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OPENSEQ.org
3190-4254
Genes: A B A+B
Length: 241 366 584
Sequences: 74704 3451 421
Seq/Len: 309.98 9.43 0.72
MirrorTree (Pazo et al. 2001) 0.51
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.08 0.56 0.01
2 0.10 0.56 0.02
5 0.12 0.57 0.20
10 0.14 0.57 0.43
20 0.18 0.57 0.69
100 0.25 0.58 1.84
∞ 0.29 0.63 3.09
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
34_L 325_L 1.49 0.66 0.00
208_Y 97_V 1.47 0.65 0.00
21_D 333_T 1.23 0.45 0.00
225_L 93_L 1.22 0.45 0.00
94_S 48_V 1.22 0.44 0.00
20_E 303_M 1.18 0.41 0.00
34_L 165_D 1.17 0.40 0.00
80_I 337_I 1.14 0.38 0.00
24_L 207_L 1.08 0.33 0.00
4_L 304_L 1.07 0.32 0.00
155_N 25_I 1.04 0.30 0.00
4_L 36_G 1.03 0.29 0.00
34_L 172_V 1.03 0.29 0.00
95_V 206_T 1.02 0.29 0.00
10_A 342_A 1.01 0.28 0.00
21_D 329_L 0.99 0.27 0.00
94_S 161_I 0.99 0.27 0.00
57_A 46_N 0.99 0.27 0.00
24_L 107_V 0.99 0.27 0.00
34_L 281_L 0.98 0.26 0.00
62_I 49_L 0.97 0.26 0.00
4_L 285_P 0.97 0.25 0.00
35_L 249_M 0.96 0.25 0.00
49_V 285_P 0.96 0.25 0.00
143_R 79_L 0.95 0.24 0.00
207_A 12_L 0.93 0.23 0.00
26_V 132_L 0.93 0.23 0.00
24_L 343_I 0.93 0.23 0.00
34_L 170_K 0.93 0.23 0.00
62_I 340_A 0.93 0.23 0.00
99_L 12_L 0.93 0.23 0.00
34_L 104_I 0.92 0.23 0.00
26_V 234_I 0.92 0.22 0.00
94_S 93_L 0.91 0.22 0.00
146_V 309_F 0.91 0.22 0.00
130_L 334_V 0.91 0.22 0.00
217_A 62_L 0.89 0.21 0.00
155_N 120_A 0.89 0.21 0.00
35_L 79_L 0.89 0.21 0.00
55_R 47_L 0.89 0.20 0.00
23_S 343_I 0.88 0.20 0.00
64_D 95_K 0.88 0.20 0.00
12_A 75_T 0.87 0.20 0.00
9_L 159_L 0.87 0.19 0.00
180_I 231_Q 0.87 0.19 0.00
95_V 253_T 0.87 0.19 0.00
132_D 274_F 0.86 0.19 0.00
147_E 54_L 0.86 0.19 0.00
7_K 282_M 0.86 0.19 0.00
192_I 60_A 0.85 0.19 0.00
193_T 66_L 0.85 0.19 0.00
24_L 288_V 0.85 0.18 0.00
67_I 112_V 0.85 0.18 0.00
44_T 65_P 0.85 0.18 0.00
156_P 287_S 0.85 0.18 0.00
214_H 165_D 0.84 0.18 0.00
90_F 172_V 0.84 0.18 0.00
208_Y 217_A 0.84 0.18 0.00
214_H 229_D 0.84 0.18 0.00
94_S 184_R 0.84 0.18 0.00
49_V 68_L 0.84 0.18 0.00
21_D 166_G 0.83 0.18 0.00
7_K 325_L 0.83 0.18 0.00
81_G 330_W 0.83 0.18 0.00
19_V 121_G 0.83 0.18 0.00
43_T 327_P 0.83 0.18 0.00
132_D 79_L 0.83 0.17 0.00
48_M 73_L 0.83 0.17 0.00
112_E 116_N 0.83 0.17 0.00
158_F 14_S 0.83 0.17 0.00
7_K 51_L 0.83 0.17 0.00
8_N 90_A 0.82 0.17 0.00
25_T 229_D 0.82 0.17 0.00
22_V 112_V 0.82 0.17 0.00
26_V 343_I 0.82 0.17 0.00
211_S 16_L 0.82 0.17 0.00
171_I 267_N 0.82 0.17 0.00
220_T 99_V 0.82 0.17 0.00
94_S 312_I 0.81 0.17 0.00
97_D 249_M 0.81 0.17 0.00
59_N 109_T 0.81 0.17 0.00
211_S 236_H 0.81 0.17 0.00
208_Y 303_M 0.81 0.17 0.00
193_T 259_T 0.81 0.17 0.00
24_L 316_L 0.81 0.16 0.00
190_V 172_V 0.80 0.16 0.00
208_Y 252_R 0.80 0.16 0.00
23_S 12_L 0.80 0.16 0.00
62_I 261_R 0.80 0.16 0.00
119_N 24_L 0.80 0.16 0.00
152_L 37_A 0.80 0.16 0.00
39_G 92_G 0.80 0.16 0.00
41_G 92_G 0.80 0.16 0.00
42_K 92_G 0.80 0.16 0.00
162_D 92_G 0.80 0.16 0.00
20_E 13_K 0.80 0.16 0.00
43_T 191_D 0.79 0.16 0.00
121_L 309_F 0.79 0.16 0.00
123_E 252_R 0.79 0.16 0.00
102_V 12_L 0.79 0.16 0.00
84_P 225_T 0.79 0.16 0.00
235_L 10_E 0.79 0.16 0.00
108_D 81_T 0.78 0.15 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 (0.57 > 0.4) of paralogs.
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