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OPENSEQ.org
StNrdDG
Genes: A B A+B
Length: 734 201 819
Sequences: 1188 1640 692
Seq/Len: 1.62 8.16 0.84
MirrorTree (Pazo et al. 2001) 0.78
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 0.00 0.00 0.63
2 0.00 0.00 0.68
5 0.00 0.01 0.73
10 0.00 0.01 0.74
20 0.00 0.01 0.74
100 0.01 0.02 0.76
∞ 0.02 0.08 0.84
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
639_A 83_Q 1.56 0.76 0.02
635_K 33_E 1.31 0.56 0.01
239_T 93_F 1.18 0.46 0.01
535_I 86_T 1.13 0.41 0.01
549_E 179_V 1.09 0.38 0.01
676_F 154_N 1.08 0.36 0.00
576_F 144_V 1.06 0.35 0.00
579_V 119_T 1.04 0.34 0.00
354_L 103_V 1.04 0.33 0.00
576_F 181_I 1.03 0.33 0.00
580_T 179_V 1.02 0.32 0.00
375_K 172_K 1.00 0.30 0.00
231_A 167_I 0.96 0.27 0.00
304_T 38_S 0.95 0.27 0.00
97_E 104_K 0.94 0.26 0.00
137_D 121_Y 0.92 0.25 0.00
375_K 153_K 0.92 0.25 0.00
231_A 86_T 0.90 0.23 0.00
641_W 177_G 0.89 0.23 0.00
548_D 178_K 0.89 0.23 0.00
432_I 134_I 0.89 0.23 0.00
434_L 173_S 0.88 0.22 0.00
82_V 99_L 0.88 0.22 0.00
161_L 57_W 0.86 0.21 0.00
230_V 86_T 0.86 0.21 0.00
183_P 38_S 0.86 0.21 0.00
163_P 177_G 0.85 0.21 0.00
85_E 39_L 0.85 0.20 0.00
680_N 155_L 0.85 0.20 0.00
582_I 115_I 0.84 0.20 0.00
342_I 20_R 0.83 0.19 0.00
247_L 24_Y 0.82 0.19 0.00
576_F 143_L 0.82 0.19 0.00
321_E 106_I 0.82 0.19 0.00
513_V 56_T 0.81 0.18 0.00
260_A 75_Q 0.81 0.18 0.00
260_A 147_R 0.81 0.18 0.00
296_T 59_F 0.81 0.18 0.00
352_R 167_I 0.81 0.18 0.00
580_T 135_E 0.81 0.18 0.00
273_D 158_Q 0.80 0.18 0.00
240_A 158_Q 0.80 0.17 0.00
544_E 152_K 0.80 0.17 0.00
531_F 144_V 0.80 0.17 0.00
680_N 152_K 0.79 0.17 0.00
545_S 20_R 0.79 0.17 0.00
554_F 147_R 0.79 0.17 0.00
172_G 84_G 0.79 0.17 0.00
579_V 99_L 0.79 0.17 0.00
274_Y 152_K 0.78 0.17 0.00
321_E 46_F 0.78 0.17 0.00
372_C 56_T 0.78 0.17 0.00
254_N 57_W 0.78 0.16 0.00
442_K 115_I 0.77 0.16 0.00
250_Y 142_I 0.77 0.16 0.00
542_A 87_L 0.77 0.16 0.00
309_L 149_D 0.77 0.16 0.00
341_A 118_W 0.76 0.16 0.00
152_V 116_W 0.76 0.16 0.00
496_F 121_Y 0.76 0.16 0.00
217_Q 167_I 0.76 0.15 0.00
433_A 173_S 0.76 0.15 0.00
578_V 86_T 0.76 0.15 0.00
436_S 38_S 0.75 0.15 0.00
676_F 35_V 0.75 0.15 0.00
527_E 168_I 0.75 0.15 0.00
528_A 153_K 0.75 0.15 0.00
550_Y 177_G 0.75 0.15 0.00
447_F 154_N 0.74 0.15 0.00
597_R 93_F 0.74 0.15 0.00
652_G 73_I 0.74 0.15 0.00
641_W 80_P 0.74 0.15 0.00
395_K 125_E 0.73 0.14 0.00
495_L 88_L 0.73 0.14 0.00
273_D 104_K 0.73 0.14 0.00
154_K 152_K 0.73 0.14 0.00
260_A 39_L 0.73 0.14 0.00
534_N 153_K 0.73 0.14 0.00
110_S 175_D 0.72 0.14 0.00
365_I 86_T 0.72 0.14 0.00
350_L 20_R 0.72 0.14 0.00
556_V 144_V 0.72 0.14 0.00
255_Y 94_L 0.72 0.14 0.00
448_E 138_H 0.72 0.14 0.00
269_E 151_T 0.72 0.14 0.00
648_V 106_I 0.71 0.14 0.00
463_E 152_K 0.71 0.14 0.00
640_V 154_N 0.71 0.14 0.00
427_L 179_V 0.71 0.14 0.00
221_A 93_F 0.71 0.14 0.00
530_T 176_Q 0.71 0.14 0.00
545_S 104_K 0.71 0.14 0.00
439_D 117_S 0.71 0.13 0.00
233_S 42_S 0.71 0.13 0.00
166_A 113_K 0.70 0.13 0.00
610_K 80_P 0.70 0.13 0.00
163_P 151_T 0.70 0.13 0.00
272_E 119_T 0.70 0.13 0.00
665_F 86_T 0.70 0.13 0.00
610_K 29_F 0.70 0.13 0.00
439_D 163_S 0.70 0.13 0.00
332_L 39_L 0.70 0.13 0.00
649_G 31_D 0.70 0.13 0.00
223_I 31_D 0.70 0.13 0.00
377_M 50_G 0.70 0.13 0.00
171_K 173_S 0.69 0.13 0.00
441_D 104_K 0.69 0.13 0.00
375_K 177_G 0.69 0.13 0.00
625_C 151_T 0.69 0.13 0.00
191_C 102_L 0.69 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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