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OPENSEQ.org
Enc_test
Genes: A B A+B
Length: 262 114 369
Sequences: 258 141 54
Seq/Len: 0.98 1.24 0.15
MirrorTree (Pazo et al. 2001) 0.62
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 0.14
2 0.01 0.00 0.14
5 0.01 0.00 0.14
10 0.01 0.00 0.14
20 0.01 0.00 0.14
100 0.01 0.00 0.14
∞ 0.01 0.01 0.14
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
63_D 23_L 1.46 0.25 0.00
176_N 30_I 1.45 0.24 0.00
72_L 89_K 1.40 0.23 0.00
240_R 111_I 1.36 0.21 0.00
191_Y 50_K 1.34 0.20 0.00
35_Y 60_M 1.33 0.20 0.00
214_D 47_T 1.32 0.19 0.00
227_L 34_A 1.32 0.19 0.00
36_G 3_D 1.31 0.19 0.00
215_A 21_R 1.30 0.19 0.00
54_P 40_V 1.30 0.19 0.00
162_F 48_V 1.29 0.18 0.00
83_A 23_L 1.23 0.17 0.00
172_T 113_K 1.21 0.16 0.00
67_V 57_D 1.20 0.15 0.00
114_V 52_L 1.19 0.15 0.00
235_I 91_I 1.19 0.15 0.00
41_D 17_R 1.18 0.15 0.00
52_A 35_W 1.18 0.15 0.00
172_T 51_I 1.17 0.15 0.00
218_V 82_R 1.16 0.14 0.00
248_F 106_G 1.16 0.14 0.00
256_R 111_I 1.15 0.14 0.00
49_E 81_L 1.13 0.14 0.00
233_L 111_I 1.13 0.14 0.00
235_I 67_L 1.12 0.13 0.00
17_K 96_E 1.12 0.13 0.00
112_R 90_P 1.12 0.13 0.00
240_R 112_R 1.11 0.13 0.00
233_L 48_V 1.11 0.13 0.00
22_I 33_V 1.10 0.13 0.00
70_W 23_L 1.10 0.13 0.00
49_E 90_P 1.09 0.13 0.00
255_S 109_L 1.08 0.12 0.00
205_K 113_K 1.08 0.12 0.00
152_L 111_I 1.08 0.12 0.00
43_E 43_T 1.07 0.12 0.00
55_L 20_V 1.06 0.12 0.00
68_V 111_I 1.06 0.12 0.00
57_E 23_L 1.05 0.12 0.00
106_S 12_L 1.05 0.12 0.00
42_V 23_L 1.05 0.12 0.00
214_D 34_A 1.05 0.12 0.00
9_R 38_Q 1.04 0.12 0.00
122_I 64_A 1.04 0.12 0.00
231_Q 96_E 1.03 0.11 0.00
42_V 20_V 1.02 0.11 0.00
7_L 10_S 1.02 0.11 0.00
206_I 8_P 1.02 0.11 0.00
190_H 21_R 1.02 0.11 0.00
44_G 68_E 1.02 0.11 0.00
259_T 77_W 1.02 0.11 0.00
246_R 30_I 1.02 0.11 0.00
233_L 75_P 1.01 0.11 0.00
204_G 35_W 1.01 0.11 0.00
55_L 40_V 1.01 0.11 0.00
112_R 84_Y 1.00 0.10 0.00
22_I 94_I 0.99 0.10 0.00
93_D 22_A 0.99 0.10 0.00
85_F 56_R 0.99 0.10 0.00
103_D 99_S 0.99 0.10 0.00
179_R 17_R 0.98 0.10 0.00
40_V 91_I 0.98 0.10 0.00
120_E 81_L 0.98 0.10 0.00
62_S 33_V 0.98 0.10 0.00
79_I 105_T 0.97 0.10 0.00
183_F 97_E 0.97 0.10 0.00
4_M 95_E 0.97 0.10 0.00
155_I 81_L 0.96 0.10 0.00
88_D 18_D 0.96 0.10 0.00
16_E 89_K 0.96 0.10 0.00
128_K 43_T 0.95 0.10 0.00
21_E 74_M 0.95 0.10 0.00
90_W 22_A 0.95 0.10 0.00
164_K 104_N 0.95 0.09 0.00
213_E 51_I 0.94 0.09 0.00
152_L 60_M 0.94 0.09 0.00
157_R 82_R 0.94 0.09 0.00
197_V 73_N 0.94 0.09 0.00
165_D 12_L 0.94 0.09 0.00
229_L 16_D 0.94 0.09 0.00
134_L 17_R 0.94 0.09 0.00
152_L 42_T 0.93 0.09 0.00
200_C 21_R 0.93 0.09 0.00
180_W 74_M 0.93 0.09 0.00
177_T 67_L 0.93 0.09 0.00
259_T 53_E 0.93 0.09 0.00
151_L 108_D 0.93 0.09 0.00
85_F 55_N 0.93 0.09 0.00
198_E 97_E 0.92 0.09 0.00
25_R 27_K 0.92 0.09 0.00
99_K 48_V 0.92 0.09 0.00
223_G 46_E 0.92 0.09 0.00
62_S 10_S 0.92 0.09 0.00
171_Y 30_I 0.92 0.09 0.00
103_D 53_E 0.92 0.09 0.00
259_T 91_I 0.92 0.09 0.00
34_L 70_L 0.92 0.09 0.00
232_D 70_L 0.92 0.09 0.00
236_G 70_L 0.92 0.09 0.00
44_G 85_L 0.92 0.09 0.00
190_H 33_V 0.91 0.09 0.00
69_K 91_I 0.91 0.09 0.00
28_E 27_K 0.91 0.09 0.00
123_F 108_D 0.91 0.09 0.00
217_V 14_G 0.91 0.09 0.00
7_L 75_P 0.90 0.09 0.00
215_A 7_E 0.90 0.09 0.00
167_I 100_G 0.90 0.09 0.00
89_L 16_D 0.90 0.09 0.00
250_T 76_G 0.90 0.09 0.00
92_L 84_Y 0.89 0.09 0.00
66_E 90_P 0.89 0.08 0.00
172_T 44_K 0.89 0.08 0.00
51_A 19_F 0.89 0.08 0.00
169_G 20_V 0.89 0.08 0.00
249_I 16_D 0.88 0.08 0.00
177_T 75_P 0.88 0.08 0.00
157_R 89_K 0.88 0.08 0.00
206_I 87_T 0.88 0.08 0.00
20_Q 30_I 0.88 0.08 0.00
76_L 77_W 0.88 0.08 0.00
49_E 13_T 0.88 0.08 0.00
94_N 45_D 0.88 0.08 0.00
95_L 67_L 0.87 0.08 0.00
44_G 71_R 0.87 0.08 0.00
189_G 30_I 0.87 0.08 0.00
207_I 7_E 0.87 0.08 0.00
119_D 22_A 0.87 0.08 0.00
93_D 26_L 0.87 0.08 0.00
94_N 20_V 0.87 0.08 0.00
157_R 92_T 0.87 0.08 0.00
100_P 83_T 0.87 0.08 0.00
197_V 13_T 0.87 0.08 0.00
34_L 86_F 0.86 0.08 0.00
232_D 86_F 0.86 0.08 0.00
236_G 86_F 0.86 0.08 0.00
177_T 43_T 0.86 0.08 0.00
159_L 51_I 0.86 0.08 0.00
107_L 78_D 0.86 0.08 0.00
256_R 38_Q 0.86 0.08 0.00
197_V 92_T 0.86 0.08 0.00
162_F 47_T 0.86 0.08 0.00
256_R 3_D 0.86 0.08 0.00
222_G 110_G 0.86 0.08 0.00
155_I 91_I 0.86 0.08 0.00
215_A 111_I 0.86 0.08 0.00
216_L 100_G 0.86 0.08 0.00
164_K 4_Q 0.86 0.08 0.00
135_L 96_E 0.85 0.08 0.00
31_K 43_T 0.85 0.08 0.00
206_I 92_T 0.85 0.08 0.00
172_T 97_E 0.85 0.08 0.00
93_D 74_M 0.85 0.08 0.00
102_V 53_E 0.85 0.08 0.00
117_F 80_A 0.85 0.08 0.00
40_V 21_R 0.85 0.08 0.00
15_T 108_D 0.85 0.08 0.00
235_I 106_G 0.85 0.08 0.00
256_R 48_V 0.85 0.08 0.00
246_R 16_D 0.85 0.08 0.00
242_K 40_V 0.85 0.08 0.00
217_V 51_I 0.84 0.08 0.00
177_T 20_V 0.84 0.08 0.00
23_D 33_V 0.84 0.08 0.00
115_A 25_S 0.84 0.08 0.00
21_E 66_L 0.84 0.08 0.00
4_M 54_H 0.84 0.08 0.00
4_M 61_E 0.84 0.08 0.00
4_M 69_W 0.84 0.08 0.00
208_T 81_L 0.84 0.07 0.00
97_R 109_L 0.84 0.07 0.00
22_I 91_I 0.83 0.07 0.00
116_E 97_E 0.83 0.07 0.00
39_F 96_E 0.83 0.07 0.00
209_T 112_R 0.83 0.07 0.00
67_V 33_V 0.83 0.07 0.00
23_D 38_Q 0.83 0.07 0.00
190_H 67_L 0.83 0.07 0.00
111_V 50_K 0.83 0.07 0.00
27_R 93_E 0.83 0.07 0.00
252_T 18_D 0.82 0.07 0.00
212_I 27_K 0.82 0.07 0.00
76_L 76_G 0.82 0.07 0.00
128_K 104_N 0.82 0.07 0.00
214_D 89_K 0.82 0.07 0.00
112_R 52_L 0.82 0.07 0.00
39_F 53_E 0.82 0.07 0.00
61_L 75_P 0.82 0.07 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
10803 0.15 Tm_S_F Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6912 0.15 Enc_test Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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