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OPENSEQ.org
fliFfliQ
Genes: A B A+B
Length: 560 89 629
Sequences: 1496 1330 939
Seq/Len: 2.67 14.94 1.49
MirrorTree (Pazo et al. 2001) 0.66
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.03
10 0.00 0.01 0.26
20 0.00 0.01 1.45
100 0.01 0.02 1.59
∞ 0.03 0.05 1.85
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
355_F 45_N 1.39 0.79 0.04
136_A 45_N 1.20 0.64 0.03
206_L 67_P 1.19 0.63 0.03
358_V 26_L 1.16 0.60 0.02
227_Y 22_L 1.14 0.58 0.02
357_T 76_F 1.14 0.58 0.02
49_A 45_N 1.13 0.57 0.02
270_I 43_Q 1.11 0.56 0.02
497_E 16_I 1.11 0.55 0.02
66_A 57_L 1.10 0.55 0.02
53_Y 88_I 1.10 0.54 0.02
41_L 45_N 1.07 0.51 0.02
81_L 7_V 1.06 0.50 0.02
190_K 30_I 1.05 0.49 0.02
182_R 64_F 1.05 0.49 0.02
12_Q 35_I 1.04 0.48 0.02
106_L 28_G 1.03 0.47 0.02
202_A 60_V 1.03 0.47 0.02
202_A 63_I 1.03 0.47 0.02
311_V 45_N 1.02 0.46 0.02
151_I 6_L 1.00 0.44 0.01
211_V 47_M 1.00 0.44 0.01
264_V 54_K 1.00 0.44 0.01
53_Y 43_Q 1.00 0.44 0.01
309_Q 52_V 0.99 0.43 0.01
11_G 35_I 0.99 0.43 0.01
427_R 34_V 0.99 0.43 0.01
217_S 22_L 0.99 0.43 0.01
264_V 25_L 0.98 0.42 0.01
107_I 54_K 0.98 0.42 0.01
201_A 47_M 0.97 0.41 0.01
212_R 55_I 0.97 0.41 0.01
133_Y 80_I 0.96 0.40 0.01
33_V 72_T 0.96 0.40 0.01
167_T 80_I 0.95 0.39 0.01
170_Q 78_E 0.95 0.39 0.01
151_I 64_F 0.95 0.39 0.01
82_E 30_I 0.95 0.39 0.01
90_P 67_P 0.94 0.38 0.01
428_V 64_F 0.94 0.38 0.01
137_I 43_Q 0.94 0.37 0.01
37_V 26_L 0.93 0.37 0.01
530_L 81_L 0.93 0.37 0.01
60_V 23_P 0.93 0.37 0.01
542_A 6_L 0.93 0.37 0.01
412_D 85_P 0.92 0.36 0.01
246_L 73_M 0.92 0.36 0.01
549_I 58_V 0.92 0.36 0.01
498_K 63_I 0.91 0.35 0.01
124_A 80_I 0.91 0.35 0.01
80_I 37_I 0.91 0.35 0.01
414_V 50_S 0.91 0.35 0.01
117_F 14_F 0.91 0.35 0.01
9_Q 35_I 0.91 0.35 0.01
38_F 35_I 0.90 0.34 0.01
345_S 66_M 0.90 0.34 0.01
23_I 88_I 0.90 0.34 0.01
463_V 43_Q 0.89 0.34 0.01
136_A 54_K 0.89 0.34 0.01
158_I 33_L 0.89 0.33 0.01
101_I 19_L 0.89 0.33 0.01
107_I 23_P 0.89 0.33 0.01
265_R 43_Q 0.89 0.33 0.01
61_D 26_L 0.88 0.32 0.01
11_G 60_V 0.88 0.32 0.01
126_N 45_N 0.88 0.32 0.01
469_Q 13_T 0.87 0.31 0.01
312_P 68_W 0.86 0.31 0.01
297_N 77_T 0.86 0.30 0.01
196_K 69_M 0.86 0.30 0.01
521_I 47_M 0.86 0.30 0.01
380_D 56_I 0.86 0.30 0.01
192_I 50_S 0.85 0.30 0.01
144_T 17_T 0.85 0.30 0.01
314_A 85_P 0.84 0.29 0.01
137_I 6_L 0.84 0.29 0.01
463_V 18_L 0.84 0.29 0.01
413_S 30_I 0.84 0.29 0.01
532_G 35_I 0.84 0.29 0.01
457_F 9_L 0.84 0.29 0.01
406_Y 75_D 0.84 0.29 0.01
303_R 12_Q 0.84 0.28 0.01
371_Y 66_M 0.84 0.28 0.01
453_A 20_L 0.83 0.28 0.01
457_F 82_N 0.83 0.28 0.01
540_E 45_N 0.83 0.28 0.01
116_A 65_L 0.83 0.28 0.01
368_D 11_V 0.83 0.28 0.01
339_T 41_T 0.83 0.28 0.01
91_Q 81_L 0.82 0.27 0.01
294_Q 76_F 0.82 0.27 0.01
493_E 76_F 0.82 0.27 0.01
114_F 43_Q 0.82 0.27 0.01
61_D 22_L 0.82 0.27 0.01
30_V 62_L 0.82 0.27 0.01
435_F 38_F 0.81 0.27 0.01
75_N 13_T 0.81 0.27 0.01
425_S 60_V 0.81 0.27 0.01
326_N 88_I 0.81 0.27 0.01
476_A 9_L 0.81 0.27 0.01
282_E 29_L 0.81 0.27 0.01
431_K 34_V 0.81 0.27 0.01
152_R 31_A 0.81 0.26 0.01
313_G 68_W 0.81 0.26 0.01
421_F 62_L 0.81 0.26 0.01
154_A 60_V 0.81 0.26 0.01
341_N 28_G 0.81 0.26 0.01
447_V 76_F 0.80 0.26 0.01
493_E 30_I 0.80 0.25 0.01
526_L 56_I 0.80 0.25 0.01
409_N 74_I 0.80 0.25 0.01
362_S 65_L 0.80 0.25 0.01
176_S 12_Q 0.80 0.25 0.01
545_L 63_I 0.80 0.25 0.01
129_Q 45_N 0.80 0.25 0.01
391_E 9_L 0.79 0.25 0.01
288_P 35_I 0.79 0.25 0.01
117_F 55_I 0.79 0.25 0.01
310_G 44_I 0.79 0.24 0.01
213_I 83_Q 0.78 0.24 0.01
197_N 62_L 0.78 0.24 0.01
290_V 64_F 0.78 0.24 0.01
94_V 43_Q 0.78 0.24 0.01
39_L 60_V 0.78 0.24 0.01
209_E 70_T 0.77 0.23 0.01
250_I 64_F 0.77 0.23 0.01
354_Q 52_V 0.77 0.23 0.01
77_V 66_M 0.77 0.23 0.01
52_G 18_L 0.77 0.23 0.01
183_E 84_I 0.77 0.23 0.01
239_K 36_S 0.77 0.23 0.01
261_T 79_N 0.77 0.23 0.01
136_A 23_P 0.77 0.23 0.01
380_D 22_L 0.77 0.23 0.01
69_V 7_V 0.77 0.23 0.01
76_N 31_A 0.77 0.23 0.01
454_I 34_V 0.76 0.23 0.01
117_F 69_M 0.76 0.23 0.01
34_G 50_S 0.76 0.23 0.01
219_V 12_Q 0.76 0.23 0.01
142_A 64_F 0.76 0.22 0.01
169_R 73_M 0.76 0.22 0.01
80_I 38_F 0.75 0.22 0.01
353_K 11_V 0.75 0.22 0.01
286_P 67_P 0.75 0.22 0.01
250_I 76_F 0.75 0.22 0.01
264_V 23_P 0.75 0.22 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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