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OPENSEQ.org
3se9 HL
Genes: A B A+B
Length: 228 208 409
Sequences: 8044 11834 51
Seq/Len: 35.28 56.89 0.12
MirrorTree (Pazo et al. 2001) 0.81
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 0.11 0.15 0.08
2 0.13 0.17 0.08
5 0.15 0.19 0.09
10 0.17 0.21 0.10
20 0.18 0.23 0.12
100 0.21 0.25 0.15
∞ 0.23 0.27 0.16
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
96_Y 80_D 1.71 0.32 0.00
37_W 33_W 1.68 0.30 0.00
152_C 33_W 1.49 0.22 0.00
37_W 86_C 1.40 0.20 0.00
206_Y 80_D 1.40 0.19 0.00
37_W 23_C 1.39 0.19 0.00
96_Y 33_W 1.36 0.18 0.00
212_H 90_E 1.36 0.18 0.00
208_C 33_W 1.35 0.18 0.00
15_G 122_G 1.35 0.18 0.00
166_W 33_W 1.33 0.17 0.00
34_L 21_L 1.31 0.17 0.00
208_C 188_C 1.30 0.16 0.00
210_V 73_I 1.29 0.16 0.00
15_G 186_Y 1.29 0.16 0.00
66_F 92_F 1.29 0.16 0.00
96_Y 188_C 1.28 0.16 0.00
37_W 142_W 1.27 0.15 0.00
206_Y 122_G 1.26 0.15 0.00
194_V 82_A 1.23 0.14 0.00
85_I 78_P 1.23 0.14 0.00
98_C 33_W 1.23 0.14 0.00
204_Q 35_Q 1.22 0.14 0.00
210_V 21_L 1.22 0.14 0.00
152_C 82_A 1.22 0.14 0.00
37_W 84_Y 1.20 0.14 0.00
186_G 73_I 1.20 0.14 0.00
22_C 142_W 1.19 0.13 0.00
83_M 192_H 1.19 0.13 0.00
95_T 42_P 1.19 0.13 0.00
152_C 23_C 1.18 0.13 0.00
152_C 86_C 1.17 0.13 0.00
208_C 128_C 1.17 0.13 0.00
123_V 122_G 1.16 0.13 0.00
175_V 128_C 1.16 0.13 0.00
92_D 140_V 1.16 0.13 0.00
59_V 49_T 1.13 0.12 0.00
204_Q 80_D 1.13 0.12 0.00
59_V 53_A 1.12 0.12 0.00
164_V 16_G 1.12 0.12 0.00
37_W 122_G 1.12 0.12 0.00
210_V 190_V 1.11 0.12 0.00
92_D 142_W 1.11 0.12 0.00
38_V 106_A 1.10 0.11 0.00
60_N 50_S 1.10 0.11 0.00
85_I 181_E 1.10 0.11 0.00
7_S 47_F 1.09 0.11 0.00
15_G 13_L 1.09 0.11 0.00
37_W 71_L 1.08 0.11 0.00
15_G 23_C 1.08 0.11 0.00
94_A 182_K 1.08 0.11 0.00
15_G 62_G 1.07 0.11 0.00
15_G 86_C 1.07 0.11 0.00
20_V 80_D 1.06 0.11 0.00
92_D 86_C 1.06 0.11 0.00
37_W 128_C 1.06 0.11 0.00
53_K 38_P 1.06 0.10 0.00
205_T 109_V 1.06 0.10 0.00
88_L 168_S 1.05 0.10 0.00
48_W 47_F 1.05 0.10 0.00
17_S 137_E 1.05 0.10 0.00
164_V 190_V 1.05 0.10 0.00
194_V 85_Y 1.04 0.10 0.00
56_T 49_T 1.04 0.10 0.00
214_P 148_L 1.04 0.10 0.00
96_Y 128_C 1.04 0.10 0.00
92_D 33_W 1.04 0.10 0.00
196_V 143_K 1.03 0.10 0.00
15_G 33_W 1.03 0.10 0.00
96_Y 23_C 1.03 0.10 0.00
208_C 23_C 1.03 0.10 0.00
37_W 188_C 1.03 0.10 0.00
59_V 50_S 1.03 0.10 0.00
33_E 38_P 1.02 0.10 0.00
206_Y 33_W 1.02 0.10 0.00
37_W 82_A 1.02 0.10 0.00
206_Y 142_W 1.02 0.10 0.00
152_C 142_W 1.02 0.10 0.00
102_K 98_L 1.01 0.10 0.00
166_W 23_C 1.01 0.10 0.00
98_C 188_C 1.00 0.10 0.00
22_C 188_C 1.00 0.09 0.00
166_W 86_C 1.00 0.09 0.00
88_L 68_Q 0.99 0.09 0.00
193_V 125_S 0.99 0.09 0.00
196_V 113_P 0.99 0.09 0.00
194_V 90_E 0.99 0.09 0.00
208_C 82_A 0.99 0.09 0.00
215_S 173_L 0.99 0.09 0.00
204_Q 184_K 0.98 0.09 0.00
208_C 86_C 0.98 0.09 0.00
96_Y 86_C 0.98 0.09 0.00
128_T 12_S 0.98 0.09 0.00
56_T 38_P 0.98 0.09 0.00
55_V 63_S 0.98 0.09 0.00
85_I 129_L 0.98 0.09 0.00
37_W 100_I 0.98 0.09 0.00
204_Q 122_G 0.97 0.09 0.00
15_G 124_A 0.97 0.09 0.00
56_T 45_L 0.96 0.09 0.00
123_V 23_C 0.96 0.09 0.00
20_V 100_I 0.96 0.09 0.00
13_K 68_Q 0.96 0.09 0.00
203_T 16_G 0.96 0.09 0.00
206_Y 23_C 0.95 0.09 0.00
210_V 80_D 0.95 0.09 0.00
57_G 52_R 0.95 0.09 0.00
121_I 35_Q 0.95 0.09 0.00
152_C 84_Y 0.95 0.09 0.00
57_G 38_P 0.94 0.08 0.00
121_I 184_K 0.94 0.08 0.00
85_I 140_V 0.94 0.08 0.00
59_V 57_P 0.93 0.08 0.00
185_S 73_I 0.93 0.08 0.00
206_Y 19_A 0.93 0.08 0.00
212_H 82_A 0.92 0.08 0.00
101_Q 78_P 0.92 0.08 0.00
88_L 60_F 0.92 0.08 0.00
212_H 50_S 0.92 0.08 0.00
20_V 184_K 0.91 0.08 0.00
85_I 34_Y 0.91 0.08 0.00
71_S 41_P 0.91 0.08 0.00
60_N 49_T 0.91 0.08 0.00
105_T 146_N 0.90 0.08 0.00
159_P 173_L 0.90 0.08 0.00
17_S 21_L 0.90 0.08 0.00
56_T 51_K 0.90 0.08 0.00
98_C 23_C 0.90 0.08 0.00
56_T 6_Q 0.89 0.08 0.00
35_I 84_Y 0.89 0.08 0.00
205_T 183_H 0.89 0.08 0.00
206_Y 173_L 0.89 0.08 0.00
63_S 54_S 0.89 0.08 0.00
59_V 48_A 0.89 0.08 0.00
66_F 21_L 0.89 0.07 0.00
163_T 19_A 0.88 0.07 0.00
37_W 184_K 0.88 0.07 0.00
79_F 35_Q 0.88 0.07 0.00
37_W 80_D 0.88 0.07 0.00
105_T 98_L 0.88 0.07 0.00
212_H 88_Q 0.88 0.07 0.00
22_C 33_W 0.88 0.07 0.00
20_V 59_R 0.88 0.07 0.00
179_P 98_L 0.88 0.07 0.00
37_W 186_Y 0.88 0.07 0.00
146_G 164_D 0.87 0.07 0.00
86_R 62_G 0.87 0.07 0.00
138_P 188_C 0.87 0.07 0.00
145_G 33_W 0.87 0.07 0.00
149_A 143_K 0.87 0.07 0.00
152_C 122_G 0.87 0.07 0.00
49_I 165_S 0.87 0.07 0.00
213_K 138_A 0.87 0.07 0.00
151_G 32_T 0.86 0.07 0.00
123_V 33_W 0.86 0.07 0.00
210_V 33_W 0.86 0.07 0.00
164_V 126_V 0.86 0.07 0.00
98_C 86_C 0.86 0.07 0.00
160_E 183_H 0.86 0.07 0.00
199_S 107_P 0.86 0.07 0.00
56_T 48_A 0.86 0.07 0.00
63_S 45_L 0.86 0.07 0.00
175_V 188_C 0.85 0.07 0.00
169_G 20_S 0.85 0.07 0.00
144_S 98_L 0.85 0.07 0.00
185_S 123_T 0.85 0.07 0.00
56_T 50_S 0.85 0.07 0.00
87_G 12_S 0.85 0.07 0.00
11_V 98_L 0.85 0.07 0.00
144_S 73_I 0.85 0.07 0.00
13_K 91_F 0.85 0.07 0.00
72_L 50_S 0.85 0.07 0.00
49_I 50_S 0.84 0.07 0.00
85_I 33_W 0.84 0.07 0.00
168_S 35_Q 0.84 0.07 0.00
122_V 32_T 0.84 0.07 0.00
61_F 49_T 0.84 0.07 0.00
94_A 156_S 0.84 0.07 0.00
112_F 7_S 0.84 0.07 0.00
166_W 93_G 0.83 0.07 0.00
25_S 31_M 0.83 0.07 0.00
144_S 79_E 0.83 0.07 0.00
60_N 51_K 0.83 0.07 0.00
54_T 53_A 0.83 0.07 0.00
88_L 108_S 0.83 0.07 0.00
125_S 27_S 0.83 0.07 0.00
94_A 33_W 0.83 0.07 0.00
88_L 25_A 0.83 0.07 0.00
92_D 59_R 0.83 0.07 0.00
152_C 71_L 0.83 0.07 0.00
52_V 107_P 0.82 0.07 0.00
164_V 81_F 0.82 0.07 0.00
41_A 44_L 0.82 0.07 0.00
210_V 42_P 0.82 0.07 0.00
121_I 47_F 0.82 0.07 0.00
166_W 142_W 0.82 0.07 0.00
96_Y 142_W 0.82 0.07 0.00
208_C 142_W 0.82 0.07 0.00
212_H 24_T 0.82 0.07 0.00
150_L 140_V 0.82 0.07 0.00
56_T 52_R 0.82 0.07 0.00
98_C 197_S 0.82 0.07 0.00
32_T 124_A 0.82 0.07 0.00
17_S 99_E 0.82 0.07 0.00
57_G 51_K 0.81 0.07 0.00
175_V 114_P 0.81 0.07 0.00
7_S 50_S 0.81 0.07 0.00
93_T 25_A 0.81 0.07 0.00
119_T 31_M 0.81 0.07 0.00
217_T 59_R 0.81 0.07 0.00
102_K 38_P 0.81 0.07 0.00
35_I 29_G 0.81 0.06 0.00
119_T 19_A 0.81 0.06 0.00
119_T 37_K 0.81 0.06 0.00
20_V 164_D 0.81 0.06 0.00
150_L 173_L 0.81 0.06 0.00
204_Q 187_A 0.81 0.06 0.00
131_P 107_P 0.81 0.06 0.00
17_S 11_L 0.80 0.06 0.00
223_V 27_S 0.80 0.06 0.00
59_V 45_L 0.80 0.06 0.00
150_L 33_W 0.80 0.06 0.00
115_W 75_R 0.80 0.06 0.00
37_W 173_L 0.80 0.06 0.00
98_C 71_L 0.80 0.06 0.00
143_T 76_M 0.80 0.06 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
5669 0.12 3se9 HL Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5657 0 3se9 HL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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