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OPENSEQ.org
prof-act
Genes: A B A+B
Length: 374 139 496
Sequences: 3302 621 96
Seq/Len: 8.83 4.47 0.19
MirrorTree (Pazo et al. 2001) 0.40
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 0.09
10 0.05 0.07 0.11
20 0.06 0.07 0.12
100 0.08 0.07 0.19
∞ 0.17 0.07 0.33
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 1.78 0.47 0.00
161_T 16_C 1.65 0.39 0.00
369_V 103_T 1.47 0.29 0.00
30_F 33_A 1.46 0.29 0.00
346_A 19_A 1.41 0.27 0.00
289_R 112_L 1.39 0.26 0.00
211_I 69_K 1.37 0.25 0.00
36_R 89_T 1.29 0.21 0.00
153_D 88_R 1.27 0.21 0.00
208_V 119_H 1.26 0.20 0.00
181_G 128_Y 1.26 0.20 0.00
296_T 80_D 1.23 0.19 0.00
157_G 114_G 1.23 0.19 0.00
271_C 5_A 1.22 0.19 0.00
356_I 124_N 1.21 0.18 0.00
238_S 8_D 1.20 0.18 0.00
185_T 66_G 1.17 0.17 0.00
303_T 111_L 1.16 0.17 0.00
308_I 65_L 1.15 0.16 0.00
218_V 72_V 1.15 0.16 0.00
292_L 88_R 1.15 0.16 0.00
262_Q 110_V 1.14 0.16 0.00
321_P 111_L 1.12 0.15 0.00
153_D 73_I 1.11 0.15 0.00
369_V 13_D 1.09 0.14 0.00
73_G 63_L 1.09 0.14 0.00
216_C 102_V 1.08 0.14 0.00
340_I 49_I 1.08 0.14 0.00
100_H 131_A 1.08 0.14 0.00
218_V 58_F 1.07 0.14 0.00
241_L 110_V 1.07 0.14 0.00
289_R 102_V 1.07 0.14 0.00
262_Q 114_G 1.06 0.14 0.00
90_Y 103_T 1.06 0.14 0.00
150_I 25_K 1.05 0.13 0.00
53_V 108_T 1.05 0.13 0.00
151_V 105_T 1.04 0.13 0.00
34_V 138_Q 1.04 0.13 0.00
131_M 1_A 1.02 0.13 0.00
317_T 79_Q 1.02 0.12 0.00
369_V 64_T 1.00 0.12 0.00
104_L 114_G 1.00 0.12 0.00
326_I 61_N 1.00 0.12 0.00
51_S 88_R 1.00 0.12 0.00
157_G 39_F 1.00 0.12 0.00
131_M 100_I 1.00 0.12 0.00
34_V 58_F 1.00 0.12 0.00
290_K 112_L 0.99 0.12 0.00
346_A 111_L 0.98 0.12 0.00
315_E 88_R 0.98 0.12 0.00
67_K 46_E 0.98 0.12 0.00
186_D 105_T 0.98 0.12 0.00
335_K 65_L 0.98 0.11 0.00
143_A 101_T 0.97 0.11 0.00
36_R 43_T 0.97 0.11 0.00
119_T 20_A 0.97 0.11 0.00
212_K 35_P 0.97 0.11 0.00
328_I 50_L 0.97 0.11 0.00
29_V 49_I 0.96 0.11 0.00
294_A 43_T 0.96 0.11 0.00
122_M 120_G 0.96 0.11 0.00
213_E 110_V 0.96 0.11 0.00
31_P 74_R 0.96 0.11 0.00
112_K 120_G 0.96 0.11 0.00
165_Y 110_V 0.95 0.11 0.00
139_L 17_Q 0.95 0.11 0.00
227_A 51_V 0.95 0.11 0.00
326_I 73_I 0.95 0.11 0.00
296_T 10_L 0.95 0.11 0.00
326_I 112_L 0.95 0.11 0.00
369_V 114_G 0.95 0.11 0.00
177_L 46_E 0.94 0.11 0.00
355_W 51_V 0.94 0.10 0.00
267_G 12_A 0.94 0.10 0.00
137_A 23_G 0.93 0.10 0.00
88_T 30_V 0.92 0.10 0.00
281_I 136_R 0.92 0.10 0.00
151_V 134_L 0.92 0.10 0.00
277_T 22_V 0.92 0.10 0.00
107_A 69_K 0.92 0.10 0.00
75_V 15_T 0.92 0.10 0.00
298_L 70_C 0.92 0.10 0.00
321_P 116_E 0.91 0.10 0.00
303_T 92_T 0.91 0.10 0.00
152_M 124_N 0.91 0.10 0.00
218_V 7_I 0.91 0.10 0.00
8_V 131_A 0.91 0.10 0.00
84_I 124_N 0.91 0.10 0.00
148_T 12_A 0.91 0.10 0.00
302_T 111_L 0.91 0.10 0.00
296_T 58_F 0.90 0.10 0.00
84_I 120_G 0.90 0.10 0.00
131_M 110_V 0.90 0.10 0.00
98_E 104_M 0.90 0.10 0.00
189_M 111_L 0.90 0.10 0.00
346_A 6_Y 0.90 0.10 0.00
167_G 19_A 0.89 0.10 0.00
16_C 112_L 0.89 0.10 0.00
319_L 58_F 0.89 0.10 0.00
157_G 138_Q 0.89 0.10 0.00
303_T 51_V 0.89 0.10 0.00
29_V 84_T 0.89 0.10 0.00
300_G 62_G 0.89 0.10 0.00
360_E 46_E 0.89 0.10 0.00
47_G 26_D 0.89 0.09 0.00
5_A 43_T 0.89 0.09 0.00
338_V 111_L 0.88 0.09 0.00
148_T 15_T 0.88 0.09 0.00
325_K 63_L 0.88 0.09 0.00
17_K 138_Q 0.88 0.09 0.00
19_G 10_L 0.88 0.09 0.00
167_G 125_K 0.88 0.09 0.00
151_V 31_W 0.88 0.09 0.00
366_P 74_R 0.88 0.09 0.00
199_F 45_A 0.87 0.09 0.00
55_D 136_R 0.87 0.09 0.00
50_D 110_V 0.87 0.09 0.00
312_M 83_F 0.87 0.09 0.00
161_T 67_G 0.86 0.09 0.00
303_T 129_E 0.86 0.09 0.00
57_A 58_F 0.86 0.09 0.00
100_H 69_K 0.86 0.09 0.00
358_K 16_C 0.86 0.09 0.00
310_D 35_P 0.85 0.09 0.00
327_K 42_I 0.85 0.09 0.00
155_G 65_L 0.85 0.09 0.00
148_T 88_R 0.85 0.09 0.00
305_Y 113_M 0.85 0.09 0.00
7_L 18_D 0.85 0.09 0.00
224_Q 131_A 0.85 0.09 0.00
9_V 36_G 0.85 0.09 0.00
257_P 99_N 0.84 0.09 0.00
366_P 48_G 0.84 0.09 0.00
260_L 74_R 0.84 0.09 0.00
33_I 88_R 0.84 0.09 0.00
281_I 86_D 0.84 0.09 0.00
36_R 64_T 0.84 0.09 0.00
356_I 49_I 0.84 0.09 0.00
296_T 1_A 0.84 0.08 0.00
65_T 120_G 0.84 0.08 0.00
340_I 51_V 0.83 0.08 0.00
260_L 44_P 0.83 0.08 0.00
139_L 39_F 0.83 0.08 0.00
259_A 12_A 0.83 0.08 0.00
334_R 30_V 0.83 0.08 0.00
249_I 12_A 0.83 0.08 0.00
340_I 124_N 0.83 0.08 0.00
301_G 62_G 0.83 0.08 0.00
99_E 110_V 0.83 0.08 0.00
292_L 70_C 0.83 0.08 0.00
156_D 102_V 0.82 0.08 0.00
302_T 135_R 0.82 0.08 0.00
207_I 123_I 0.82 0.08 0.00
273_I 65_L 0.82 0.08 0.00
241_L 128_Y 0.82 0.08 0.00
148_T 44_P 0.82 0.08 0.00
38_R 102_V 0.82 0.08 0.00
211_I 59_F 0.82 0.08 0.00
78_W 39_F 0.82 0.08 0.00
350_T 70_C 0.82 0.08 0.00
105_T 90_K 0.82 0.08 0.00
33_I 11_M 0.82 0.08 0.00
352_Q 81_G 0.82 0.08 0.00
342_G 56_S 0.81 0.08 0.00
192_L 9_N 0.81 0.08 0.00
296_T 13_D 0.81 0.08 0.00
93_L 109_L 0.81 0.08 0.00
328_I 135_R 0.81 0.08 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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