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OPENSEQ.org
2BTF
Genes: A B A+B
Length: 374 139 481
Sequences: 3302 621 62
Seq/Len: 8.83 4.47 0.13
MirrorTree (Pazo et al. 2001) 0.43
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 0.04 0.06 0.01
2 0.05 0.07 0.02
5 0.05 0.07 0.08
10 0.05 0.07 0.10
20 0.06 0.07 0.12
100 0.08 0.07 0.19
∞ 0.17 0.07 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
362_D 111_L 2.27 0.62 0.12
369_V 103_T 2.11 0.54 0.08
157_G 114_G 1.83 0.39 0.04
63_I 67_G 1.58 0.27 0.02
241_L 103_T 1.56 0.27 0.02
289_R 112_L 1.52 0.25 0.02
260_L 101_T 1.48 0.23 0.01
185_T 66_G 1.48 0.23 0.01
107_A 69_K 1.47 0.23 0.01
218_V 7_I 1.40 0.20 0.01
208_V 119_H 1.36 0.19 0.01
340_I 49_I 1.36 0.19 0.01
34_V 58_F 1.34 0.18 0.01
260_L 114_G 1.33 0.18 0.01
212_K 35_P 1.30 0.17 0.01
359_Q 109_L 1.30 0.17 0.01
262_Q 110_V 1.27 0.16 0.01
65_T 88_R 1.25 0.16 0.01
326_I 58_F 1.23 0.15 0.01
323_T 83_F 1.21 0.14 0.01
137_A 23_G 1.20 0.14 0.01
183_D 23_G 1.19 0.14 0.01
306_P 105_T 1.19 0.14 0.01
369_V 114_G 1.18 0.14 0.01
183_D 84_T 1.17 0.14 0.01
317_T 79_Q 1.17 0.14 0.01
137_A 18_D 1.16 0.13 0.01
336_Y 124_N 1.16 0.13 0.01
122_M 136_R 1.14 0.13 0.01
284_C 100_I 1.14 0.13 0.01
334_R 30_V 1.14 0.13 0.01
167_G 19_A 1.13 0.13 0.01
216_C 102_V 1.13 0.12 0.01
213_E 110_V 1.11 0.12 0.00
220_L 33_A 1.11 0.12 0.00
292_L 88_R 1.11 0.12 0.00
350_T 86_D 1.10 0.12 0.00
153_D 88_R 1.10 0.12 0.00
148_T 88_R 1.10 0.12 0.00
238_S 8_D 1.10 0.12 0.00
307_G 73_I 1.10 0.12 0.00
131_M 100_I 1.10 0.12 0.00
170_L 114_G 1.09 0.12 0.00
198_S 111_L 1.09 0.12 0.00
243_D 124_N 1.08 0.12 0.00
112_K 120_G 1.08 0.11 0.00
226_M 36_G 1.08 0.11 0.00
175_L 47_V 1.07 0.11 0.00
271_C 138_Q 1.07 0.11 0.00
302_T 111_L 1.06 0.11 0.00
292_L 120_G 1.05 0.11 0.00
172_H 80_D 1.05 0.11 0.00
131_M 137_S 1.04 0.10 0.00
294_A 106_A 1.04 0.10 0.00
315_E 73_I 1.03 0.10 0.00
344_I 30_V 1.03 0.10 0.00
75_V 135_R 1.02 0.10 0.00
157_G 103_T 1.02 0.10 0.00
227_A 100_I 1.01 0.10 0.00
117_K 50_L 1.00 0.10 0.00
236_E 89_T 1.00 0.10 0.00
356_I 49_I 1.00 0.10 0.00
220_L 100_I 1.00 0.10 0.00
63_I 65_L 0.99 0.10 0.00
157_G 138_Q 0.99 0.10 0.00
197_Y 84_T 0.99 0.10 0.00
308_I 68_Q 0.99 0.10 0.00
122_M 73_I 0.99 0.10 0.00
241_L 135_R 0.99 0.10 0.00
346_A 19_A 0.98 0.10 0.00
286_V 124_N 0.98 0.10 0.00
273_I 68_Q 0.98 0.10 0.00
340_I 51_V 0.98 0.09 0.00
369_V 13_D 0.98 0.09 0.00
29_V 49_I 0.98 0.09 0.00
51_S 88_R 0.98 0.09 0.00
47_G 26_D 0.97 0.09 0.00
65_T 69_K 0.97 0.09 0.00
143_A 101_T 0.97 0.09 0.00
145_G 81_G 0.96 0.09 0.00
317_T 4_N 0.96 0.09 0.00
262_Q 114_G 0.96 0.09 0.00
90_Y 103_T 0.96 0.09 0.00
308_I 65_L 0.96 0.09 0.00
88_T 82_E 0.95 0.09 0.00
97_P 89_T 0.95 0.09 0.00
131_M 131_A 0.95 0.09 0.00
215_L 83_F 0.95 0.09 0.00
303_T 58_F 0.95 0.09 0.00
131_M 110_V 0.95 0.09 0.00
29_V 100_I 0.95 0.09 0.00
167_G 125_K 0.94 0.09 0.00
319_L 112_L 0.94 0.09 0.00
84_I 120_G 0.94 0.09 0.00
303_T 111_L 0.94 0.09 0.00
357_S 17_Q 0.94 0.09 0.00
216_C 35_P 0.94 0.09 0.00
84_I 114_G 0.94 0.09 0.00
315_E 88_R 0.94 0.09 0.00
211_I 60_V 0.94 0.09 0.00
199_F 45_A 0.93 0.09 0.00
369_V 64_T 0.93 0.09 0.00
260_L 9_N 0.93 0.09 0.00
211_I 69_K 0.93 0.09 0.00
5_A 19_A 0.93 0.09 0.00
48_Q 109_L 0.93 0.09 0.00
88_T 119_H 0.93 0.09 0.00
76_T 69_K 0.93 0.09 0.00
281_I 134_L 0.93 0.09 0.00
310_D 35_P 0.92 0.08 0.00
53_V 114_G 0.92 0.08 0.00
107_A 88_R 0.92 0.08 0.00
108_P 88_R 0.92 0.08 0.00
50_D 61_N 0.92 0.08 0.00
28_A 30_V 0.92 0.08 0.00
142_Y 58_F 0.92 0.08 0.00
148_T 15_T 0.92 0.08 0.00
304_M 103_T 0.92 0.08 0.00
198_S 19_A 0.92 0.08 0.00
260_L 81_G 0.91 0.08 0.00
241_L 82_E 0.91 0.08 0.00
161_T 67_G 0.91 0.08 0.00
127_N 47_V 0.91 0.08 0.00
224_Q 111_L 0.91 0.08 0.00
330_A 65_L 0.91 0.08 0.00
151_V 31_W 0.90 0.08 0.00
36_R 89_T 0.90 0.08 0.00
314_K 63_L 0.90 0.08 0.00
167_G 30_V 0.90 0.08 0.00
66_L 124_N 0.90 0.08 0.00
73_G 63_L 0.89 0.08 0.00
292_L 80_D 0.89 0.08 0.00
100_H 115_K 0.89 0.08 0.00
13_S 44_P 0.89 0.08 0.00
17_K 69_K 0.89 0.08 0.00
53_V 73_I 0.89 0.08 0.00
131_M 128_Y 0.88 0.08 0.00
241_L 128_Y 0.88 0.08 0.00
340_I 124_N 0.88 0.08 0.00
183_D 116_E 0.88 0.08 0.00
274_H 126_K 0.88 0.08 0.00
355_W 51_V 0.88 0.08 0.00
59_S 19_A 0.87 0.07 0.00
354_M 120_G 0.87 0.07 0.00
330_A 42_I 0.86 0.07 0.00
148_T 26_D 0.86 0.07 0.00
95_V 119_H 0.86 0.07 0.00
350_T 101_T 0.86 0.07 0.00
303_T 92_T 0.86 0.07 0.00
362_D 4_N 0.86 0.07 0.00
205_R 13_D 0.86 0.07 0.00
296_T 80_D 0.86 0.07 0.00
325_K 107_K 0.86 0.07 0.00
366_P 63_L 0.86 0.07 0.00
172_H 105_T 0.86 0.07 0.00
247_I 85_M 0.86 0.07 0.00
323_T 70_C 0.86 0.07 0.00
307_G 42_I 0.85 0.07 0.00
128_T 122_M 0.85 0.07 0.00
241_L 19_A 0.85 0.07 0.00
172_H 135_R 0.85 0.07 0.00
273_I 9_N 0.85 0.07 0.00
68_Y 33_A 0.85 0.07 0.00
289_R 51_V 0.85 0.07 0.00
33_I 69_K 0.85 0.07 0.00
74_I 138_Q 0.84 0.07 0.00
36_R 84_T 0.84 0.07 0.00
364_S 67_G 0.84 0.07 0.00
165_Y 103_T 0.84 0.07 0.00
278_F 112_L 0.84 0.07 0.00
97_P 7_I 0.84 0.07 0.00
310_D 19_A 0.84 0.07 0.00
328_I 43_T 0.84 0.07 0.00
348_L 63_L 0.84 0.07 0.00
185_T 115_K 0.84 0.07 0.00
47_G 88_R 0.84 0.07 0.00
357_S 66_G 0.83 0.07 0.00
181_G 103_T 0.83 0.07 0.00
34_V 114_G 0.83 0.07 0.00
57_A 112_L 0.83 0.07 0.00
75_V 15_T 0.83 0.07 0.00
102_V 122_M 0.82 0.07 0.00
260_L 103_T 0.82 0.07 0.00
50_D 110_V 0.82 0.07 0.00
108_P 66_G 0.82 0.07 0.00
221_D 7_I 0.82 0.07 0.00
104_L 69_K 0.82 0.07 0.00
35_G 129_E 0.82 0.07 0.00
151_V 134_L 0.82 0.07 0.00
183_D 74_R 0.82 0.07 0.00
323_T 60_V 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
10587 0.13 2BTF Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.12 Done
10125 0.19 prof-act Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10099 0 prof-act Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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