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OPENSEQ.org
TA a
Genes: A B A+B
Length: 154 111 246
Sequences: 149 133 116
Seq/Len: 0.97 1.2 0.47
MirrorTree (Pazo et al. 2001) 0.89
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 0.01 0.00 0.44
2 0.01 0.00 0.44
5 0.01 0.00 0.43
10 0.01 0.00 0.43
20 0.01 0.00 0.43
100 0.01 0.00 0.44
∞ 0.04 0.04 0.44
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 2.12 0.89 0.40
68_A 41_S 1.88 0.79 0.25
107_I 66_M 1.71 0.69 0.16
77_S 105_D 1.65 0.66 0.14
92_R 20_R 1.53 0.57 0.10
89_G 107_I 1.46 0.51 0.08
79_K 29_V 1.41 0.48 0.07
104_K 102_N 1.36 0.44 0.06
62_V 46_I 1.33 0.42 0.05
119_T 107_I 1.28 0.38 0.04
7_V 65_T 1.26 0.36 0.04
117_L 94_K 1.23 0.34 0.04
124_T 31_E 1.21 0.33 0.03
67_P 101_V 1.20 0.33 0.03
119_T 20_R 1.20 0.33 0.03
69_F 75_A 1.20 0.32 0.03
69_F 16_K 1.19 0.31 0.03
89_G 21_G 1.18 0.31 0.03
14_A 91_Q 1.18 0.31 0.03
75_L 50_G 1.16 0.30 0.03
52_V 107_I 1.16 0.29 0.03
107_I 99_M 1.16 0.29 0.03
78_G 58_G 1.15 0.29 0.03
23_D 91_Q 1.15 0.29 0.03
58_E 94_K 1.14 0.28 0.03
101_E 31_E 1.13 0.28 0.03
42_R 101_V 1.13 0.28 0.03
103_E 78_Q 1.12 0.28 0.02
13_Y 84_T 1.12 0.28 0.02
43_K 20_R 1.11 0.27 0.02
22_Y 39_Q 1.11 0.27 0.02
69_F 73_L 1.10 0.26 0.02
91_G 107_I 1.10 0.26 0.02
115_N 105_D 1.10 0.26 0.02
93_Y 107_I 1.09 0.26 0.02
65_S 57_L 1.09 0.26 0.02
19_Q 87_F 1.09 0.26 0.02
32_L 14_E 1.07 0.25 0.02
149_E 94_K 1.06 0.24 0.02
30_E 91_Q 1.06 0.24 0.02
79_K 47_L 1.06 0.24 0.02
142_D 93_K 1.06 0.24 0.02
89_G 27_A 1.05 0.23 0.02
79_K 80_N 1.05 0.23 0.02
126_A 23_T 1.05 0.23 0.02
58_E 41_S 1.04 0.23 0.02
69_F 54_M 1.04 0.23 0.02
74_S 64_H 1.03 0.23 0.02
79_K 39_Q 1.03 0.23 0.02
48_L 44_Y 1.03 0.22 0.02
44_A 107_I 1.02 0.22 0.02
52_V 44_Y 1.02 0.22 0.02
57_E 16_K 1.01 0.21 0.02
132_K 55_C 1.01 0.21 0.02
142_D 101_V 1.01 0.21 0.01
150_T 105_D 1.01 0.21 0.01
93_Y 40_D 1.01 0.21 0.01
86_V 67_N 1.01 0.21 0.01
150_T 25_I 1.00 0.21 0.01
142_D 83_K 0.99 0.20 0.01
49_L 81_P 0.99 0.20 0.01
132_K 49_G 0.98 0.20 0.01
117_L 41_S 0.98 0.20 0.01
65_S 55_C 0.98 0.20 0.01
148_R 59_D 0.98 0.20 0.01
38_E 86_P 0.98 0.20 0.01
18_F 23_T 0.97 0.19 0.01
108_L 90_Q 0.96 0.19 0.01
82_D 64_H 0.96 0.19 0.01
104_K 71_R 0.96 0.19 0.01
99_Y 82_Q 0.96 0.19 0.01
57_E 38_G 0.96 0.19 0.01
120_Y 81_P 0.96 0.19 0.01
88_F 23_T 0.96 0.19 0.01
56_I 25_I 0.95 0.18 0.01
91_G 106_E 0.95 0.18 0.01
48_L 107_I 0.94 0.18 0.01
138_H 56_R 0.94 0.18 0.01
59_H 56_R 0.94 0.18 0.01
63_N 74_D 0.94 0.18 0.01
5_Q 86_P 0.94 0.18 0.01
93_Y 88_N 0.94 0.18 0.01
56_I 53_F 0.93 0.18 0.01
44_A 38_G 0.93 0.18 0.01
123_K 83_K 0.93 0.17 0.01
145_T 104_D 0.93 0.17 0.01
12_L 78_Q 0.93 0.17 0.01
26_V 91_Q 0.93 0.17 0.01
24_A 62_E 0.93 0.17 0.01
28_E 21_G 0.93 0.17 0.01
93_Y 21_G 0.93 0.17 0.01
150_T 66_M 0.93 0.17 0.01
34_G 62_E 0.92 0.17 0.01
131_S 59_D 0.92 0.17 0.01
28_E 44_Y 0.92 0.17 0.01
28_E 13_T 0.92 0.17 0.01
43_K 44_Y 0.91 0.17 0.01
20_E 91_Q 0.91 0.17 0.01
123_K 98_G 0.91 0.17 0.01
49_L 23_T 0.91 0.17 0.01
105_V 36_K 0.91 0.16 0.01
89_G 38_G 0.90 0.16 0.01
131_S 98_G 0.90 0.16 0.01
93_Y 20_R 0.90 0.16 0.01
88_F 81_P 0.90 0.16 0.01
117_L 17_V 0.90 0.16 0.01
114_E 49_G 0.90 0.16 0.01
38_E 55_C 0.90 0.16 0.01
144_E 100_D 0.90 0.16 0.01
131_S 74_D 0.90 0.16 0.01
143_W 56_R 0.89 0.16 0.01
147_T 91_Q 0.89 0.16 0.01
126_A 81_P 0.89 0.16 0.01
92_R 106_E 0.88 0.15 0.01
73_K 16_K 0.88 0.15 0.01
100_S 41_S 0.87 0.15 0.01
92_R 35_L 0.87 0.15 0.01
44_A 21_G 0.87 0.15 0.01
32_L 65_T 0.87 0.15 0.01
46_T 72_F 0.87 0.15 0.01
68_A 36_K 0.86 0.15 0.01
24_A 101_V 0.86 0.15 0.01
145_T 86_P 0.86 0.15 0.01
18_F 50_G 0.86 0.15 0.01
107_I 77_I 0.86 0.15 0.01
44_A 66_M 0.86 0.14 0.01
37_P 76_D 0.86 0.14 0.01
23_D 86_P 0.86 0.14 0.01
33_K 54_M 0.85 0.14 0.01
10_W 76_D 0.85 0.14 0.01
77_S 28_P 0.85 0.14 0.01
44_A 27_A 0.85 0.14 0.01
28_E 34_K 0.85 0.14 0.01
107_I 68_A 0.85 0.14 0.01
48_L 21_G 0.84 0.14 0.01
101_E 39_Q 0.84 0.14 0.01
63_N 39_Q 0.84 0.14 0.01
18_F 81_P 0.84 0.14 0.01
45_A 20_R 0.84 0.14 0.01
144_E 85_R 0.84 0.14 0.01
59_H 53_F 0.84 0.14 0.01
55_V 27_A 0.83 0.14 0.01
124_T 90_Q 0.83 0.14 0.01
49_L 96_V 0.83 0.14 0.01
122_K 25_I 0.83 0.14 0.01
89_G 41_S 0.83 0.13 0.01
89_G 40_D 0.83 0.13 0.01
42_R 103_I 0.83 0.13 0.01
40_Y 56_R 0.82 0.13 0.01
73_K 47_L 0.82 0.13 0.01
46_T 58_G 0.82 0.13 0.01
60_I 72_F 0.82 0.13 0.01
61_T 16_K 0.82 0.13 0.01
28_E 20_R 0.82 0.13 0.01
108_L 91_Q 0.81 0.13 0.01
48_L 19_I 0.81 0.13 0.01
84_S 105_D 0.81 0.13 0.01
67_P 42_I 0.81 0.13 0.01
91_G 40_D 0.81 0.13 0.01
119_T 17_V 0.81 0.13 0.01
109_G 76_D 0.81 0.13 0.01
11_A 78_Q 0.81 0.13 0.01
101_E 51_Q 0.81 0.13 0.01
55_V 21_G 0.80 0.13 0.01
57_E 11_L 0.80 0.13 0.01
4_P 17_V 0.80 0.12 0.01
36_D 79_N 0.80 0.12 0.01
12_L 87_F 0.80 0.12 0.01
89_G 20_R 0.80 0.12 0.01
117_L 107_I 0.80 0.12 0.01
105_V 79_N 0.80 0.12 0.01
128_T 14_E 0.80 0.12 0.01
53_H 27_A 0.80 0.12 0.01
91_G 20_R 0.79 0.12 0.01
12_L 90_Q 0.79 0.12 0.01
120_Y 23_T 0.79 0.12 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
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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