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OPENSEQ.org
wspEwspB
Genes: A B A+B
Length: 769 171 918
Sequences: 1031 3789 434
Seq/Len: 1.34 22.16 0.47
MirrorTree (Pazo et al. 2001) 0.88
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 0.01 0.04 0.04
2 0.01 0.07 0.23
5 0.01 0.10 0.46
10 0.01 0.11 0.46
20 0.01 0.11 0.46
100 0.02 0.15 0.48
∞ 0.07 0.22 0.61
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
463_L 64_V 1.51 0.55 0.00
402_L 53_V 1.47 0.52 0.00
491_R 62_V 1.41 0.47 0.00
15_F 68_D 1.38 0.45 0.00
594_V 49_A 1.37 0.45 0.00
211_V 31_A 1.26 0.37 0.00
341_V 87_V 1.24 0.35 0.00
292_L 153_L 1.23 0.34 0.00
208_K 58_S 1.21 0.33 0.00
82_G 67_L 1.18 0.31 0.00
611_I 67_L 1.17 0.30 0.00
455_A 120_F 1.14 0.28 0.00
200_D 40_L 1.13 0.28 0.00
10_S 37_V 1.12 0.27 0.00
253_A 118_S 1.11 0.27 0.00
343_E 151_A 1.11 0.27 0.00
469_M 104_L 1.10 0.26 0.00
58_R 65_P 1.10 0.26 0.00
558_P 61_G 1.07 0.25 0.00
101_L 113_L 1.07 0.24 0.00
446_V 144_V 1.07 0.24 0.00
230_Q 18_L 1.07 0.24 0.00
463_L 73_A 1.06 0.24 0.00
353_L 152_L 1.06 0.24 0.00
413_Q 34_V 1.06 0.24 0.00
583_V 46_I 1.04 0.23 0.00
193_R 49_A 1.03 0.22 0.00
663_K 65_P 1.03 0.22 0.00
206_S 65_P 1.02 0.22 0.00
428_L 39_P 1.02 0.22 0.00
356_A 109_A 1.02 0.22 0.00
571_V 76_R 1.02 0.22 0.00
411_N 73_A 1.01 0.21 0.00
661_E 144_V 1.01 0.21 0.00
353_L 153_L 1.01 0.21 0.00
418_E 18_L 1.00 0.21 0.00
343_E 132_Y 1.00 0.21 0.00
708_V 65_P 1.00 0.21 0.00
123_I 22_M 1.00 0.21 0.00
509_I 64_V 0.99 0.20 0.00
101_L 88_L 0.99 0.20 0.00
618_L 66_V 0.98 0.20 0.00
400_I 93_A 0.98 0.20 0.00
394_S 104_L 0.97 0.19 0.00
139_P 119_A 0.97 0.19 0.00
471_Q 49_A 0.97 0.19 0.00
378_I 108_Q 0.97 0.19 0.00
420_A 41_L 0.97 0.19 0.00
562_V 86_I 0.97 0.19 0.00
692_L 145_Q 0.97 0.19 0.00
58_R 59_H 0.96 0.19 0.00
57_A 141_R 0.96 0.19 0.00
684_A 53_V 0.95 0.18 0.00
193_R 120_F 0.95 0.18 0.00
479_F 103_G 0.95 0.18 0.00
72_M 29_L 0.95 0.18 0.00
559_V 66_V 0.95 0.18 0.00
582_L 59_H 0.94 0.18 0.00
341_V 53_V 0.94 0.18 0.00
764_I 120_F 0.94 0.18 0.00
79_A 117_P 0.94 0.18 0.00
388_M 57_F 0.94 0.18 0.00
76_L 136_V 0.93 0.17 0.00
279_D 92_R 0.93 0.17 0.00
483_V 27_Y 0.93 0.17 0.00
96_Q 29_L 0.93 0.17 0.00
460_V 130_A 0.92 0.17 0.00
607_S 88_L 0.92 0.17 0.00
52_S 153_L 0.92 0.17 0.00
341_V 56_V 0.92 0.17 0.00
356_A 38_L 0.91 0.17 0.00
469_M 148_R 0.91 0.17 0.00
520_I 104_L 0.91 0.17 0.00
603_L 23_E 0.91 0.16 0.00
305_A 28_A 0.90 0.16 0.00
545_L 22_M 0.90 0.16 0.00
91_I 135_P 0.90 0.16 0.00
725_V 65_P 0.90 0.16 0.00
438_S 53_V 0.90 0.16 0.00
479_F 60_R 0.89 0.16 0.00
562_V 30_D 0.89 0.16 0.00
424_S 37_V 0.89 0.16 0.00
357_V 145_Q 0.89 0.16 0.00
365_E 118_S 0.89 0.16 0.00
319_G 37_V 0.89 0.16 0.00
52_S 132_Y 0.89 0.16 0.00
440_R 52_W 0.89 0.16 0.00
531_Y 152_L 0.88 0.15 0.00
585_M 58_S 0.88 0.15 0.00
314_M 28_A 0.88 0.15 0.00
203_L 87_V 0.88 0.15 0.00
471_Q 82_T 0.88 0.15 0.00
757_L 106_L 0.88 0.15 0.00
571_V 21_R 0.88 0.15 0.00
576_F 87_V 0.88 0.15 0.00
124_D 45_R 0.87 0.15 0.00
420_A 47_P 0.87 0.15 0.00
389_L 65_P 0.87 0.15 0.00
439_M 74_F 0.87 0.15 0.00
483_V 72_M 0.87 0.15 0.00
597_V 45_R 0.86 0.15 0.00
509_I 48_E 0.86 0.15 0.00
215_R 152_L 0.86 0.15 0.00
298_A 23_E 0.86 0.15 0.00
507_A 125_L 0.86 0.15 0.00
511_R 85_R 0.86 0.14 0.00
273_Q 34_V 0.86 0.14 0.00
459_M 72_M 0.85 0.14 0.00
763_L 85_R 0.85 0.14 0.00
404_R 150_E 0.85 0.14 0.00
30_L 25_D 0.85 0.14 0.00
603_L 28_A 0.85 0.14 0.00
429_L 89_V 0.84 0.14 0.00
591_L 132_Y 0.84 0.14 0.00
215_R 63_L 0.84 0.14 0.00
455_A 41_L 0.84 0.14 0.00
610_L 65_P 0.84 0.14 0.00
20_E 68_D 0.84 0.14 0.00
264_I 90_E 0.84 0.14 0.00
192_L 161_L 0.84 0.14 0.00
605_D 34_V 0.84 0.14 0.00
343_E 64_V 0.84 0.14 0.00
28_A 105_I 0.84 0.14 0.00
406_R 34_V 0.84 0.14 0.00
726_S 146_W 0.84 0.14 0.00
538_L 35_V 0.84 0.14 0.00
462_Q 109_A 0.84 0.14 0.00
387_G 148_R 0.84 0.14 0.00
352_L 47_P 0.83 0.14 0.00
728_K 136_V 0.83 0.14 0.00
579_E 68_D 0.83 0.14 0.00
282_A 109_A 0.83 0.14 0.00
52_S 56_V 0.83 0.14 0.00
210_L 41_L 0.83 0.14 0.00
192_L 18_L 0.83 0.14 0.00
601_A 58_S 0.83 0.13 0.00
598_S 49_A 0.83 0.13 0.00
718_Q 153_L 0.83 0.13 0.00
561_V 105_I 0.83 0.13 0.00
340_D 53_V 0.82 0.13 0.00
311_Q 87_V 0.82 0.13 0.00
427_E 132_Y 0.82 0.13 0.00
277_D 31_A 0.82 0.13 0.00
582_L 107_E 0.82 0.13 0.00
488_S 151_A 0.82 0.13 0.00
527_Q 85_R 0.82 0.13 0.00
124_D 30_D 0.82 0.13 0.00
605_D 111_D 0.82 0.13 0.00
515_L 66_V 0.82 0.13 0.00
382_A 59_H 0.82 0.13 0.00
119_G 133_L 0.81 0.13 0.00
674_V 65_P 0.81 0.13 0.00
495_V 23_E 0.81 0.13 0.00
406_R 89_V 0.81 0.13 0.00
322_L 65_P 0.81 0.13 0.00
107_P 86_I 0.81 0.13 0.00
735_R 47_P 0.81 0.13 0.00
405_L 28_A 0.81 0.13 0.00
281_F 152_L 0.81 0.13 0.00
701_R 107_E 0.81 0.13 0.00
405_L 56_V 0.81 0.13 0.00
386_A 135_P 0.81 0.13 0.00
486_T 133_L 0.81 0.13 0.00
639_Q 22_M 0.81 0.13 0.00
649_L 147_V 0.80 0.13 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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