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OPENSEQ.org
ExH
Genes: A B A+B
Length: 98 276 330
Sequences: 888 457 244
Seq/Len: 9.06 1.66 0.74
MirrorTree (Pazo et al. 2001) 0.70
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 0.00
2 0.00 0.00 0.02
5 0.00 0.00 0.65
10 0.00 0.00 0.65
20 0.00 0.00 0.65
100 0.01 0.00 0.65
∞ 0.01 0.00 0.73
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
54_I 265_R 1.89 0.89 0.28
95_R 256_G 1.69 0.80 0.18
55_A 137_F 1.54 0.71 0.12
83_R 241_D 1.47 0.66 0.10
95_R 166_I 1.36 0.57 0.07
75_S 239_S 1.35 0.56 0.07
98_I 164_N 1.34 0.56 0.07
41_N 201_A 1.30 0.52 0.06
95_R 236_I 1.27 0.50 0.05
82_V 189_L 1.26 0.48 0.05
96_T 129_G 1.25 0.48 0.05
78_F 180_I 1.23 0.46 0.04
75_S 161_N 1.16 0.40 0.04
55_A 239_S 1.15 0.39 0.03
68_A 92_M 1.13 0.37 0.03
45_E 127_K 1.12 0.37 0.03
35_N 126_T 1.11 0.36 0.03
86_A 265_R 1.10 0.35 0.03
61_D 58_E 1.08 0.34 0.03
81_E 257_N 1.08 0.34 0.03
82_V 268_K 1.08 0.33 0.03
47_G 241_D 1.07 0.33 0.03
42_K 96_I 1.06 0.32 0.03
95_R 252_I 1.06 0.32 0.02
32_M 92_M 1.04 0.31 0.02
84_N 125_F 1.03 0.30 0.02
82_V 133_A 1.03 0.30 0.02
43_A 110_F 1.03 0.30 0.02
81_E 124_K 1.03 0.30 0.02
82_V 181_A 1.03 0.30 0.02
50_A 132_K 1.02 0.29 0.02
31_K 184_V 1.02 0.29 0.02
74_S 261_N 1.01 0.29 0.02
71_K 249_V 1.00 0.28 0.02
47_G 222_D 1.00 0.28 0.02
71_K 265_R 0.99 0.27 0.02
81_E 217_K 0.99 0.27 0.02
98_I 179_D 0.99 0.27 0.02
48_E 182_K 0.99 0.27 0.02
91_K 253_S 0.97 0.26 0.02
67_I 230_F 0.96 0.25 0.02
54_I 77_F 0.96 0.25 0.02
24_G 262_L 0.96 0.25 0.02
81_E 207_E 0.95 0.25 0.02
84_N 241_D 0.95 0.25 0.02
68_A 74_I 0.95 0.25 0.02
51_M 223_Y 0.95 0.25 0.02
54_I 223_Y 0.95 0.25 0.02
70_T 251_I 0.95 0.25 0.02
38_N 79_P 0.95 0.24 0.02
98_I 68_A 0.94 0.24 0.01
98_I 185_I 0.94 0.24 0.01
36_E 248_S 0.94 0.24 0.01
42_K 184_V 0.94 0.24 0.01
98_I 136_E 0.93 0.23 0.01
51_M 207_E 0.93 0.23 0.01
60_K 99_L 0.93 0.23 0.01
72_A 109_E 0.92 0.23 0.01
37_I 118_L 0.92 0.23 0.01
96_T 133_A 0.91 0.22 0.01
79_M 172_E 0.91 0.22 0.01
83_R 176_T 0.91 0.22 0.01
94_T 265_R 0.91 0.22 0.01
96_T 253_S 0.90 0.21 0.01
55_A 260_S 0.89 0.21 0.01
94_T 260_S 0.89 0.21 0.01
28_E 175_D 0.89 0.21 0.01
13_I 135_E 0.88 0.21 0.01
88_S 166_I 0.88 0.20 0.01
91_K 263_N 0.88 0.20 0.01
87_I 150_K 0.87 0.20 0.01
92_E 94_S 0.87 0.20 0.01
60_K 91_E 0.87 0.20 0.01
43_A 234_A 0.87 0.20 0.01
34_K 119_E 0.87 0.20 0.01
62_L 219_N 0.86 0.20 0.01
47_G 243_A 0.86 0.20 0.01
58_Q 177_A 0.86 0.20 0.01
51_M 266_L 0.85 0.19 0.01
40_L 266_L 0.85 0.19 0.01
44_Q 273_V 0.85 0.19 0.01
71_K 218_V 0.84 0.18 0.01
43_A 222_D 0.84 0.18 0.01
95_R 270_K 0.84 0.18 0.01
24_G 238_I 0.83 0.18 0.01
66_A 132_K 0.83 0.18 0.01
31_K 197_A 0.82 0.17 0.01
76_M 256_G 0.82 0.17 0.01
63_H 102_Q 0.82 0.17 0.01
62_L 257_N 0.82 0.17 0.01
62_L 177_A 0.82 0.17 0.01
74_S 180_I 0.82 0.17 0.01
76_M 265_R 0.82 0.17 0.01
75_S 167_E 0.82 0.17 0.01
82_V 94_S 0.81 0.17 0.01
58_Q 72_T 0.81 0.17 0.01
82_V 85_L 0.81 0.17 0.01
88_S 155_L 0.81 0.17 0.01
87_I 166_I 0.81 0.17 0.01
98_I 80_S 0.81 0.17 0.01
51_M 219_N 0.81 0.17 0.01
35_N 143_D 0.81 0.17 0.01
30_A 91_E 0.81 0.17 0.01
79_M 257_N 0.81 0.17 0.01
53_D 114_L 0.81 0.17 0.01
58_Q 250_V 0.80 0.17 0.01
85_K 92_M 0.80 0.17 0.01
94_T 137_F 0.80 0.16 0.01
86_A 189_L 0.80 0.16 0.01
67_I 254_D 0.80 0.16 0.01
63_H 226_L 0.80 0.16 0.01
61_D 256_G 0.80 0.16 0.01
75_S 237_K 0.80 0.16 0.01
62_L 217_K 0.80 0.16 0.01
54_I 217_K 0.79 0.16 0.01
89_A 125_F 0.79 0.16 0.01
64_Q 205_I 0.79 0.16 0.01
87_I 202_K 0.79 0.16 0.01
77_K 235_H 0.79 0.16 0.01
82_V 180_I 0.79 0.16 0.01
60_K 257_N 0.78 0.15 0.01
70_T 90_D 0.78 0.15 0.01
55_A 184_V 0.78 0.15 0.01
49_A 205_I 0.78 0.15 0.01
37_I 115_N 0.78 0.15 0.01
47_G 127_K 0.78 0.15 0.01
11_N 198_Y 0.78 0.15 0.01
51_M 162_L 0.78 0.15 0.01
21_N 102_Q 0.77 0.15 0.01
64_Q 153_A 0.77 0.15 0.01
71_K 202_K 0.77 0.15 0.01
82_V 193_S 0.77 0.15 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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