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OPENSEQ.org
137
Genes: A B A+B
Length: 286 467 692
Sequences: 10046 2226 698
Seq/Len: 35.13 4.77 1.01
MirrorTree (Pazo et al. 2001) 0.72
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 0.55 0.53
2 0.03 0.57 0.67
5 0.03 0.57 0.86
10 0.05 0.59 0.90
20 0.06 0.61 0.93
100 0.10 0.62 1.03
∞ 0.19 0.63 1.11
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
103_I 147_G 1.44 0.73 0.01
238_D 120_K 1.36 0.67 0.01
59_E 257_L 1.19 0.52 0.01
158_M 340_L 1.17 0.49 0.01
54_Q 212_I 1.16 0.48 0.00
114_A 68_I 1.12 0.45 0.00
5_C 165_I 1.10 0.43 0.00
83_V 254_K 1.09 0.42 0.00
246_K 225_S 1.08 0.41 0.00
32_K 189_V 1.05 0.39 0.00
211_V 364_T 1.04 0.38 0.00
157_A 388_Y 1.01 0.35 0.00
78_A 306_S 1.00 0.34 0.00
116_E 109_D 0.98 0.33 0.00
202_K 454_L 0.98 0.33 0.00
33_V 165_I 0.97 0.32 0.00
228_I 259_L 0.96 0.31 0.00
201_N 304_D 0.96 0.31 0.00
83_V 406_D 0.96 0.31 0.00
105_A 338_V 0.94 0.30 0.00
257_N 309_K 0.94 0.29 0.00
255_I 207_P 0.94 0.29 0.00
232_P 442_G 0.93 0.28 0.00
188_N 321_E 0.92 0.28 0.00
83_V 426_R 0.92 0.28 0.00
211_V 259_L 0.91 0.27 0.00
50_H 418_F 0.91 0.27 0.00
231_D 189_V 0.90 0.27 0.00
182_L 373_D 0.90 0.26 0.00
238_D 247_S 0.90 0.26 0.00
74_D 153_V 0.90 0.26 0.00
249_D 152_S 0.90 0.26 0.00
247_V 378_M 0.89 0.26 0.00
73_E 210_V 0.89 0.26 0.00
3_R 166_V 0.88 0.25 0.00
151_C 407_L 0.88 0.25 0.00
211_V 166_V 0.88 0.25 0.00
182_L 375_D 0.88 0.25 0.00
269_M 410_S 0.88 0.25 0.00
266_E 299_I 0.87 0.24 0.00
83_V 304_D 0.87 0.24 0.00
48_I 81_A 0.87 0.24 0.00
74_D 278_G 0.87 0.24 0.00
23_V 424_P 0.87 0.24 0.00
238_D 379_K 0.87 0.24 0.00
212_P 72_P 0.86 0.24 0.00
47_L 236_C 0.85 0.23 0.00
242_A 248_E 0.85 0.23 0.00
108_F 74_G 0.85 0.23 0.00
170_K 70_H 0.85 0.23 0.00
118_D 356_D 0.85 0.23 0.00
81_G 196_K 0.85 0.23 0.00
225_M 191_D 0.85 0.23 0.00
63_E 402_R 0.85 0.23 0.00
223_R 301_A 0.84 0.23 0.00
191_R 276_K 0.84 0.22 0.00
109_L 212_I 0.84 0.22 0.00
235_K 250_E 0.84 0.22 0.00
201_N 120_K 0.84 0.22 0.00
80_Y 388_Y 0.84 0.22 0.00
61_A 364_T 0.83 0.22 0.00
223_R 105_F 0.83 0.22 0.00
240_Y 435_G 0.83 0.22 0.00
203_L 392_T 0.83 0.22 0.00
82_G 338_V 0.83 0.21 0.00
59_E 386_L 0.82 0.21 0.00
202_K 357_L 0.82 0.21 0.00
151_C 193_V 0.82 0.21 0.00
191_R 210_V 0.81 0.21 0.00
33_V 93_V 0.81 0.21 0.00
63_E 324_A 0.81 0.21 0.00
247_V 247_S 0.81 0.20 0.00
75_V 325_V 0.81 0.20 0.00
80_Y 306_S 0.81 0.20 0.00
14_G 439_G 0.81 0.20 0.00
15_K 439_G 0.81 0.20 0.00
177_V 400_V 0.81 0.20 0.00
201_N 278_G 0.81 0.20 0.00
111_E 210_V 0.81 0.20 0.00
22_L 424_P 0.80 0.20 0.00
63_E 379_K 0.80 0.20 0.00
178_R 164_T 0.80 0.20 0.00
269_M 229_L 0.80 0.20 0.00
53_A 236_C 0.80 0.20 0.00
122_V 234_L 0.80 0.20 0.00
245_R 259_L 0.80 0.20 0.00
249_D 402_R 0.80 0.20 0.00
205_T 189_V 0.79 0.19 0.00
151_C 279_I 0.79 0.19 0.00
194_E 231_E 0.79 0.19 0.00
88_S 418_F 0.79 0.19 0.00
201_N 228_L 0.79 0.19 0.00
7_I 359_M 0.79 0.19 0.00
201_N 230_E 0.78 0.19 0.00
171_Y 109_D 0.78 0.19 0.00
176_S 137_V 0.78 0.19 0.00
60_M 59_W 0.78 0.19 0.00
11_G 439_G 0.78 0.19 0.00
259_I 110_I 0.78 0.19 0.00
182_L 234_L 0.78 0.18 0.00
80_Y 325_V 0.78 0.18 0.00
56_T 376_R 0.78 0.18 0.00
63_E 320_P 0.78 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.61 > 0.4) of paralogs.
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