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OPENSEQ.org
aaab
Genes: A B A+B
Length: 397 1000 1337
Sequences: 13428 3133 2617
Seq/Len: 33.82 3.13 1.96
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 0.02 0.02 1.75
2 0.03 0.02 1.82
5 0.04 0.02 1.84
10 0.06 0.03 1.85
20 0.07 0.03 1.87
100 0.13 0.06 1.94
∞ 0.21 0.17 2.09
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
349_V 597_Y 1.23 0.75 0.03
127_N 732_D 1.08 0.60 0.02
132_L 211_N 1.03 0.55 0.01
214_V 474_I 1.01 0.53 0.01
276_L 291_I 0.98 0.50 0.01
199_Q 701_Q 0.96 0.48 0.01
361_I 450_S 0.94 0.45 0.01
351_E 349_I 0.94 0.45 0.01
361_I 662_M 0.92 0.42 0.01
85_S 349_I 0.91 0.42 0.01
305_A 162_M 0.89 0.40 0.01
93_L 422_E 0.89 0.40 0.01
95_Q 544_L 0.89 0.40 0.01
54_T 788_D 0.88 0.39 0.01
202_A 542_L 0.88 0.39 0.01
295_A 493_C 0.88 0.39 0.01
38_P 319_S 0.87 0.38 0.01
180_I 892_Y 0.85 0.36 0.01
130_Q 251_L 0.85 0.36 0.01
271_T 30_L 0.85 0.35 0.01
344_G 782_L 0.84 0.35 0.01
126_V 799_V 0.84 0.34 0.01
180_I 466_I 0.84 0.34 0.01
272_G 193_L 0.84 0.34 0.01
361_I 385_A 0.83 0.34 0.01
147_L 166_I 0.83 0.34 0.01
352_G 243_T 0.83 0.33 0.01
206_V 370_I 0.83 0.33 0.01
355_A 207_I 0.82 0.33 0.01
361_I 531_V 0.82 0.32 0.01
287_L 857_Y 0.82 0.32 0.01
363_G 478_M 0.81 0.32 0.01
323_V 483_L 0.81 0.32 0.01
280_F 827_I 0.81 0.31 0.01
206_V 321_L 0.81 0.31 0.01
26_D 349_I 0.81 0.31 0.01
349_V 531_V 0.80 0.31 0.01
206_V 804_F 0.80 0.31 0.01
181_S 909_V 0.80 0.31 0.01
183_R 699_R 0.80 0.30 0.01
344_G 198_L 0.80 0.30 0.01
313_V 172_V 0.80 0.30 0.01
212_I 908_G 0.80 0.30 0.01
273_S 800_P 0.79 0.30 0.01
136_Q 946_V 0.79 0.30 0.01
76_I 847_L 0.79 0.29 0.01
331_K 337_I 0.79 0.29 0.01
184_I 357_L 0.78 0.28 0.01
349_V 713_L 0.78 0.28 0.01
243_K 799_V 0.78 0.28 0.01
214_V 741_V 0.77 0.28 0.01
192_G 461_G 0.77 0.28 0.01
87_I 186_I 0.77 0.28 0.01
60_T 918_F 0.77 0.28 0.01
93_L 699_R 0.77 0.28 0.01
198_G 826_E 0.77 0.28 0.01
368_R 45_I 0.76 0.27 0.01
375_A 594_V 0.76 0.27 0.01
197_N 141_G 0.76 0.27 0.01
189_V 140_V 0.76 0.27 0.01
307_L 746_I 0.76 0.27 0.01
30_A 551_G 0.76 0.27 0.01
76_I 219_L 0.76 0.27 0.01
356_G 62_T 0.75 0.26 0.01
305_A 414_E 0.75 0.26 0.01
324_L 31_P 0.75 0.26 0.01
345_D 5_F 0.75 0.26 0.01
23_T 827_I 0.75 0.26 0.01
272_G 780_R 0.75 0.26 0.01
195_V 439_Q 0.74 0.26 0.01
33_G 308_A 0.74 0.26 0.01
252_I 629_V 0.74 0.25 0.01
246_L 749_T 0.74 0.25 0.01
68_V 42_A 0.74 0.25 0.01
256_Q 496_M 0.74 0.25 0.01
93_L 546_L 0.74 0.25 0.01
205_T 142_V 0.74 0.25 0.01
139_S 572_F 0.73 0.25 0.01
218_Q 321_L 0.73 0.24 0.01
269_Q 980_L 0.73 0.24 0.01
349_V 510_K 0.73 0.24 0.01
89_A 429_E 0.73 0.24 0.01
353_L 116_P 0.73 0.24 0.01
359_V 997_S 0.73 0.24 0.01
255_P 268_I 0.73 0.24 0.01
323_V 447_M 0.72 0.24 0.01
178_S 750_L 0.72 0.24 0.01
49_P 899_F 0.72 0.24 0.01
357_D 406_V 0.72 0.24 0.01
268_D 844_M 0.72 0.24 0.01
88_E 596_H 0.72 0.23 0.01
196_Q 844_M 0.72 0.23 0.01
276_L 90_I 0.71 0.23 0.01
206_V 216_A 0.71 0.23 0.01
243_K 311_A 0.71 0.23 0.01
308_V 579_P 0.71 0.23 0.01
203_L 251_L 0.71 0.23 0.01
192_G 373_P 0.71 0.23 0.01
258_G 622_Q 0.70 0.22 0.01
349_V 662_M 0.70 0.22 0.01
295_A 786_I 0.70 0.22 0.01
89_A 268_I 0.70 0.22 0.01
294_R 219_L 0.70 0.22 0.01
44_T 311_A 0.70 0.22 0.01
171_L 90_I 0.70 0.22 0.01
97_D 980_L 0.70 0.22 0.01
30_A 704_A 0.70 0.22 0.01
152_Q 282_N 0.70 0.22 0.01
144_D 574_T 0.70 0.22 0.01
140_K 7_D 0.70 0.22 0.01
192_G 408_D 0.70 0.22 0.01
58_G 623_N 0.69 0.22 0.01
205_T 364_A 0.69 0.22 0.01
139_S 46_S 0.69 0.22 0.01
344_G 920_G 0.69 0.21 0.01
178_S 410_I 0.69 0.21 0.01
154_N 17_I 0.69 0.21 0.01
374_K 463_T 0.69 0.21 0.01
139_S 53_D 0.69 0.21 0.01
95_Q 460_G 0.69 0.21 0.01
359_V 261_L 0.69 0.21 0.01
101_Y 59_D 0.69 0.21 0.01
338_V 245_E 0.69 0.21 0.01
313_V 5_F 0.68 0.21 0.01
47_T 245_E 0.68 0.21 0.01
88_E 314_E 0.68 0.21 0.01
184_I 799_V 0.68 0.21 0.01
120_N 265_V 0.68 0.21 0.01
294_R 236_A 0.68 0.21 0.01
155_A 353_L 0.68 0.20 0.01
56_L 456_M 0.68 0.20 0.01
115_A 801_F 0.68 0.20 0.01
354_K 742_S 0.68 0.20 0.01
258_G 75_L 0.68 0.20 0.01
171_L 985_G 0.67 0.20 0.01
270_T 588_Q 0.67 0.20 0.01
371_V 834_G 0.67 0.20 0.01
357_D 701_Q 0.67 0.20 0.01
308_V 574_T 0.67 0.20 0.01
361_I 536_R 0.67 0.20 0.01
243_K 308_A 0.67 0.20 0.01
349_V 241_T 0.67 0.20 0.01
149_D 111_L 0.67 0.20 0.01
244_V 483_L 0.67 0.20 0.01
127_N 710_P 0.67 0.20 0.01
218_Q 808_R 0.67 0.20 0.01
41_G 322_K 0.67 0.20 0.01
202_A 287_S 0.67 0.20 0.01
79_R 412_V 0.67 0.20 0.01
145_Q 745_D 0.67 0.20 0.01
220_S 614_G 0.67 0.20 0.01
265_V 397_G 0.67 0.20 0.01
71_Q 287_S 0.67 0.20 0.01
87_I 366_L 0.66 0.19 0.01
358_R 701_Q 0.66 0.19 0.01
70_P 454_V 0.66 0.19 0.01
204_A 749_T 0.66 0.19 0.01
142_E 594_V 0.66 0.19 0.01
176_V 323_I 0.66 0.19 0.00
128_R 565_P 0.66 0.19 0.00
336_P 544_L 0.66 0.19 0.00
48_E 799_V 0.66 0.19 0.00
258_G 284_Q 0.66 0.19 0.00
60_T 284_Q 0.66 0.19 0.00
312_G 547_I 0.66 0.19 0.00
258_G 949_A 0.66 0.19 0.00
68_V 266_A 0.66 0.19 0.00
45_V 647_I 0.66 0.19 0.00
253_K 827_I 0.66 0.19 0.00
313_V 346_E 0.66 0.19 0.00
323_V 791_V 0.66 0.19 0.00
259_T 625_G 0.66 0.19 0.00
353_L 839_E 0.66 0.19 0.00
337_I 310_L 0.66 0.19 0.00
130_Q 808_R 0.66 0.19 0.00
189_V 157_Y 0.66 0.19 0.00
206_V 535_L 0.66 0.19 0.00
357_D 48_S 0.66 0.19 0.00
278_A 458_F 0.66 0.19 0.00
217_T 258_S 0.65 0.19 0.00
243_K 533_G 0.65 0.19 0.00
355_A 728_K 0.65 0.19 0.00
267_V 763_I 0.65 0.19 0.00
48_E 234_I 0.65 0.18 0.00
125_T 190_P 0.65 0.18 0.00
282_N 18_I 0.65 0.18 0.00
355_A 551_G 0.65 0.18 0.00
357_D 700_N 0.65 0.18 0.00
313_V 366_L 0.65 0.18 0.00
197_N 839_E 0.65 0.18 0.00
130_Q 820_N 0.65 0.18 0.00
252_I 198_L 0.65 0.18 0.00
325_V 606_V 0.65 0.18 0.00
147_L 61_V 0.65 0.18 0.00
268_D 966_D 0.65 0.18 0.00
76_I 914_L 0.64 0.18 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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