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OPENSEQ.org
139
Genes: A B A+B
Length: 286 468 692
Sequences: 10046 2228 707
Seq/Len: 35.13 4.76 1.02
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 0.68
5 0.03 0.57 0.86
10 0.05 0.59 0.91
20 0.06 0.61 0.94
100 0.10 0.62 1.02
∞ 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 1.45 0.74 0.01
238_D 120_K 1.19 0.52 0.01
59_E 257_L 1.17 0.49 0.01
158_M 340_L 1.14 0.47 0.01
114_A 68_I 1.11 0.45 0.01
32_K 189_V 1.06 0.40 0.00
54_Q 212_I 1.06 0.40 0.00
211_V 364_T 1.06 0.39 0.00
73_E 210_V 1.05 0.39 0.00
83_V 304_D 1.02 0.37 0.00
238_D 247_S 1.01 0.35 0.00
157_A 388_Y 1.00 0.34 0.00
83_V 254_K 0.99 0.33 0.00
228_I 259_L 0.99 0.33 0.00
3_R 166_V 0.96 0.32 0.00
63_E 404_K 0.95 0.30 0.00
232_P 442_G 0.94 0.30 0.00
32_K 375_D 0.94 0.29 0.00
182_L 373_D 0.94 0.29 0.00
188_N 321_E 0.94 0.29 0.00
5_C 165_I 0.93 0.29 0.00
61_A 364_T 0.92 0.28 0.00
147_I 122_I 0.92 0.28 0.00
23_V 424_P 0.92 0.28 0.00
33_V 165_I 0.92 0.28 0.00
201_N 228_L 0.91 0.28 0.00
78_A 306_S 0.91 0.27 0.00
105_A 338_V 0.91 0.27 0.00
50_H 418_F 0.91 0.27 0.00
245_R 259_L 0.91 0.27 0.00
83_V 406_D 0.91 0.27 0.00
116_E 109_D 0.91 0.27 0.00
246_K 225_S 0.90 0.27 0.00
63_E 402_R 0.90 0.27 0.00
201_N 304_D 0.90 0.27 0.00
202_K 454_L 0.89 0.26 0.00
194_E 231_E 0.89 0.26 0.00
247_V 378_M 0.89 0.26 0.00
80_Y 163_K 0.89 0.26 0.00
81_G 196_K 0.88 0.25 0.00
191_R 276_K 0.88 0.25 0.00
257_N 309_K 0.88 0.25 0.00
235_K 250_E 0.88 0.25 0.00
74_D 278_G 0.88 0.25 0.00
242_A 248_E 0.88 0.25 0.00
48_I 81_A 0.88 0.25 0.00
108_F 74_G 0.87 0.24 0.00
29_M 372_D 0.87 0.24 0.00
151_C 407_L 0.86 0.24 0.00
212_P 72_P 0.86 0.24 0.00
269_M 410_S 0.86 0.24 0.00
73_E 324_A 0.86 0.23 0.00
80_Y 306_S 0.85 0.23 0.00
170_K 70_H 0.84 0.23 0.00
151_C 193_V 0.84 0.23 0.00
203_L 392_T 0.84 0.22 0.00
223_R 105_F 0.84 0.22 0.00
118_D 356_D 0.83 0.22 0.00
211_V 259_L 0.83 0.22 0.00
109_L 212_I 0.83 0.22 0.00
177_V 400_V 0.83 0.22 0.00
27_A 321_E 0.83 0.22 0.00
118_D 225_S 0.83 0.22 0.00
240_Y 435_G 0.82 0.21 0.00
231_D 189_V 0.82 0.21 0.00
249_D 152_S 0.82 0.21 0.00
59_E 386_L 0.82 0.21 0.00
201_N 278_G 0.82 0.21 0.00
122_V 234_L 0.81 0.21 0.00
47_L 236_C 0.81 0.20 0.00
74_D 153_V 0.80 0.20 0.00
83_V 426_R 0.80 0.20 0.00
82_G 338_V 0.80 0.20 0.00
259_I 110_I 0.80 0.20 0.00
80_Y 388_Y 0.80 0.20 0.00
7_I 143_I 0.80 0.20 0.00
182_L 375_D 0.80 0.20 0.00
171_Y 109_D 0.80 0.20 0.00
178_R 164_T 0.79 0.20 0.00
247_V 247_S 0.79 0.19 0.00
204_G 103_S 0.79 0.19 0.00
266_E 299_I 0.79 0.19 0.00
255_I 207_P 0.79 0.19 0.00
249_D 402_R 0.79 0.19 0.00
53_A 236_C 0.79 0.19 0.00
50_H 294_E 0.78 0.19 0.00
22_L 424_P 0.78 0.19 0.00
225_M 191_D 0.78 0.19 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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