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OPENSEQ.org
FxQ
Genes: A B A+B
Length: 560 89 628
Sequences: 1492 1330 1034
Seq/Len: 2.66 14.94 1.65
MirrorTree (Pazo et al. 2001) 0.65
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 1.46
100 0.01 0.02 1.59
∞ 0.03 0.05 1.87
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
206_L 67_P 1.25 0.72 0.01
355_F 45_N 1.25 0.72 0.01
311_V 45_N 1.24 0.70 0.01
133_Y 80_I 1.17 0.64 0.01
53_Y 88_I 1.17 0.64 0.01
107_I 54_K 1.12 0.60 0.01
495_A 31_A 1.11 0.58 0.01
66_A 57_L 1.10 0.57 0.01
49_A 45_N 1.10 0.57 0.01
358_V 26_L 1.09 0.56 0.01
53_Y 43_Q 1.08 0.55 0.01
136_A 45_N 1.07 0.55 0.01
530_L 81_L 1.06 0.53 0.01
190_K 30_I 1.05 0.53 0.01
173_P 35_I 1.05 0.52 0.01
270_I 43_Q 1.03 0.50 0.01
264_V 54_K 1.03 0.50 0.01
106_L 28_G 1.02 0.49 0.01
137_I 43_Q 1.02 0.48 0.01
486_N 80_I 1.01 0.48 0.01
264_V 25_L 1.01 0.48 0.01
90_P 67_P 1.00 0.47 0.01
227_Y 22_L 0.99 0.46 0.01
201_A 47_M 0.99 0.45 0.01
41_L 45_N 0.98 0.45 0.01
497_E 16_I 0.98 0.45 0.01
187_L 35_I 0.97 0.44 0.01
357_T 76_F 0.97 0.44 0.01
23_I 88_I 0.97 0.43 0.01
294_Q 76_F 0.97 0.43 0.01
211_V 47_M 0.97 0.43 0.01
152_R 31_A 0.95 0.41 0.01
12_Q 35_I 0.94 0.41 0.01
136_A 54_K 0.94 0.41 0.01
11_G 60_V 0.93 0.40 0.01
446_P 34_V 0.91 0.38 0.01
60_V 23_P 0.91 0.37 0.01
351_T 84_I 0.91 0.37 0.01
414_V 50_S 0.90 0.37 0.01
489_L 35_I 0.90 0.37 0.01
117_F 14_F 0.90 0.36 0.01
34_G 50_S 0.89 0.36 0.01
116_A 65_L 0.89 0.36 0.01
303_R 12_Q 0.89 0.36 0.01
107_I 23_P 0.89 0.35 0.01
9_Q 35_I 0.89 0.35 0.01
82_E 30_I 0.88 0.35 0.01
521_I 47_M 0.88 0.35 0.01
154_A 60_V 0.88 0.35 0.01
312_P 68_W 0.88 0.34 0.01
338_V 73_M 0.88 0.34 0.01
30_I 62_L 0.87 0.34 0.01
408_A 62_L 0.87 0.34 0.01
52_G 18_L 0.87 0.34 0.01
446_P 36_S 0.87 0.33 0.01
213_I 31_A 0.86 0.33 0.01
170_Q 78_E 0.86 0.33 0.01
91_Q 81_L 0.86 0.33 0.01
332_T 60_V 0.86 0.33 0.01
27_A 88_I 0.86 0.32 0.01
114_F 43_Q 0.86 0.32 0.01
94_V 43_Q 0.86 0.32 0.01
167_T 80_I 0.85 0.32 0.01
217_S 22_L 0.85 0.32 0.01
450_F 44_I 0.85 0.32 0.01
166_F 45_N 0.85 0.32 0.01
388_L 54_K 0.85 0.32 0.01
28_S 14_F 0.85 0.32 0.00
313_G 68_W 0.85 0.32 0.00
552_D 44_I 0.85 0.32 0.00
81_L 7_V 0.85 0.32 0.00
341_N 28_G 0.85 0.32 0.00
468_T 26_L 0.85 0.31 0.00
250_I 64_F 0.84 0.31 0.00
37_V 26_L 0.84 0.31 0.00
380_D 22_L 0.84 0.30 0.00
129_Q 45_N 0.83 0.30 0.00
158_I 33_L 0.83 0.30 0.00
353_K 11_V 0.83 0.30 0.00
7_L 35_I 0.83 0.30 0.00
169_R 21_S 0.83 0.29 0.00
202_A 63_I 0.82 0.29 0.00
202_A 60_V 0.82 0.29 0.00
257_F 50_S 0.82 0.29 0.00
412_D 85_P 0.82 0.29 0.00
38_F 35_I 0.82 0.29 0.00
265_K 43_Q 0.82 0.29 0.00
80_K 37_I 0.82 0.29 0.00
60_V 54_K 0.82 0.29 0.00
515_N 9_L 0.82 0.29 0.00
73_E 38_F 0.82 0.29 0.00
309_Q 52_V 0.82 0.29 0.00
427_R 34_V 0.81 0.28 0.00
532_G 35_I 0.81 0.28 0.00
10_I 37_I 0.81 0.28 0.00
182_R 64_F 0.81 0.28 0.00
463_V 18_L 0.80 0.28 0.00
274_F 13_T 0.80 0.28 0.00
75_N 38_F 0.80 0.28 0.00
144_T 17_T 0.80 0.27 0.00
11_G 35_I 0.80 0.27 0.00
159_A 45_N 0.80 0.27 0.00
483_Q 9_L 0.80 0.27 0.00
106_L 54_K 0.80 0.27 0.00
528_E 56_I 0.79 0.27 0.00
393_L 9_L 0.79 0.27 0.00
362_S 55_I 0.79 0.26 0.00
408_A 35_I 0.79 0.26 0.00
243_E 65_L 0.79 0.26 0.00
63_S 54_K 0.79 0.26 0.00
288_P 35_I 0.79 0.26 0.00
409_T 30_I 0.78 0.26 0.00
75_N 13_T 0.78 0.26 0.00
334_K 57_L 0.78 0.26 0.00
542_A 6_L 0.78 0.26 0.00
268_V 28_G 0.78 0.25 0.00
94_V 6_L 0.77 0.25 0.00
137_I 6_L 0.77 0.25 0.00
387_P 76_F 0.77 0.25 0.00
136_A 23_P 0.77 0.25 0.00
164_S 19_L 0.77 0.25 0.00
537_K 28_G 0.77 0.24 0.00
61_S 22_L 0.77 0.24 0.00
339_T 41_T 0.76 0.24 0.00
551_N 49_L 0.76 0.24 0.00
174_T 70_T 0.76 0.24 0.00
80_K 38_F 0.76 0.24 0.00
449_Y 43_Q 0.76 0.24 0.00
540_E 45_N 0.76 0.24 0.00
38_F 12_Q 0.76 0.24 0.00
161_P 31_A 0.76 0.24 0.00
345_S 66_M 0.76 0.24 0.00
523_Y 45_N 0.76 0.24 0.00
57_V 43_Q 0.76 0.24 0.00
391_E 9_L 0.75 0.24 0.00
202_A 58_V 0.75 0.23 0.00
455_L 69_M 0.75 0.23 0.00
368_D 11_V 0.75 0.23 0.00
43_R 35_I 0.75 0.23 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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