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OPENSEQ.org
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Genes: A B A+B
Length: 675 89 741
Sequences: 1449 1545 1024
Seq/Len: 2.15 17.36 1.38
MirrorTree (Pazo et al. 2001) 0.79
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 0.01 0.07
2 0.01 0.01 0.16
5 0.01 0.01 1.01
10 0.01 0.01 1.21
20 0.01 0.01 1.34
100 0.02 0.01 1.49
∞ 0.08 0.07 1.68
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
107_F 54_K 1.41 0.79 0.04
200_I 43_Q 1.36 0.75 0.04
249_I 47_Q 1.34 0.74 0.03
135_A 27_A 1.32 0.73 0.03
295_V 7_V 1.25 0.67 0.03
654_S 38_V 1.24 0.66 0.03
118_V 35_I 1.23 0.65 0.02
607_P 46_D 1.12 0.54 0.02
471_F 53_L 1.11 0.53 0.02
596_Q 36_S 1.10 0.52 0.02
87_T 50_P 1.09 0.51 0.02
499_R 30_V 1.05 0.47 0.01
107_F 25_V 1.05 0.47 0.01
82_S 8_Q 1.02 0.44 0.01
323_K 26_I 1.01 0.42 0.01
255_G 36_S 1.00 0.42 0.01
86_S 51_F 1.00 0.42 0.01
306_V 28_A 1.00 0.42 0.01
484_F 8_Q 0.99 0.41 0.01
64_L 51_F 0.99 0.41 0.01
297_A 85_P 0.99 0.41 0.01
609_R 80_I 0.98 0.40 0.01
68_S 41_I 0.98 0.40 0.01
486_G 58_V 0.97 0.39 0.01
150_M 6_F 0.97 0.39 0.01
469_I 13_T 0.96 0.38 0.01
252_V 67_H 0.96 0.38 0.01
632_A 43_Q 0.96 0.38 0.01
287_L 38_V 0.96 0.38 0.01
375_W 33_I 0.95 0.37 0.01
139_A 12_Q 0.93 0.35 0.01
283_S 43_Q 0.93 0.35 0.01
436_K 53_L 0.93 0.35 0.01
48_S 7_V 0.93 0.35 0.01
402_F 6_F 0.93 0.35 0.01
545_S 76_F 0.92 0.35 0.01
243_A 45_Q 0.92 0.34 0.01
621_M 58_V 0.92 0.34 0.01
469_I 18_F 0.92 0.34 0.01
127_Q 47_Q 0.92 0.34 0.01
409_I 31_L 0.91 0.34 0.01
649_S 73_I 0.91 0.33 0.01
86_S 3_T 0.90 0.32 0.01
56_L 40_A 0.90 0.32 0.01
474_K 38_V 0.89 0.31 0.01
404_L 38_V 0.89 0.31 0.01
123_I 29_S 0.88 0.31 0.01
91_I 23_P 0.88 0.31 0.01
27_V 47_Q 0.88 0.30 0.01
577_L 85_P 0.88 0.30 0.01
566_I 66_Y 0.88 0.30 0.01
208_V 81_F 0.87 0.30 0.01
247_A 43_Q 0.87 0.30 0.01
373_M 76_F 0.86 0.29 0.01
414_L 58_V 0.86 0.29 0.01
404_L 76_F 0.85 0.29 0.01
105_G 68_W 0.85 0.28 0.01
552_V 25_V 0.85 0.28 0.01
72_I 56_I 0.85 0.28 0.01
89_R 6_F 0.85 0.28 0.01
505_V 31_L 0.85 0.28 0.01
165_V 43_Q 0.85 0.28 0.01
103_S 56_I 0.84 0.28 0.01
515_S 43_Q 0.84 0.28 0.01
169_L 35_I 0.84 0.28 0.01
99_D 56_I 0.84 0.28 0.01
34_L 81_F 0.84 0.28 0.01
293_M 19_I 0.84 0.28 0.01
437_L 59_F 0.84 0.28 0.01
109_V 68_W 0.84 0.27 0.01
411_K 26_I 0.84 0.27 0.01
531_I 69_M 0.84 0.27 0.01
86_S 47_Q 0.84 0.27 0.01
192_M 53_L 0.84 0.27 0.01
380_E 45_Q 0.84 0.27 0.01
225_F 73_I 0.83 0.27 0.01
49_T 60_A 0.83 0.27 0.01
196_K 43_Q 0.83 0.27 0.01
132_T 84_I 0.83 0.27 0.01
225_F 20_L 0.83 0.27 0.01
20_A 40_A 0.83 0.27 0.01
547_K 76_F 0.83 0.27 0.01
482_K 30_V 0.83 0.27 0.01
184_F 53_L 0.83 0.27 0.01
73_L 84_I 0.83 0.26 0.01
166_I 76_F 0.83 0.26 0.01
400_I 53_L 0.83 0.26 0.01
561_A 47_Q 0.83 0.26 0.01
254_A 15_W 0.83 0.26 0.01
118_V 85_P 0.82 0.26 0.01
100_I 29_S 0.82 0.26 0.01
553_I 14_L 0.82 0.26 0.01
311_A 6_F 0.82 0.26 0.01
377_F 22_L 0.82 0.26 0.01
493_L 57_A 0.82 0.26 0.01
215_L 73_I 0.82 0.26 0.01
543_F 33_I 0.81 0.25 0.01
541_L 68_W 0.81 0.25 0.01
163_A 76_F 0.81 0.25 0.01
582_I 26_I 0.81 0.25 0.01
150_M 38_V 0.81 0.25 0.01
518_V 45_Q 0.80 0.25 0.01
586_I 12_Q 0.80 0.24 0.01
317_I 55_I 0.80 0.24 0.01
566_I 64_L 0.80 0.24 0.01
38_V 27_A 0.80 0.24 0.01
530_S 48_T 0.80 0.24 0.01
119_I 26_I 0.80 0.24 0.01
517_I 62_L 0.80 0.24 0.01
169_L 30_V 0.79 0.24 0.01
125_I 7_V 0.79 0.24 0.01
585_D 73_I 0.79 0.24 0.01
71_T 2_E 0.79 0.24 0.01
640_K 45_Q 0.79 0.24 0.01
472_L 53_L 0.79 0.23 0.01
629_I 69_M 0.79 0.23 0.01
104_F 40_A 0.79 0.23 0.01
58_I 40_A 0.79 0.23 0.01
501_Y 18_F 0.79 0.23 0.01
162_R 53_L 0.79 0.23 0.01
187_S 17_I 0.78 0.23 0.01
309_F 82_E 0.78 0.23 0.01
126_V 58_V 0.78 0.23 0.01
483_E 44_L 0.78 0.23 0.01
617_L 20_L 0.78 0.23 0.01
385_L 17_I 0.78 0.23 0.01
407_E 62_L 0.78 0.23 0.01
537_I 84_I 0.78 0.23 0.01
570_Y 20_L 0.78 0.23 0.01
656_Q 36_S 0.78 0.23 0.01
621_M 30_V 0.77 0.22 0.01
536_T 13_T 0.77 0.22 0.01
37_V 31_L 0.77 0.22 0.01
563_R 52_L 0.77 0.22 0.01
408_S 72_T 0.77 0.22 0.01
619_N 34_I 0.77 0.22 0.01
631_T 11_V 0.77 0.22 0.01
380_E 30_V 0.76 0.22 0.01
85_V 10_C 0.76 0.22 0.01
308_L 58_V 0.76 0.21 0.01
222_D 35_I 0.76 0.21 0.01
126_V 64_L 0.76 0.21 0.01
95_H 9_L 0.76 0.21 0.01
463_A 53_L 0.76 0.21 0.01
41_I 20_L 0.76 0.21 0.01
232_F 44_L 0.76 0.21 0.01
55_M 52_L 0.76 0.21 0.01
135_A 46_D 0.76 0.21 0.01
533_D 13_T 0.75 0.21 0.01
438_S 53_L 0.75 0.21 0.01
308_L 22_L 0.75 0.21 0.01
378_F 25_V 0.75 0.21 0.01
520_I 61_T 0.75 0.21 0.01
529_V 19_I 0.75 0.21 0.01
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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