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OPENSEQ.org
23
Genes: A B A+B
Length: 646 340 946
Sequences: 2963 4321 910
Seq/Len: 4.59 12.71 0.96
MirrorTree (Pazo et al. 2001) 0.43
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 0.06 0.06 0.29
2 0.06 0.06 0.33
5 0.06 0.06 0.35
10 0.06 0.06 0.35
20 0.07 0.06 0.37
100 0.07 0.07 0.50
∞ 0.10 0.12 0.92
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
237_M 253_D 1.23 0.53 0.00
209_I 270_T 1.20 0.51 0.00
536_V 16_S 1.10 0.41 0.00
440_I 284_V 1.08 0.40 0.00
173_I 47_E 1.07 0.39 0.00
192_E 22_R 1.06 0.39 0.00
305_L 8_T 1.05 0.37 0.00
321_L 57_D 1.03 0.36 0.00
297_I 130_P 0.98 0.32 0.00
119_V 260_I 0.97 0.30 0.00
24_G 1_M 0.95 0.29 0.00
290_G 218_I 0.95 0.29 0.00
238_V 273_V 0.95 0.29 0.00
326_L 171_S 0.94 0.28 0.00
65_N 221_P 0.93 0.28 0.00
298_T 273_V 0.92 0.27 0.00
312_G 22_R 0.90 0.26 0.00
121_S 321_I 0.90 0.26 0.00
312_G 298_P 0.90 0.26 0.00
486_L 337_V 0.90 0.25 0.00
310_F 190_L 0.89 0.25 0.00
331_I 11_L 0.89 0.24 0.00
121_S 20_I 0.89 0.24 0.00
514_D 8_T 0.87 0.24 0.00
356_G 273_V 0.87 0.24 0.00
238_V 320_V 0.87 0.23 0.00
436_P 16_S 0.87 0.23 0.00
574_C 311_R 0.87 0.23 0.00
423_K 168_L 0.86 0.23 0.00
221_S 22_R 0.86 0.23 0.00
74_I 7_Q 0.86 0.23 0.00
412_V 208_V 0.85 0.22 0.00
140_T 250_D 0.85 0.22 0.00
68_F 239_L 0.84 0.22 0.00
211_T 253_D 0.84 0.21 0.00
115_Y 31_Y 0.84 0.21 0.00
236_R 254_V 0.83 0.21 0.00
543_E 5_Y 0.83 0.21 0.00
258_R 172_L 0.82 0.20 0.00
208_S 161_D 0.82 0.20 0.00
331_I 334_L 0.81 0.20 0.00
513_E 19_E 0.81 0.20 0.00
412_V 170_V 0.81 0.20 0.00
244_E 30_R 0.81 0.20 0.00
49_R 303_P 0.81 0.20 0.00
129_E 66_R 0.80 0.19 0.00
163_T 13_R 0.80 0.19 0.00
500_K 75_S 0.80 0.19 0.00
463_G 11_L 0.80 0.19 0.00
272_R 71_G 0.79 0.19 0.00
511_S 204_L 0.79 0.19 0.00
517_R 243_P 0.79 0.18 0.00
377_A 226_Q 0.78 0.18 0.00
298_T 327_P 0.78 0.18 0.00
343_I 291_P 0.78 0.18 0.00
310_F 168_L 0.78 0.18 0.00
281_S 8_T 0.77 0.18 0.00
517_R 200_E 0.77 0.17 0.00
515_I 31_Y 0.77 0.17 0.00
243_A 303_P 0.76 0.17 0.00
118_E 101_M 0.76 0.17 0.00
65_N 40_G 0.76 0.17 0.00
602_V 261_S 0.76 0.17 0.00
440_I 36_N 0.76 0.17 0.00
537_S 316_I 0.76 0.17 0.00
463_G 306_K 0.76 0.17 0.00
297_I 59_R 0.76 0.17 0.00
394_L 28_A 0.75 0.17 0.00
157_A 278_G 0.75 0.16 0.00
513_E 15_A 0.75 0.16 0.00
516_E 304_L 0.74 0.16 0.00
243_A 19_E 0.74 0.16 0.00
198_F 300_E 0.74 0.16 0.00
233_F 53_D 0.74 0.16 0.00
118_E 56_S 0.74 0.16 0.00
598_E 16_S 0.74 0.16 0.00
22_Q 77_P 0.73 0.16 0.00
514_D 43_E 0.73 0.16 0.00
241_F 332_T 0.73 0.16 0.00
70_A 20_I 0.73 0.16 0.00
221_S 13_R 0.73 0.15 0.00
541_S 20_I 0.73 0.15 0.00
312_G 248_K 0.73 0.15 0.00
546_A 18_E 0.73 0.15 0.00
263_L 320_V 0.73 0.15 0.00
121_S 316_I 0.72 0.15 0.00
427_T 192_P 0.72 0.15 0.00
198_F 44_K 0.72 0.15 0.00
600_E 54_V 0.72 0.15 0.00
489_S 16_S 0.72 0.15 0.00
216_I 303_P 0.71 0.15 0.00
59_V 208_V 0.71 0.15 0.00
129_E 71_G 0.71 0.15 0.00
220_K 143_N 0.71 0.14 0.00
321_L 260_I 0.71 0.14 0.00
27_E 14_G 0.71 0.14 0.00
432_S 176_Y 0.71 0.14 0.00
70_A 48_I 0.71 0.14 0.00
581_L 70_E 0.71 0.14 0.00
49_R 261_S 0.70 0.14 0.00
524_K 326_I 0.70 0.14 0.00
207_V 314_L 0.70 0.14 0.00
516_E 201_D 0.70 0.14 0.00
392_L 28_A 0.70 0.14 0.00
99_G 67_Y 0.70 0.14 0.00
223_A 7_Q 0.70 0.14 0.00
310_F 158_K 0.70 0.14 0.00
139_V 283_V 0.70 0.14 0.00
115_Y 220_F 0.70 0.14 0.00
325_K 171_S 0.69 0.14 0.00
257_K 260_I 0.69 0.14 0.00
139_V 35_K 0.69 0.14 0.00
441_Q 299_G 0.69 0.14 0.00
379_I 181_K 0.69 0.14 0.00
361_K 30_R 0.69 0.14 0.00
375_V 18_E 0.69 0.14 0.00
221_S 311_R 0.69 0.14 0.00
418_T 16_S 0.69 0.14 0.00
209_I 245_N 0.69 0.14 0.00
502_T 170_V 0.69 0.14 0.00
464_I 331_R 0.68 0.13 0.00
198_F 72_L 0.68 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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