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OPENSEQ.org
ExI
Genes: A B A+B
Length: 98 461 524
Sequences: 888 5981 613
Seq/Len: 9.06 12.97 1.17
MirrorTree (Pazo et al. 2001) 0.57
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 0.00 0.22 0.01
2 0.00 0.48 0.01
5 0.00 0.50 1.06
10 0.00 0.52 1.08
20 0.00 0.53 1.08
100 0.01 0.56 1.10
∞ 0.01 0.58 1.17
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
71_K 144_V 1.53 0.83 0.07
71_K 182_S 1.50 0.81 0.07
28_E 192_I 1.28 0.64 0.04
37_I 424_N 1.19 0.56 0.03
73_E 144_V 1.18 0.55 0.03
34_K 201_E 1.17 0.54 0.03
81_E 267_G 1.15 0.52 0.02
19_S 213_D 1.13 0.50 0.02
38_N 45_L 1.12 0.49 0.02
61_D 275_T 1.11 0.48 0.02
80_L 280_P 1.11 0.48 0.02
70_T 146_V 1.10 0.48 0.02
72_A 382_N 1.10 0.48 0.02
95_R 178_I 1.07 0.45 0.02
67_I 23_T 1.07 0.44 0.02
79_M 230_Y 1.04 0.42 0.02
30_A 320_I 1.04 0.41 0.02
62_L 377_S 1.04 0.41 0.02
83_R 239_A 1.03 0.41 0.02
88_S 29_S 1.02 0.39 0.02
79_M 312_D 1.02 0.39 0.02
84_N 239_A 1.01 0.39 0.01
63_H 261_M 1.01 0.39 0.01
67_I 226_L 1.01 0.39 0.01
94_T 35_L 1.00 0.38 0.01
54_I 35_L 0.99 0.37 0.01
50_A 182_S 0.98 0.36 0.01
83_R 384_V 0.98 0.36 0.01
91_K 123_M 0.98 0.36 0.01
76_M 256_V 0.98 0.36 0.01
51_M 275_T 0.97 0.35 0.01
65_A 230_Y 0.96 0.34 0.01
79_M 306_F 0.96 0.34 0.01
88_S 399_L 0.95 0.33 0.01
67_I 349_I 0.95 0.33 0.01
62_L 407_E 0.94 0.33 0.01
97_Q 231_G 0.94 0.33 0.01
83_R 340_D 0.94 0.32 0.01
20_Q 146_V 0.93 0.32 0.01
33_L 412_F 0.93 0.31 0.01
30_A 98_E 0.92 0.31 0.01
98_I 146_V 0.92 0.31 0.01
81_E 373_K 0.92 0.31 0.01
78_F 227_M 0.92 0.31 0.01
55_A 179_V 0.92 0.30 0.01
63_H 127_R 0.92 0.30 0.01
47_G 379_L 0.92 0.30 0.01
37_I 360_I 0.91 0.30 0.01
33_L 320_I 0.91 0.30 0.01
97_Q 179_V 0.90 0.29 0.01
87_I 38_G 0.90 0.29 0.01
96_T 256_V 0.89 0.28 0.01
28_E 338_L 0.88 0.28 0.01
88_S 430_L 0.88 0.28 0.01
84_N 250_L 0.88 0.27 0.01
83_R 215_V 0.88 0.27 0.01
62_L 103_V 0.87 0.27 0.01
61_D 359_D 0.87 0.26 0.01
24_G 349_I 0.86 0.26 0.01
69_I 32_I 0.86 0.26 0.01
81_E 286_L 0.86 0.26 0.01
92_E 311_V 0.86 0.26 0.01
37_I 16_S 0.86 0.26 0.01
31_K 353_A 0.86 0.26 0.01
76_M 78_F 0.85 0.26 0.01
36_E 216_I 0.85 0.25 0.01
93_I 154_T 0.85 0.25 0.01
28_E 10_L 0.85 0.25 0.01
32_M 312_D 0.84 0.25 0.01
64_Q 45_L 0.84 0.24 0.01
63_H 372_F 0.84 0.24 0.01
27_D 55_T 0.83 0.24 0.01
37_I 370_R 0.83 0.23 0.01
41_N 277_K 0.82 0.23 0.01
74_S 104_V 0.82 0.23 0.01
75_S 97_D 0.82 0.23 0.01
79_M 406_K 0.82 0.23 0.01
92_E 388_I 0.82 0.23 0.01
81_E 48_N 0.81 0.23 0.01
50_A 342_G 0.81 0.23 0.01
95_R 350_Q 0.80 0.22 0.01
87_I 259_F 0.80 0.22 0.01
82_V 362_S 0.80 0.22 0.01
30_A 39_V 0.80 0.22 0.01
16_T 344_Y 0.80 0.21 0.01
76_M 30_I 0.79 0.21 0.01
62_L 137_L 0.79 0.21 0.01
92_E 185_P 0.79 0.21 0.01
91_K 382_N 0.79 0.21 0.01
40_L 241_Y 0.79 0.21 0.01
33_L 80_I 0.79 0.21 0.01
90_Y 303_I 0.78 0.21 0.01
82_V 340_D 0.78 0.20 0.01
72_A 378_L 0.78 0.20 0.01
80_L 42_I 0.78 0.20 0.01
61_D 84_A 0.78 0.20 0.01
61_D 280_P 0.78 0.20 0.01
95_R 235_A 0.77 0.20 0.01
37_I 73_S 0.77 0.20 0.01
74_S 302_T 0.77 0.20 0.01
20_Q 104_V 0.77 0.20 0.01
27_D 147_K 0.77 0.20 0.01
40_L 47_S 0.77 0.20 0.01
28_E 386_L 0.77 0.20 0.01
56_T 297_E 0.77 0.20 0.01
77_K 397_K 0.76 0.20 0.01
87_I 430_L 0.76 0.19 0.01
65_A 236_M 0.76 0.19 0.01
62_L 374_R 0.76 0.19 0.01
20_Q 371_K 0.76 0.19 0.01
60_K 374_R 0.76 0.19 0.01
31_K 428_E 0.76 0.19 0.01
67_I 373_K 0.76 0.19 0.01
52_T 424_N 0.76 0.19 0.01
78_F 29_S 0.76 0.19 0.01
87_I 45_L 0.76 0.19 0.01
56_T 349_I 0.75 0.19 0.01
62_L 269_A 0.75 0.19 0.01
55_A 382_N 0.75 0.19 0.01
84_N 148_T 0.75 0.19 0.01
76_M 245_Q 0.75 0.19 0.01
78_F 179_V 0.75 0.18 0.01
54_I 374_R 0.75 0.18 0.01
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 (0.56 > 0.4) of paralogs.
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