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OPENSEQ.org
Sitanan
Genes: A B A+B
Length: 500 619 1035
Sequences: 4285 1323 1101
Seq/Len: 8.57 2.14 1.06
MirrorTree (Pazo et al. 2001) 0.07
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 0.03 0.09 0.00
2 0.03 0.09 0.00
5 0.03 0.09 0.01
10 0.03 0.09 0.01
20 0.03 0.09 0.04
100 0.05 0.09 0.20
∞ 0.20 0.09 0.98
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
45_I 149_V 1.29 0.62 0.00
190_D 188_I 1.18 0.52 0.00
403_A 300_V 1.15 0.49 0.00
387_F 62_S 1.14 0.48 0.00
271_P 386_L 1.13 0.47 0.00
179_P 500_M 1.13 0.47 0.00
378_L 291_R 1.11 0.46 0.00
141_L 369_V 1.09 0.43 0.00
151_R 291_R 1.08 0.42 0.00
217_F 131_S 1.05 0.40 0.00
150_Y 259_T 1.04 0.39 0.00
186_D 71_L 1.03 0.38 0.00
277_P 78_V 1.01 0.36 0.00
130_M 306_L 1.00 0.35 0.00
338_Q 42_V 0.99 0.35 0.00
137_S 352_I 0.99 0.34 0.00
93_S 579_P 0.98 0.34 0.00
283_V 96_Y 0.98 0.33 0.00
353_L 140_R 0.97 0.32 0.00
169_L 569_A 0.96 0.32 0.00
275_Y 170_Q 0.96 0.32 0.00
183_D 272_R 0.96 0.32 0.00
218_P 96_Y 0.96 0.32 0.00
107_I 30_E 0.95 0.32 0.00
164_T 349_V 0.95 0.31 0.00
283_V 230_S 0.95 0.31 0.00
169_L 486_P 0.95 0.31 0.00
308_V 560_I 0.95 0.31 0.00
186_D 505_M 0.95 0.31 0.00
234_T 111_I 0.94 0.31 0.00
140_A 184_F 0.94 0.30 0.00
189_I 369_V 0.94 0.30 0.00
163_A 29_V 0.93 0.30 0.00
339_L 385_I 0.91 0.28 0.00
197_V 327_V 0.91 0.28 0.00
39_A 103_V 0.91 0.28 0.00
190_D 120_L 0.91 0.28 0.00
183_D 594_A 0.91 0.28 0.00
186_D 209_E 0.91 0.28 0.00
427_I 272_R 0.91 0.28 0.00
190_D 548_T 0.90 0.27 0.00
150_Y 290_L 0.90 0.27 0.00
212_L 131_S 0.90 0.27 0.00
168_L 245_I 0.89 0.27 0.00
329_S 360_H 0.89 0.27 0.00
215_H 52_H 0.89 0.26 0.00
297_A 20_E 0.88 0.26 0.00
187_D 42_V 0.88 0.26 0.00
51_N 52_H 0.87 0.25 0.00
250_K 569_A 0.87 0.25 0.00
479_I 230_S 0.86 0.25 0.00
363_V 579_P 0.86 0.24 0.00
490_V 62_S 0.86 0.24 0.00
325_D 472_V 0.86 0.24 0.00
375_R 113_V 0.85 0.24 0.00
160_G 174_V 0.85 0.24 0.00
185_F 131_S 0.85 0.24 0.00
108_V 85_E 0.84 0.23 0.00
189_I 20_E 0.84 0.23 0.00
214_A 47_I 0.84 0.23 0.00
371_L 265_S 0.84 0.23 0.00
206_V 140_R 0.84 0.23 0.00
175_G 244_R 0.84 0.23 0.00
338_Q 352_I 0.83 0.23 0.00
186_D 208_Y 0.83 0.23 0.00
171_L 144_V 0.83 0.23 0.00
18_L 147_Q 0.83 0.22 0.00
338_Q 569_A 0.83 0.22 0.00
19_L 250_K 0.83 0.22 0.00
180_Y 565_A 0.82 0.22 0.00
211_L 243_V 0.82 0.22 0.00
111_N 52_H 0.82 0.22 0.00
89_S 184_F 0.82 0.22 0.00
189_I 197_R 0.82 0.22 0.00
93_S 307_R 0.82 0.22 0.00
250_K 113_V 0.82 0.22 0.00
376_K 78_V 0.82 0.22 0.00
59_I 225_D 0.82 0.22 0.00
253_L 266_E 0.82 0.22 0.00
184_F 95_L 0.82 0.21 0.00
215_H 131_S 0.81 0.21 0.00
490_V 4_E 0.81 0.21 0.00
197_V 62_S 0.80 0.20 0.00
131_K 565_A 0.80 0.20 0.00
19_L 103_V 0.80 0.20 0.00
199_S 565_A 0.80 0.20 0.00
363_V 478_R 0.79 0.20 0.00
129_V 45_N 0.79 0.20 0.00
100_T 516_I 0.79 0.20 0.00
284_N 72_I 0.79 0.20 0.00
170_D 147_Q 0.79 0.20 0.00
36_E 100_D 0.79 0.20 0.00
284_N 166_L 0.79 0.20 0.00
402_L 138_D 0.79 0.20 0.00
195_F 349_V 0.79 0.20 0.00
481_Q 572_K 0.79 0.20 0.00
119_P 502_E 0.78 0.19 0.00
148_A 322_V 0.78 0.19 0.00
445_C 75_Q 0.78 0.19 0.00
67_V 385_I 0.78 0.19 0.00
338_Q 31_F 0.78 0.19 0.00
32_A 351_K 0.78 0.19 0.00
47_P 190_I 0.78 0.19 0.00
232_R 190_I 0.78 0.19 0.00
154_D 512_P 0.77 0.19 0.00
134_Q 212_A 0.77 0.19 0.00
399_G 382_L 0.77 0.18 0.00
192_L 579_P 0.77 0.18 0.00
45_I 45_N 0.77 0.18 0.00
264_F 113_V 0.77 0.18 0.00
130_M 484_E 0.77 0.18 0.00
97_Q 479_T 0.77 0.18 0.00
46_A 103_V 0.76 0.18 0.00
195_F 79_V 0.76 0.18 0.00
165_R 267_P 0.76 0.18 0.00
100_T 113_V 0.76 0.18 0.00
499_L 484_E 0.76 0.18 0.00
197_V 195_L 0.76 0.18 0.00
232_R 579_P 0.76 0.18 0.00
385_V 62_S 0.76 0.18 0.00
17_R 200_Y 0.76 0.18 0.00
31_V 113_V 0.75 0.18 0.00
182_L 98_E 0.75 0.18 0.00
170_D 276_S 0.75 0.18 0.00
86_D 471_K 0.75 0.18 0.00
189_I 110_R 0.75 0.18 0.00
310_P 184_F 0.75 0.17 0.00
338_Q 259_T 0.75 0.17 0.00
387_F 349_V 0.75 0.17 0.00
425_L 31_F 0.75 0.17 0.00
155_Q 268_T 0.75 0.17 0.00
481_Q 512_P 0.75 0.17 0.00
87_I 150_R 0.75 0.17 0.00
216_E 225_D 0.75 0.17 0.00
189_I 165_F 0.74 0.17 0.00
183_D 95_L 0.74 0.17 0.00
400_E 361_L 0.74 0.17 0.00
141_L 155_L 0.74 0.17 0.00
375_R 142_R 0.74 0.17 0.00
108_V 352_I 0.74 0.17 0.00
491_G 252_G 0.74 0.17 0.00
412_I 267_P 0.74 0.17 0.00
189_I 362_P 0.74 0.17 0.00
441_L 155_L 0.74 0.17 0.00
187_D 525_A 0.74 0.17 0.00
142_R 398_G 0.73 0.17 0.00
243_H 79_V 0.73 0.17 0.00
491_G 259_T 0.73 0.17 0.00
372_D 149_V 0.73 0.17 0.00
190_D 327_V 0.73 0.17 0.00
159_H 500_M 0.73 0.17 0.00
126_H 95_L 0.73 0.17 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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