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OPENSEQ.org
cutseq
Genes: A B A+B
Length: 529 314 770
Sequences: 1217 4315 952
Seq/Len: 2.3 13.74 1.24
MirrorTree (Pazo et al. 2001) 0.55
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 0.01 0.18 0.48
2 0.01 0.20 0.94
5 0.01 0.27 1.00
10 0.01 0.31 1.05
20 0.01 0.36 1.13
100 0.01 0.41 1.17
∞ 0.04 0.47 1.27
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
17_T 34_S 1.17 0.56 0.00
503_Y 74_I 1.17 0.56 0.00
510_L 314_Q 1.16 0.55 0.00
259_N 269_A 1.15 0.54 0.00
503_Y 29_L 1.04 0.43 0.00
517_V 290_I 1.03 0.42 0.00
499_Q 295_G 1.01 0.41 0.00
524_A 297_Y 0.99 0.38 0.00
334_T 284_N 0.98 0.38 0.00
403_Q 257_N 0.98 0.38 0.00
517_V 294_S 0.96 0.36 0.00
108_L 128_N 0.95 0.34 0.00
352_L 94_T 0.93 0.33 0.00
495_T 253_T 0.92 0.32 0.00
136_L 137_L 0.91 0.31 0.00
23_K 287_K 0.91 0.31 0.00
395_S 30_S 0.90 0.30 0.00
415_F 296_S 0.90 0.30 0.00
284_T 231_A 0.90 0.30 0.00
388_L 87_K 0.90 0.30 0.00
409_P 137_L 0.90 0.30 0.00
90_L 269_A 0.89 0.30 0.00
409_P 135_K 0.89 0.29 0.00
340_G 99_A 0.88 0.29 0.00
28_E 272_Q 0.88 0.29 0.00
500_W 252_V 0.88 0.29 0.00
313_D 81_A 0.88 0.29 0.00
136_L 71_A 0.88 0.28 0.00
326_T 289_N 0.87 0.28 0.00
319_V 287_K 0.87 0.28 0.00
514_L 11_A 0.87 0.28 0.00
279_L 154_N 0.87 0.28 0.00
512_Q 278_F 0.86 0.27 0.00
15_V 132_F 0.86 0.27 0.00
397_D 105_S 0.86 0.27 0.00
412_T 29_L 0.86 0.27 0.00
389_N 276_V 0.86 0.27 0.00
271_R 56_S 0.86 0.27 0.00
50_L 94_T 0.85 0.26 0.00
351_I 226_A 0.85 0.26 0.00
138_F 309_V 0.85 0.26 0.00
351_I 79_D 0.84 0.26 0.00
324_A 136_Q 0.84 0.26 0.00
289_K 71_A 0.84 0.26 0.00
493_Y 16_A 0.84 0.26 0.00
154_T 300_A 0.83 0.25 0.00
334_T 276_V 0.83 0.24 0.00
63_A 113_Q 0.82 0.24 0.00
108_L 147_F 0.82 0.24 0.00
308_M 117_N 0.82 0.24 0.00
51_T 278_F 0.81 0.23 0.00
506_I 11_A 0.81 0.23 0.00
196_D 99_A 0.81 0.23 0.00
54_K 42_A 0.81 0.23 0.00
56_K 52_D 0.81 0.23 0.00
418_N 123_L 0.81 0.23 0.00
395_S 99_A 0.80 0.23 0.00
28_E 64_A 0.80 0.22 0.00
473_N 252_V 0.79 0.22 0.00
347_I 92_I 0.79 0.22 0.00
32_R 295_G 0.79 0.22 0.00
519_N 5_I 0.79 0.22 0.00
252_L 280_S 0.79 0.22 0.00
520_M 253_T 0.78 0.21 0.00
510_L 284_N 0.78 0.21 0.00
64_V 252_V 0.78 0.21 0.00
173_K 295_G 0.78 0.21 0.00
178_G 286_S 0.78 0.21 0.00
9_L 16_A 0.77 0.21 0.00
510_L 286_S 0.77 0.20 0.00
496_M 160_T 0.77 0.20 0.00
454_L 108_T 0.76 0.20 0.00
322_L 143_T 0.76 0.20 0.00
339_Q 286_S 0.76 0.20 0.00
262_F 248_I 0.76 0.20 0.00
308_M 194_N 0.76 0.20 0.00
173_K 17_N 0.76 0.20 0.00
497_A 276_V 0.76 0.20 0.00
296_D 99_A 0.75 0.20 0.00
383_D 74_I 0.75 0.20 0.00
496_M 290_I 0.75 0.20 0.00
285_L 243_A 0.75 0.19 0.00
412_T 143_T 0.75 0.19 0.00
12_G 27_A 0.75 0.19 0.00
298_Q 213_G 0.74 0.19 0.00
338_L 68_G 0.74 0.19 0.00
382_Q 217_L 0.74 0.19 0.00
197_S 296_S 0.74 0.19 0.00
482_K 282_S 0.74 0.19 0.00
204_G 235_I 0.74 0.19 0.00
189_T 276_V 0.74 0.19 0.00
103_I 301_Q 0.74 0.19 0.00
101_M 308_N 0.74 0.18 0.00
47_Q 15_K 0.74 0.18 0.00
507_L 29_L 0.74 0.18 0.00
383_D 56_S 0.73 0.18 0.00
46_K 4_R 0.73 0.18 0.00
62_T 14_A 0.73 0.18 0.00
138_F 130_T 0.73 0.18 0.00
48_K 7_T 0.73 0.18 0.00
509_K 257_N 0.73 0.18 0.00
6_L 239_D 0.73 0.18 0.00
269_M 105_S 0.73 0.18 0.00
31_A 268_A 0.73 0.18 0.00
265_D 82_M 0.72 0.18 0.00
270_F 260_T 0.72 0.18 0.00
16_L 289_N 0.72 0.17 0.00
409_P 298_A 0.72 0.17 0.00
484_S 253_T 0.71 0.17 0.00
457_M 256_I 0.71 0.17 0.00
350_S 252_V 0.71 0.17 0.00
144_E 96_A 0.71 0.17 0.00
405_V 82_M 0.71 0.17 0.00
20_T 288_A 0.71 0.17 0.00
346_S 82_M 0.71 0.17 0.00
504_E 93_K 0.71 0.17 0.00
470_S 253_T 0.71 0.17 0.00
78_V 19_D 0.71 0.17 0.00
464_I 277_D 0.71 0.17 0.00
315_Y 53_S 0.71 0.17 0.00
112_D 29_L 0.71 0.17 0.00
522_N 74_I 0.71 0.17 0.00
78_V 228_M 0.70 0.17 0.00
338_L 304_S 0.70 0.17 0.00
513_Q 276_V 0.70 0.17 0.00
504_E 75_L 0.70 0.17 0.00
156_R 123_L 0.70 0.17 0.00
520_M 13_N 0.70 0.17 0.00
60_F 56_S 0.70 0.17 0.00
326_T 226_A 0.70 0.17 0.00
388_L 84_E 0.70 0.16 0.00
475_I 16_A 0.70 0.16 0.00
512_Q 304_S 0.70 0.16 0.00
466_K 74_I 0.70 0.16 0.00
50_L 137_L 0.69 0.16 0.00
76_R 276_V 0.69 0.16 0.00
54_K 156_T 0.69 0.16 0.00
381_M 234_A 0.69 0.16 0.00
461_D 54_L 0.69 0.16 0.00
489_I 52_D 0.69 0.16 0.00
474_D 10_A 0.69 0.16 0.00
272_S 51_A 0.69 0.16 0.00
507_L 94_T 0.69 0.16 0.00
36_Y 287_K 0.69 0.16 0.00
496_M 14_A 0.69 0.16 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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