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OPENSEQ.org
3ip4 A vs B
Genes: A B A+B
Length: 485 483 933
Sequences: 9591 2608 1489
Seq/Len: 19.78 5.4 1.6
MirrorTree (Pazo et al. 2001) 0.76
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 0.05 0.09 1.31
2 0.06 0.09 1.40
5 0.06 0.09 1.47
10 0.06 0.09 1.51
20 0.08 0.09 1.54
100 0.12 0.10 1.63
∞ 0.20 0.11 2.08
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
99_F 44_Y 1.65 0.93 0.55
329_Y 44_Y 1.54 0.89 0.46
329_Y 43_A 1.43 0.84 0.37
102_I 44_Y 1.31 0.76 0.28
376_K 272_E 1.16 0.62 0.17
201_F 40_I 0.98 0.44 0.09
238_S 50_V 0.96 0.41 0.08
370_Y 95_F 0.96 0.41 0.08
238_S 276_V 0.95 0.41 0.08
209_S 273_P 0.87 0.33 0.06
315_S 205_F 0.84 0.31 0.05
368_S 225_E 0.84 0.30 0.05
410_N 437_K 0.83 0.30 0.05
261_V 426_L 0.82 0.29 0.05
317_A 327_F 0.81 0.27 0.04
375_Y 275_I 0.80 0.27 0.04
439_I 234_E 0.80 0.26 0.04
370_Y 96_D 0.79 0.26 0.04
11_L 409_L 0.78 0.25 0.04
236_N 40_I 0.78 0.25 0.04
184_A 455_S 0.77 0.24 0.04
312_I 317_L 0.76 0.24 0.04
427_L 182_V 0.76 0.23 0.04
131_G 275_I 0.76 0.23 0.04
109_E 40_I 0.75 0.23 0.04
328_R 42_L 0.74 0.22 0.03
179_I 11_V 0.74 0.22 0.03
328_R 296_P 0.74 0.22 0.03
265_K 61_R 0.74 0.22 0.03
315_S 59_A 0.73 0.22 0.03
132_S 422_V 0.73 0.22 0.03
468_V 347_G 0.72 0.21 0.03
206_F 123_M 0.72 0.20 0.03
43_F 339_L 0.71 0.20 0.03
324_F 247_R 0.71 0.20 0.03
407_T 153_S 0.70 0.20 0.03
308_S 211_L 0.70 0.19 0.03
294_V 113_T 0.69 0.19 0.03
137_Y 137_S 0.68 0.18 0.03
339_L 89_A 0.68 0.18 0.02
364_F 217_F 0.68 0.18 0.02
146_D 436_Y 0.68 0.18 0.02
433_L 99_I 0.68 0.18 0.02
473_E 138_L 0.67 0.18 0.02
466_Y 86_N 0.67 0.17 0.02
431_V 467_L 0.67 0.17 0.02
274_D 116_I 0.66 0.17 0.02
117_V 376_I 0.66 0.17 0.02
206_F 460_N 0.66 0.17 0.02
139_K 76_F 0.65 0.16 0.02
433_L 76_F 0.65 0.16 0.02
91_C 41_D 0.64 0.16 0.02
460_F 167_L 0.64 0.16 0.02
272_V 99_I 0.64 0.16 0.02
99_F 47_V 0.64 0.15 0.02
333_S 253_G 0.64 0.15 0.02
185_Y 223_G 0.63 0.15 0.02
18_K 95_F 0.63 0.15 0.02
146_D 199_P 0.63 0.15 0.02
173_S 220_V 0.63 0.15 0.02
366_L 270_F 0.63 0.15 0.02
185_Y 159_S 0.62 0.15 0.02
95_M 161_K 0.62 0.15 0.02
365_A 263_G 0.62 0.15 0.02
98_G 379_G 0.62 0.15 0.02
132_S 445_G 0.62 0.15 0.02
203_L 63_A 0.62 0.14 0.02
324_F 74_S 0.62 0.14 0.02
86_G 417_T 0.61 0.14 0.02
85_N 400_A 0.61 0.14 0.02
59_D 255_T 0.61 0.14 0.02
218_R 281_D 0.61 0.14 0.02
171_L 43_A 0.61 0.14 0.02
184_A 123_M 0.61 0.14 0.02
340_E 139_V 0.61 0.14 0.02
408_A 166_Y 0.61 0.14 0.02
95_M 47_V 0.60 0.14 0.02
441_V 466_Q 0.60 0.14 0.02
56_Q 69_E 0.60 0.14 0.02
272_V 353_N 0.60 0.13 0.02
100_V 280_I 0.60 0.13 0.02
239_T 80_N 0.60 0.13 0.02
322_S 415_E 0.59 0.13 0.02
208_S 48_L 0.59 0.13 0.02
201_F 39_V 0.59 0.13 0.02
439_I 18_D 0.59 0.13 0.01
339_L 141_L 0.59 0.13 0.01
410_N 61_R 0.59 0.13 0.01
319_S 350_E 0.59 0.13 0.01
229_A 444_M 0.59 0.13 0.01
315_S 382_S 0.59 0.13 0.01
259_L 472_L 0.59 0.13 0.01
396_Y 443_A 0.59 0.13 0.01
213_I 248_F 0.59 0.13 0.01
363_T 275_I 0.59 0.13 0.01
439_I 348_V 0.58 0.13 0.01
364_F 264_S 0.58 0.13 0.01
364_F 62_A 0.58 0.13 0.01
146_D 451_I 0.58 0.13 0.01
289_S 116_I 0.58 0.13 0.01
455_F 250_E 0.58 0.13 0.01
141_T 13_V 0.58 0.12 0.01
94_K 311_A 0.58 0.12 0.01
328_R 82_F 0.58 0.12 0.01
256_I 19_S 0.58 0.12 0.01
109_E 437_K 0.58 0.12 0.01
149_A 58_W 0.58 0.12 0.01
206_F 418_L 0.57 0.12 0.01
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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