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OPENSEQ.org
HscAIscX
Genes: A B A+B
Length: 616 66 681
Sequences: 5109 324 218
Seq/Len: 8.29 4.91 0.32
MirrorTree (Pazo et al. 2001) 0.51
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 0.02 0.00 0.01
2 0.02 0.00 0.29
5 0.03 0.00 0.32
10 0.03 0.00 0.32
20 0.03 0.00 0.33
100 0.05 0.00 0.34
∞ 0.09 0.00 0.43
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
320_K 26_T 1.53 0.46 0.00
138_A 41_D 1.32 0.32 0.00
408_V 48_A 1.31 0.31 0.00
584_A 14_A 1.28 0.30 0.00
303_L 27_V 1.24 0.28 0.00
167_G 60_V 1.18 0.24 0.00
152_V 60_V 1.17 0.24 0.00
509_I 21_D 1.16 0.23 0.00
435_I 47_Q 1.15 0.23 0.00
7_S 14_A 1.14 0.22 0.00
279_S 12_G 1.13 0.22 0.00
245_L 30_T 1.12 0.21 0.00
89_M 17_D 1.12 0.21 0.00
455_A 30_T 1.09 0.20 0.00
601_D 63_D 1.09 0.20 0.00
519_Y 17_D 1.08 0.20 0.00
542_S 58_L 1.08 0.20 0.00
7_S 27_V 1.08 0.20 0.00
514_K 14_A 1.08 0.19 0.00
515_D 66_E 1.07 0.19 0.00
551_A 13_E 1.06 0.19 0.00
463_P 40_E 1.06 0.18 0.00
312_L 14_A 1.04 0.18 0.00
601_D 66_E 1.03 0.18 0.00
125_N 52_K 1.03 0.17 0.00
176_G 28_R 1.01 0.17 0.00
217_I 13_E 1.01 0.17 0.00
202_V 8_S 1.00 0.16 0.00
116_M 40_E 0.99 0.16 0.00
384_S 4_K 0.98 0.16 0.00
229_A 48_A 0.98 0.16 0.00
125_N 57_I 0.98 0.16 0.00
351_F 53_I 0.98 0.16 0.00
233_D 31_D 0.98 0.15 0.00
120_A 33_H 0.98 0.15 0.00
107_F 43_D 0.98 0.15 0.00
327_D 27_V 0.97 0.15 0.00
601_D 18_A 0.97 0.15 0.00
286_V 38_D 0.97 0.15 0.00
588_V 57_I 0.96 0.15 0.00
604_V 53_I 0.96 0.15 0.00
128_R 66_E 0.96 0.15 0.00
496_I 53_I 0.96 0.15 0.00
103_L 49_S 0.96 0.15 0.00
234_S 32_M 0.96 0.15 0.00
279_S 49_S 0.95 0.15 0.00
488_K 8_S 0.95 0.14 0.00
293_G 27_V 0.94 0.14 0.00
272_I 58_L 0.94 0.14 0.00
316_R 17_D 0.94 0.14 0.00
314_A 3_L 0.94 0.14 0.00
52_L 33_H 0.94 0.14 0.00
511_S 33_H 0.93 0.14 0.00
204_A 31_D 0.93 0.14 0.00
473_F 40_E 0.93 0.14 0.00
414_T 35_W 0.92 0.14 0.00
128_R 40_E 0.92 0.14 0.00
178_H 12_G 0.92 0.14 0.00
514_K 65_A 0.92 0.13 0.00
609_K 38_D 0.91 0.13 0.00
496_I 4_K 0.91 0.13 0.00
572_V 14_A 0.90 0.13 0.00
135_K 6_T 0.90 0.13 0.00
132_D 30_T 0.90 0.13 0.00
385_E 60_V 0.90 0.13 0.00
408_V 3_L 0.89 0.13 0.00
422_D 31_D 0.89 0.12 0.00
7_S 40_E 0.89 0.12 0.00
513_I 40_E 0.89 0.12 0.00
540_L 12_G 0.88 0.12 0.00
48_E 17_D 0.88 0.12 0.00
43_T 3_L 0.88 0.12 0.00
530_A 30_T 0.88 0.12 0.00
586_K 26_T 0.88 0.12 0.00
585_I 27_V 0.88 0.12 0.00
455_A 36_I 0.87 0.12 0.00
520_A 46_P 0.87 0.12 0.00
414_T 65_A 0.87 0.12 0.00
540_L 53_I 0.87 0.12 0.00
89_M 58_L 0.87 0.12 0.00
138_A 60_V 0.87 0.12 0.00
167_G 8_S 0.87 0.12 0.00
150_D 17_D 0.86 0.12 0.00
233_D 35_W 0.86 0.12 0.00
513_I 32_M 0.86 0.12 0.00
592_T 14_A 0.86 0.12 0.00
272_I 62_L 0.86 0.12 0.00
364_K 33_H 0.86 0.12 0.00
542_S 13_E 0.85 0.12 0.00
413_T 46_P 0.85 0.12 0.00
91_R 57_I 0.85 0.12 0.00
93_L 40_E 0.85 0.12 0.00
545_G 13_E 0.85 0.11 0.00
114_L 60_V 0.84 0.11 0.00
513_I 12_G 0.84 0.11 0.00
605_R 59_L 0.84 0.11 0.00
234_S 65_A 0.84 0.11 0.00
528_M 48_A 0.84 0.11 0.00
148_E 16_Y 0.84 0.11 0.00
473_F 3_L 0.84 0.11 0.00
254_G 3_L 0.83 0.11 0.00
583_Q 32_M 0.83 0.11 0.00
45_A 22_L 0.83 0.11 0.00
407_K 63_D 0.82 0.11 0.00
270_A 38_D 0.82 0.11 0.00
94_A 18_A 0.82 0.11 0.00
167_G 58_L 0.82 0.11 0.00
295_I 47_Q 0.82 0.10 0.00
493_E 36_I 0.82 0.10 0.00
308_V 50_N 0.82 0.10 0.00
521_E 21_D 0.82 0.10 0.00
497_Q 52_K 0.82 0.10 0.00
530_A 59_L 0.82 0.10 0.00
463_P 28_R 0.81 0.10 0.00
592_T 13_E 0.81 0.10 0.00
276_I 12_G 0.81 0.10 0.00
389_L 24_P 0.81 0.10 0.00
604_V 37_C 0.81 0.10 0.00
215_I 40_E 0.81 0.10 0.00
586_K 59_L 0.81 0.10 0.00
368_I 3_L 0.81 0.10 0.00
609_K 35_W 0.81 0.10 0.00
414_T 27_V 0.81 0.10 0.00
164_Q 24_P 0.81 0.10 0.00
146_A 6_T 0.81 0.10 0.00
297_R 62_L 0.81 0.10 0.00
135_K 26_T 0.80 0.10 0.00
552_A 38_D 0.80 0.10 0.00
591_Q 13_E 0.80 0.10 0.00
191_I 57_I 0.80 0.10 0.00
608_L 17_D 0.80 0.10 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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