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OPENSEQ.org
dlta-dltc_bs
Genes: A B A+B
Length: 503 78 567
Sequences: 38038 190 217
Seq/Len: 75.62 2.44 0.38
MirrorTree (Pazo et al. 2001) 0.82
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 0.08 0.08 0.05
2 0.10 0.08 0.36
5 0.14 0.08 0.37
10 0.17 0.08 0.37
20 0.19 0.08 0.37
100 0.24 0.08 0.38
∞ 0.30 0.09 0.39
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
302_V 30_E 1.50 0.48 0.00
298_A 65_N 1.49 0.47 0.00
149_I 67_P 1.48 0.46 0.00
220_V 37_F 1.47 0.46 0.00
168_L 67_P 1.41 0.42 0.00
401_I 52_I 1.39 0.40 0.00
320_V 16_Q 1.29 0.34 0.00
210_G 42_L 1.29 0.34 0.00
274_V 47_E 1.26 0.32 0.00
55_I 11_L 1.25 0.31 0.00
460_A 7_V 1.25 0.31 0.00
412_E 52_I 1.22 0.29 0.00
233_S 57_T 1.21 0.29 0.00
202_L 58_E 1.20 0.28 0.00
275_S 10_V 1.15 0.26 0.00
494_R 20_V 1.15 0.25 0.00
39_A 67_P 1.12 0.24 0.00
497_I 47_E 1.11 0.23 0.00
149_I 42_L 1.11 0.23 0.00
200_M 67_P 1.11 0.23 0.00
235_L 63_V 1.11 0.23 0.00
487_T 20_V 1.10 0.23 0.00
141_K 37_F 1.09 0.22 0.00
100_A 15_C 1.09 0.22 0.00
5_H 12_A 1.09 0.22 0.00
412_E 24_P 1.09 0.22 0.00
446_P 51_D 1.07 0.21 0.00
247_M 41_E 1.07 0.21 0.00
222_K 37_F 1.06 0.21 0.00
43_I 19_I 1.06 0.21 0.00
492_I 6_E 1.06 0.21 0.00
494_R 19_I 1.06 0.21 0.00
239_T 15_C 1.04 0.20 0.00
278_K 7_V 1.04 0.20 0.00
61_M 56_I 1.03 0.19 0.00
268_C 11_L 1.03 0.19 0.00
266_M 51_D 1.02 0.19 0.00
122_S 8_L 1.02 0.19 0.00
240_S 25_D 1.01 0.19 0.00
164_S 15_C 1.01 0.19 0.00
471_A 53_L 1.01 0.18 0.00
86_I 31_E 1.01 0.18 0.00
368_A 65_N 1.00 0.18 0.00
329_I 30_E 1.00 0.18 0.00
477_K 44_L 0.99 0.18 0.00
154_S 16_Q 0.99 0.18 0.00
228_E 5_Q 0.99 0.18 0.00
72_S 15_C 0.99 0.18 0.00
258_L 57_T 0.98 0.17 0.00
348_V 26_I 0.98 0.17 0.00
408_M 56_I 0.98 0.17 0.00
439_Y 16_Q 0.98 0.17 0.00
359_L 64_W 0.98 0.17 0.00
413_I 62_D 0.97 0.17 0.00
360_G 16_Q 0.97 0.17 0.00
312_I 50_F 0.97 0.17 0.00
432_Q 46_I 0.96 0.17 0.00
240_S 66_T 0.96 0.17 0.00
222_K 47_E 0.96 0.17 0.00
399_F 11_L 0.96 0.16 0.00
69_F 58_E 0.95 0.16 0.00
239_T 56_I 0.95 0.16 0.00
250_M 64_W 0.95 0.16 0.00
470_P 46_I 0.94 0.16 0.00
193_F 14_V 0.94 0.15 0.00
480_Y 55_P 0.93 0.15 0.00
442_A 61_R 0.93 0.15 0.00
444_I 71_V 0.93 0.15 0.00
434_N 37_F 0.93 0.15 0.00
404_H 67_P 0.93 0.15 0.00
406_Y 8_L 0.93 0.15 0.00
440_L 61_R 0.93 0.15 0.00
22_S 71_V 0.93 0.15 0.00
184_G 20_V 0.92 0.15 0.00
121_V 42_L 0.92 0.15 0.00
306_E 65_N 0.92 0.15 0.00
179_F 55_P 0.92 0.15 0.00
199_V 67_P 0.92 0.15 0.00
12_E 30_E 0.91 0.15 0.00
494_R 26_I 0.91 0.15 0.00
476_R 15_C 0.91 0.14 0.00
423_V 72_N 0.91 0.14 0.00
347_I 50_F 0.91 0.14 0.00
477_K 16_Q 0.91 0.14 0.00
423_V 9_D 0.91 0.14 0.00
364_L 57_T 0.90 0.14 0.00
20_F 56_I 0.90 0.14 0.00
77_H 58_E 0.90 0.14 0.00
205_C 44_L 0.90 0.14 0.00
248_C 50_F 0.90 0.14 0.00
440_L 34_L 0.89 0.14 0.00
436_T 14_V 0.89 0.14 0.00
304_S 60_D 0.89 0.14 0.00
231_K 56_I 0.89 0.14 0.00
413_I 37_F 0.89 0.14 0.00
251_D 58_E 0.89 0.14 0.00
287_A 51_D 0.89 0.14 0.00
411_E 14_V 0.89 0.14 0.00
215_V 52_I 0.88 0.14 0.00
50_E 37_F 0.88 0.14 0.00
52_K 76_E 0.88 0.14 0.00
470_P 57_T 0.88 0.14 0.00
302_V 11_L 0.88 0.13 0.00
22_S 27_E 0.88 0.13 0.00
324_K 55_P 0.87 0.13 0.00
201_D 67_P 0.87 0.13 0.00
494_R 17_D 0.87 0.13 0.00
56_L 49_R 0.87 0.13 0.00
144_E 50_F 0.87 0.13 0.00
77_H 38_G 0.87 0.13 0.00
240_S 68_N 0.87 0.13 0.00
463_K 51_D 0.86 0.13 0.00
335_E 3_F 0.86 0.13 0.00
420_S 17_D 0.86 0.13 0.00
245_V 50_F 0.86 0.13 0.00
411_E 39_T 0.86 0.13 0.00
406_Y 65_N 0.86 0.13 0.00
379_R 33_L 0.86 0.13 0.00
36_S 50_F 0.86 0.13 0.00
347_I 38_G 0.85 0.13 0.00
250_M 37_F 0.85 0.13 0.00
28_T 72_N 0.85 0.13 0.00
273_P 38_G 0.85 0.13 0.00
426_A 60_D 0.85 0.12 0.00
462_K 6_E 0.85 0.12 0.00
312_I 4_K 0.85 0.12 0.00
404_H 33_L 0.85 0.12 0.00
200_M 39_T 0.85 0.12 0.00
414_E 20_V 0.84 0.12 0.00
72_S 48_N 0.84 0.12 0.00
187_F 13_E 0.84 0.12 0.00
459_S 75_S 0.84 0.12 0.00
263_D 37_F 0.84 0.12 0.00
287_A 38_G 0.84 0.12 0.00
265_F 66_T 0.83 0.12 0.00
99_G 46_I 0.83 0.12 0.00
1_M 6_E 0.83 0.12 0.00
20_F 55_P 0.83 0.12 0.00
238_W 66_T 0.83 0.12 0.00
401_I 10_V 0.83 0.12 0.00
14_Y 30_E 0.83 0.12 0.00
306_E 11_L 0.82 0.12 0.00
367_K 12_A 0.82 0.12 0.00
303_T 9_D 0.82 0.12 0.00
436_T 29_F 0.82 0.12 0.00
410_L 55_P 0.82 0.12 0.00
311_V 75_S 0.82 0.12 0.00
56_L 44_L 0.82 0.12 0.00
397_L 7_V 0.82 0.12 0.00
223_P 74_L 0.82 0.12 0.00
368_A 44_L 0.81 0.11 0.00
38_R 50_F 0.81 0.11 0.00
91_I 22_E 0.81 0.11 0.00
122_S 45_A 0.81 0.11 0.00
246_Q 58_E 0.81 0.11 0.00
474_I 54_V 0.81 0.11 0.00
19_A 18_D 0.81 0.11 0.00
422_Y 62_D 0.81 0.11 0.00
301_A 61_R 0.81 0.11 0.00
412_E 19_I 0.81 0.11 0.00
214_C 31_E 0.80 0.11 0.00
104_I 13_E 0.80 0.11 0.00
455_F 44_L 0.80 0.11 0.00
150_Y 71_V 0.80 0.11 0.00
412_E 77_L 0.80 0.11 0.00
74_K 39_T 0.80 0.11 0.00
308_T 21_K 0.80 0.11 0.00
217_K 67_P 0.80 0.11 0.00
420_S 19_I 0.80 0.11 0.00
462_K 7_V 0.80 0.11 0.00
310_D 72_N 0.80 0.11 0.00
456_Q 26_I 0.80 0.11 0.00
102_L 47_E 0.80 0.11 0.00
444_I 56_I 0.80 0.11 0.00
223_P 37_F 0.79 0.11 0.00
62_E 30_E 0.79 0.11 0.00
80_I 49_R 0.79 0.11 0.00
331_I 53_L 0.79 0.11 0.00
34_E 27_E 0.79 0.11 0.00
67_V 67_P 0.79 0.11 0.00
451_F 30_E 0.79 0.11 0.00
348_V 54_V 0.79 0.11 0.00
80_I 64_W 0.79 0.11 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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