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OPENSEQ.org
ExF
Genes: A B A+B
Length: 98 560 633
Sequences: 888 1492 763
Seq/Len: 9.06 2.66 1.21
MirrorTree (Pazo et al. 2001) 0.66
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 0.00 1.12
2 0.00 0.00 1.12
5 0.00 0.00 1.16
10 0.00 0.00 1.16
20 0.00 0.00 1.16
100 0.01 0.01 1.16
∞ 0.01 0.03 1.21
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
92_E 462_K 1.52 0.83 0.07
36_E 351_T 1.41 0.75 0.05
70_T 216_Q 1.31 0.68 0.04
80_L 316_S 1.28 0.65 0.04
94_T 212_K 1.27 0.64 0.04
86_A 125_T 1.26 0.63 0.04
85_K 351_T 1.23 0.60 0.03
82_V 291_R 1.21 0.58 0.03
74_S 357_T 1.20 0.57 0.03
67_I 91_Q 1.19 0.57 0.03
81_E 417_Q 1.13 0.51 0.02
97_Q 335_K 1.10 0.48 0.02
88_S 104_E 1.10 0.48 0.02
80_L 414_V 1.09 0.47 0.02
39_D 471_M 1.08 0.46 0.02
89_A 273_D 1.07 0.46 0.02
75_S 451_I 1.06 0.45 0.02
92_E 522_Q 1.06 0.45 0.02
69_I 111_R 1.06 0.44 0.02
86_A 30_I 1.05 0.43 0.02
48_E 57_V 1.04 0.43 0.02
83_R 344_L 1.04 0.42 0.02
67_I 467_F 1.03 0.41 0.02
95_R 388_L 1.02 0.40 0.02
67_I 246_L 1.02 0.40 0.02
34_K 536_D 1.01 0.40 0.02
41_N 158_I 1.01 0.40 0.02
80_L 236_I 1.01 0.39 0.02
70_T 256_P 1.00 0.39 0.01
50_A 404_I 1.00 0.38 0.01
93_I 245_A 0.99 0.38 0.01
40_L 18_T 0.99 0.38 0.01
75_S 139_G 0.98 0.37 0.01
73_E 216_Q 0.98 0.37 0.01
74_S 268_V 0.97 0.36 0.01
28_E 391_E 0.97 0.36 0.01
28_E 390_K 0.97 0.35 0.01
75_S 522_Q 0.96 0.35 0.01
61_D 142_A 0.96 0.34 0.01
87_I 126_N 0.95 0.34 0.01
35_N 34_G 0.95 0.34 0.01
71_K 363_A 0.94 0.33 0.01
73_E 530_L 0.94 0.33 0.01
92_E 395_S 0.94 0.33 0.01
49_A 262_D 0.93 0.33 0.01
55_A 168_E 0.93 0.32 0.01
73_E 174_T 0.93 0.32 0.01
53_D 22_R 0.92 0.32 0.01
62_L 231_L 0.92 0.32 0.01
54_I 148_L 0.91 0.30 0.01
96_T 202_A 0.91 0.30 0.01
65_A 537_K 0.90 0.30 0.01
55_A 125_T 0.90 0.30 0.01
37_I 206_L 0.90 0.30 0.01
87_I 63_S 0.90 0.30 0.01
92_E 206_L 0.89 0.29 0.01
53_D 192_I 0.89 0.29 0.01
72_A 498_K 0.89 0.29 0.01
92_E 209_E 0.89 0.29 0.01
91_K 355_F 0.89 0.29 0.01
85_K 533_L 0.88 0.28 0.01
50_A 290_V 0.88 0.28 0.01
27_D 151_I 0.88 0.28 0.01
79_M 470_K 0.88 0.28 0.01
96_T 551_N 0.88 0.28 0.01
72_A 198_I 0.87 0.28 0.01
43_A 51_N 0.87 0.27 0.01
62_L 278_E 0.87 0.27 0.01
64_Q 99_M 0.86 0.27 0.01
92_E 362_S 0.86 0.27 0.01
49_A 116_A 0.86 0.27 0.01
86_A 100_F 0.86 0.27 0.01
95_R 360_R 0.86 0.27 0.01
74_S 457_F 0.86 0.27 0.01
30_A 178_V 0.86 0.27 0.01
63_H 128_E 0.86 0.27 0.01
94_T 236_I 0.86 0.27 0.01
38_N 207_T 0.86 0.26 0.01
20_Q 358_V 0.86 0.26 0.01
54_I 539_E 0.85 0.26 0.01
84_N 151_I 0.85 0.26 0.01
81_E 333_Y 0.85 0.26 0.01
97_Q 83_S 0.85 0.26 0.01
91_K 164_S 0.85 0.26 0.01
93_I 362_S 0.84 0.25 0.01
65_A 148_L 0.84 0.25 0.01
73_E 136_A 0.84 0.25 0.01
69_I 17_L 0.84 0.25 0.01
30_A 227_Y 0.84 0.25 0.01
71_K 345_S 0.84 0.25 0.01
81_E 139_G 0.84 0.25 0.01
53_D 142_A 0.83 0.25 0.01
47_G 188_T 0.83 0.25 0.01
79_M 194_G 0.83 0.24 0.01
67_I 286_P 0.83 0.24 0.01
64_Q 126_N 0.83 0.24 0.01
76_M 320_P 0.83 0.24 0.01
71_K 107_I 0.82 0.24 0.01
51_M 243_E 0.82 0.24 0.01
36_E 128_E 0.82 0.24 0.01
58_Q 177_V 0.82 0.24 0.01
66_A 166_F 0.82 0.23 0.01
36_E 366_T 0.82 0.23 0.01
56_T 276_K 0.82 0.23 0.01
79_M 144_T 0.81 0.23 0.01
93_I 515_N 0.81 0.23 0.01
83_R 151_I 0.81 0.23 0.01
87_I 68_I 0.81 0.23 0.01
11_N 176_S 0.81 0.23 0.01
39_D 87_I 0.81 0.23 0.01
45_E 206_L 0.81 0.23 0.01
62_L 438_R 0.81 0.23 0.01
93_I 327_K 0.81 0.23 0.01
95_R 179_V 0.81 0.23 0.01
77_K 235_Q 0.81 0.23 0.01
22_S 308_I 0.80 0.23 0.01
71_K 154_A 0.80 0.22 0.01
98_I 450_F 0.80 0.22 0.01
35_N 91_Q 0.80 0.22 0.01
47_G 456_L 0.80 0.22 0.01
44_Q 314_A 0.80 0.22 0.01
97_Q 294_Q 0.79 0.22 0.01
31_K 67_A 0.79 0.22 0.01
62_L 39_L 0.79 0.22 0.01
30_A 480_E 0.79 0.22 0.01
71_K 289_I 0.79 0.21 0.01
37_I 413_S 0.79 0.21 0.01
79_M 396_V 0.78 0.21 0.01
95_R 355_F 0.78 0.21 0.01
80_L 346_K 0.78 0.21 0.01
72_A 89_V 0.78 0.21 0.01
62_L 458_I 0.78 0.21 0.01
27_D 215_D 0.78 0.21 0.01
38_N 459_F 0.78 0.21 0.01
92_E 86_K 0.78 0.21 0.01
63_H 138_E 0.78 0.21 0.01
87_I 141_L 0.78 0.21 0.01
54_I 230_D 0.77 0.21 0.01
37_I 152_R 0.77 0.21 0.01
36_E 533_L 0.77 0.21 0.01
65_A 355_F 0.77 0.20 0.01
19_S 57_V 0.77 0.20 0.01
65_A 262_D 0.77 0.20 0.01
79_M 270_I 0.77 0.20 0.01
62_L 359_L 0.77 0.20 0.01
70_T 257_F 0.77 0.20 0.01
63_H 18_T 0.77 0.20 0.01
78_F 121_A 0.77 0.20 0.01
91_K 549_I 0.77 0.20 0.01
41_N 145_I 0.77 0.20 0.01
70_T 84_E 0.77 0.20 0.01
58_Q 165_V 0.77 0.20 0.01
44_Q 179_V 0.77 0.20 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)
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