 0.13 0.01
92_R 35_L 0.88 0.13 0.01
17_C 21_G 0.88 0.13 0.01
92_R 37_P 0.87 0.13 0.01
91_G 35_L 0.87 0.13 0.01
132_K 45_E 0.87 0.13 0.01
54_K 72_F 0.87 0.13 0.01
117_L 27_A 0.87 0.13 0.01
73_K 47_L 0.87 0.13 0.01
19_Q 87_F 0.87 0.13 0.01
56_I 82_Q 0.87 0.12 0.01
142_D 83_K 0.86 0.12 0.01
82_D 64_H 0.86 0.12 0.01
81_K 49_G 0.86 0.12 0.01
143_W 32_A 0.86 0.12 0.01
93_Y 88_N 0.86 0.12 0.01
123_K 98_G 0.86 0.12 0.01
58_E 41_S 0.85 0.12 0.01
58_E 62_E 0.85 0.12 0.01
107_I 97_A 0.85 0.12 0.01
30_E 67_N 0.85 0.12 0.01
117_L 38_G 0.85 0.12 0.01
65_S 28_P 0.84 0.12 0.01
132_K 16_K 0.84 0.12 0.01
147_T 91_Q 0.84 0.12 0.01
73_K 16_K 0.84 0.12 0.01
11_A 77_I 0.84 0.12 0.01
91_G 99_M 0.84 0.12 0.01
132_K 49_G 0.84 0.12 0.01
46_T 58_G 0.84 0.12 0.01
32_L 28_P 0.83 0.12 0.01
104_K 105_D 0.83 0.12 0.01
56_I 16_K 0.83 0.12 0.01
37_P 76_D 0.83 0.12 0.01
126_A 23_T 0.83 0.12 0.01
58_E 94_K 0.83 0.12 0.01
44_A 46_I 0.83 0.11 0.01
24_A 62_E 0.83 0.11 0.01
36_D 25_I 0.83 0.11 0.01
105_V 31_E 0.82 0.11 0.01
46_T 100_D 0.82 0.11 0.01
86_V 67_N 0.82 0.11 0.01
17_C 41_S 0.82 0.11 0.01
4_P 88_N 0.82 0.11 0.01
55_V 21_G 0.82 0.11 0.01
136_R 100_D 0.82 0.11 0.01
115_N 68_A 0.82 0.11 0.01
28_E 44_Y 0.82 0.11 0.01
46_T 34_K 0.81 0.11 0.01
52_V 17_V 0.81 0.11 0.00
46_T 44_Y 0.81 0.11 0.00
5_Q 51_Q 0.81 0.11 0.00
29_V 76_D 0.81 0.11 0.00
100_S 41_S 0.81 0.11 0.00
135_K 96_V 0.81 0.11 0.00
112_N 18_T 0.81 0.11 0.00
150_T 94_K 0.81 0.11 0.00
39_N 79_N 0.81 0.11 0.00
142_D 60_E 0.81 0.11 0.00
81_K 104_D 0.81 0.11 0.00
117_L 94_K 0.80 0.11 0.00
31_T 101_V 0.80 0.11 0.00
46_T 75_A 0.80 0.11 0.00
93_Y 35_L 0.80 0.11 0.00
40_Y 55_C 0.80 0.11 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
4740 0.47 TA a Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2015_06) 0.40 Done - Shared
4739 0.47 TA a Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2015_06) 0.42 Done - Shared
4738 0.35 TA Δgene:(1, 1) A:(1E-04, 4) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
4737 0.35 TA Δgene:(1, 20) A:(1E-04, 4) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.36 Done - Shared
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