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OPENSEQ.org
mbma
Genes: A B A+B
Length: 383 1000 1325
Sequences: 14469 3126 2730
Seq/Len: 37.78 3.13 2.06
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 1.84
2 0.02 0.02 1.91
5 0.04 0.02 1.93
10 0.05 0.03 1.96
20 0.07 0.03 1.97
100 0.14 0.06 2.04
∞ 0.21 0.17 2.17
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
334_V 597_Y 1.15 0.69 0.01
93_Q 544_I 1.08 0.62 0.01
290_A 162_I 1.07 0.61 0.01
346_T 662_M 1.01 0.54 0.01
121_K 251_L 1.00 0.53 0.01
334_V 712_L 1.00 0.53 0.01
280_A 493_C 1.00 0.53 0.01
123_L 211_N 0.98 0.51 0.01
261_I 291_I 0.97 0.50 0.01
130_S 46_Q 0.97 0.50 0.01
198_V 740_V 0.96 0.48 0.01
258_S 799_P 0.92 0.44 0.01
181_N 141_G 0.92 0.44 0.01
196_I 907_G 0.90 0.41 0.01
183_Q 701_K 0.88 0.40 0.01
164_I 891_Y 0.88 0.39 0.01
316_K 337_I 0.87 0.39 0.01
91_L 699_R 0.87 0.39 0.01
165_S 908_V 0.87 0.38 0.01
354_P 244_E 0.85 0.37 0.01
309_L 31_P 0.85 0.37 0.01
91_L 422_E 0.85 0.36 0.01
293_A 142_V 0.85 0.36 0.01
52_T 787_K 0.84 0.36 0.01
118_Q 731_D 0.84 0.36 0.01
25_G 349_L 0.83 0.34 0.00
348_G 478_M 0.83 0.34 0.00
337_G 243_A 0.82 0.34 0.00
83_S 349_L 0.82 0.34 0.00
261_I 90_I 0.82 0.33 0.00
291_I 65_I 0.81 0.33 0.00
329_G 781_N 0.81 0.33 0.00
339_N 268_V 0.81 0.32 0.00
293_A 579_P 0.81 0.32 0.00
74_I 5_F 0.81 0.32 0.00
18_I 310_I 0.81 0.32 0.00
36_P 319_Q 0.81 0.32 0.00
257_G 779_R 0.81 0.32 0.00
22_S 826_I 0.81 0.32 0.00
190_V 321_M 0.80 0.32 0.00
272_L 856_Y 0.80 0.32 0.00
181_N 745_I 0.80 0.32 0.00
74_I 846_I 0.80 0.31 0.00
345_I 741_S 0.80 0.31 0.00
257_G 193_L 0.79 0.31 0.00
340_A 207_I 0.79 0.31 0.00
85_V 186_I 0.79 0.30 0.00
346_T 385_A 0.79 0.30 0.00
179_V 313_L 0.79 0.30 0.00
298_V 172_V 0.79 0.30 0.00
187_M 242_T 0.78 0.30 0.00
77_R 186_I 0.78 0.30 0.00
66_V 256_D 0.78 0.29 0.00
164_I 466_I 0.78 0.29 0.00
308_A 447_M 0.78 0.29 0.00
91_L 546_V 0.77 0.29 0.00
186_A 542_L 0.77 0.29 0.00
58_T 917_M 0.77 0.29 0.00
168_I 798_V 0.77 0.29 0.00
346_T 450_S 0.77 0.29 0.00
263_A 458_F 0.77 0.29 0.00
86_K 596_E 0.77 0.28 0.00
135_A 574_A 0.77 0.28 0.00
345_I 251_L 0.77 0.28 0.00
176_G 461_G 0.77 0.28 0.00
149_E 981_I 0.76 0.28 0.00
190_V 535_L 0.76 0.27 0.00
278_V 730_I 0.75 0.27 0.00
241_L 496_M 0.75 0.27 0.00
329_G 960_E 0.75 0.27 0.00
293_A 574_A 0.75 0.27 0.00
103_Y 251_L 0.75 0.27 0.00
360_T 594_M 0.74 0.26 0.00
317_V 359_L 0.74 0.26 0.00
168_I 353_L 0.74 0.26 0.00
50_L 291_I 0.74 0.26 0.00
134_Y 205_S 0.74 0.26 0.00
321_V 544_I 0.74 0.26 0.00
130_S 53_S 0.74 0.26 0.00
330_D 5_F 0.74 0.26 0.00
238_Q 826_I 0.74 0.26 0.00
56_G 623_S 0.74 0.26 0.00
256_T 871_Q 0.74 0.26 0.00
167_R 699_R 0.73 0.26 0.00
341_G 62_V 0.73 0.25 0.00
180_T 772_L 0.73 0.25 0.00
298_V 5_F 0.72 0.25 0.00
58_T 284_S 0.72 0.25 0.00
237_S 629_I 0.72 0.24 0.00
343_K 701_K 0.72 0.24 0.00
269_N 803_F 0.72 0.24 0.00
121_K 819_N 0.72 0.24 0.00
108_A 372_V 0.72 0.24 0.00
117_A 798_V 0.72 0.24 0.00
21_L 1_M 0.71 0.24 0.00
148_V 260_V 0.71 0.24 0.00
328_I 244_E 0.71 0.24 0.00
130_S 111_L 0.71 0.24 0.00
79_F 682_L 0.71 0.24 0.00
230_S 547_V 0.71 0.24 0.00
189_T 142_V 0.71 0.24 0.00
190_V 803_F 0.71 0.23 0.00
292_L 745_I 0.71 0.23 0.00
130_S 572_L 0.71 0.23 0.00
336_E 349_L 0.70 0.23 0.00
18_I 543_L 0.70 0.23 0.00
80_K 451_A 0.70 0.23 0.00
198_V 474_I 0.70 0.23 0.00
45_A 245_Q 0.70 0.23 0.00
42_T 311_A 0.70 0.23 0.00
245_L 798_V 0.70 0.23 0.00
168_I 741_S 0.70 0.23 0.00
165_S 17_L 0.70 0.23 0.00
290_A 414_E 0.70 0.22 0.00
202_Q 291_I 0.70 0.22 0.00
309_L 114_A 0.69 0.22 0.00
291_I 75_L 0.69 0.22 0.00
325_D 606_V 0.69 0.22 0.00
324_A 47_V 0.69 0.22 0.00
248_S 315_P 0.69 0.22 0.00
341_G 477_A 0.69 0.22 0.00
339_N 596_E 0.69 0.22 0.00
180_T 699_R 0.69 0.22 0.00
125_A 322_K 0.69 0.22 0.00
254_E 978_L 0.68 0.21 0.00
241_L 249_I 0.68 0.21 0.00
159_K 312_N 0.68 0.21 0.00
54_L 456_M 0.68 0.21 0.00
318_E 540_P 0.68 0.21 0.00
342_D 420_M 0.68 0.21 0.00
231_L 839_A 0.68 0.21 0.00
168_I 606_V 0.68 0.21 0.00
197_Y 749_V 0.68 0.21 0.00
127_Q 188_L 0.67 0.21 0.00
140_A 489_T 0.67 0.21 0.00
284_E 349_L 0.67 0.21 0.00
68_P 269_G 0.67 0.21 0.00
114_Q 147_G 0.67 0.20 0.00
340_A 551_G 0.67 0.20 0.00
152_R 805_T 0.67 0.20 0.00
201_T 258_S 0.67 0.20 0.00
334_V 531_V 0.67 0.20 0.00
240_P 282_N 0.67 0.20 0.00
338_L 838_D 0.67 0.20 0.00
107_Q 265_V 0.67 0.20 0.00
190_V 370_I 0.67 0.20 0.00
210_L 439_Q 0.67 0.20 0.00
79_F 443_V 0.67 0.20 0.00
322_I 313_L 0.67 0.20 0.00
279_H 219_L 0.66 0.20 0.00
196_I 891_Y 0.66 0.20 0.00
181_N 838_D 0.66 0.20 0.00
133_Q 594_M 0.66 0.20 0.00
161_L 198_L 0.66 0.20 0.00
159_K 543_L 0.66 0.20 0.00
155_L 787_K 0.66 0.20 0.00
338_L 260_V 0.66 0.20 0.00
310_V 606_V 0.66 0.20 0.00
94_I 587_T 0.66 0.20 0.00
291_I 88_M 0.66 0.20 0.00
243_G 75_L 0.66 0.20 0.00
90_Q 693_E 0.66 0.20 0.00
308_A 740_V 0.66 0.19 0.00
353_Q 45_V 0.66 0.19 0.00
348_G 337_I 0.66 0.19 0.00
101_A 827_L 0.65 0.19 0.00
300_R 478_M 0.65 0.19 0.00
176_G 373_P 0.65 0.19 0.00
340_A 727_K 0.65 0.19 0.00
260_T 798_V 0.65 0.19 0.00
83_S 175_F 0.65 0.19 0.00
99_Y 59_D 0.65 0.19 0.00
142_L 287_S 0.65 0.19 0.00
182_G 409_A 0.65 0.19 0.00
165_S 308_Q 0.65 0.19 0.00
280_A 584_A 0.65 0.19 0.00
322_I 244_E 0.65 0.19 0.00
277_F 965_A 0.65 0.19 0.00
69_Q 819_N 0.65 0.19 0.00
197_Y 337_I 0.65 0.19 0.00
283_Q 743_A 0.65 0.19 0.00
181_N 981_I 0.65 0.19 0.00
98_T 802_A 0.65 0.19 0.00
335_T 267_D 0.65 0.19 0.00
66_V 266_A 0.65 0.19 0.00
272_L 141_G 0.65 0.19 0.00
21_L 874_A 0.65 0.19 0.00
152_R 959_V 0.65 0.19 0.00
345_I 73_D 0.65 0.19 0.00
51_N 308_Q 0.65 0.19 0.00
95_D 978_L 0.65 0.19 0.00
162_S 410_I 0.65 0.19 0.00
298_V 884_F 0.65 0.19 0.00
74_I 597_Y 0.65 0.19 0.00
160_V 323_V 0.65 0.19 0.00
322_I 961_A 0.65 0.19 0.00
181_N 205_S 0.65 0.19 0.00
278_V 770_V 0.65 0.19 0.00
38_V 234_I 0.64 0.19 0.00
54_L 981_I 0.64 0.19 0.00
212_R 726_Y 0.64 0.18 0.00
201_T 962_A 0.64 0.18 0.00
93_Q 872_A 0.64 0.18 0.00
349_L 64_V 0.64 0.18 0.00
149_E 492_L 0.64 0.18 0.00
243_G 948_A 0.64 0.18 0.00
346_T 531_V 0.64 0.18 0.00
29_A 551_G 0.64 0.18 0.00
118_Q 710_P 0.64 0.18 0.00
273_L 749_V 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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