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OPENSEQ.org
1234
Genes: A B A+B
Length: 490 396 835
Sequences: 6314 24071 651
Seq/Len: 12.89 60.79 0.78
MirrorTree (Pazo et al. 2001) 0.45
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 0.02 0.25
2 0.04 0.03 0.32
5 0.05 0.04 0.44
10 0.05 0.05 0.56
20 0.05 0.07 0.73
100 0.07 0.15 1.85
∞ 0.16 0.22 4.14
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
99_V 123_V 1.67 0.81 0.04
122_I 298_L 1.17 0.42 0.01
465_V 375_V 1.09 0.36 0.01
124_I 239_I 1.09 0.35 0.01
99_V 323_Q 1.08 0.35 0.01
105_V 256_G 1.07 0.34 0.01
99_V 92_D 1.06 0.34 0.01
337_E 67_G 1.04 0.32 0.01
294_L 356_E 1.03 0.31 0.01
104_I 199_Q 1.01 0.30 0.01
278_M 110_A 1.01 0.30 0.01
294_L 375_V 1.00 0.29 0.01
469_Y 124_W 0.98 0.28 0.01
427_E 125_V 0.97 0.27 0.01
180_I 125_V 0.96 0.26 0.01
249_R 270_R 0.93 0.24 0.01
191_F 209_L 0.93 0.24 0.01
251_Y 47_T 0.92 0.24 0.01
122_I 57_L 0.92 0.24 0.01
337_E 295_A 0.92 0.23 0.01
290_T 157_L 0.91 0.23 0.00
39_D 110_A 0.91 0.23 0.00
99_V 195_Q 0.90 0.22 0.00
423_A 277_A 0.89 0.22 0.00
200_F 265_S 0.89 0.22 0.00
429_M 366_G 0.89 0.22 0.00
334_T 356_E 0.89 0.21 0.00
93_L 175_V 0.87 0.21 0.00
333_L 371_A 0.87 0.21 0.00
51_T 253_E 0.87 0.20 0.00
288_L 195_Q 0.87 0.20 0.00
251_Y 107_L 0.86 0.20 0.00
187_V 106_A 0.85 0.20 0.00
296_V 278_A 0.85 0.19 0.00
347_K 298_L 0.85 0.19 0.00
340_E 124_W 0.84 0.19 0.00
43_L 357_Q 0.84 0.19 0.00
208_L 141_G 0.83 0.19 0.00
99_V 290_G 0.83 0.18 0.00
481_F 246_K 0.83 0.18 0.00
67_A 172_G 0.83 0.18 0.00
286_E 141_G 0.83 0.18 0.00
101_V 231_F 0.82 0.18 0.00
471_D 243_S 0.82 0.18 0.00
294_L 142_L 0.82 0.18 0.00
63_L 54_Q 0.81 0.18 0.00
334_T 239_I 0.81 0.17 0.00
92_S 175_V 0.81 0.17 0.00
70_I 364_E 0.81 0.17 0.00
429_M 199_Q 0.81 0.17 0.00
104_I 58_E 0.81 0.17 0.00
32_L 323_Q 0.81 0.17 0.00
203_V 383_D 0.81 0.17 0.00
473_K 255_V 0.81 0.17 0.00
248_E 208_P 0.80 0.17 0.00
340_E 157_L 0.80 0.17 0.00
201_T 209_L 0.80 0.17 0.00
44_F 265_S 0.79 0.17 0.00
445_C 373_G 0.79 0.16 0.00
194_Y 239_I 0.79 0.16 0.00
88_K 293_V 0.79 0.16 0.00
476_R 319_Q 0.79 0.16 0.00
93_L 255_V 0.78 0.16 0.00
333_L 271_A 0.78 0.16 0.00
210_G 375_V 0.78 0.16 0.00
195_L 131_P 0.78 0.16 0.00
433_G 373_G 0.78 0.16 0.00
339_I 52_A 0.78 0.16 0.00
297_F 73_E 0.77 0.15 0.00
298_I 273_S 0.77 0.15 0.00
470_L 119_S 0.77 0.15 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)
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