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OPENSEQ.org
etftrim
Genes: A B A+B
Length: 255 377 610
Sequences: 2620 12601 554
Seq/Len: 10.27 33.42 0.91
MirrorTree (Pazo et al. 2001) 0.52
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 0.01 0.02 0.22
2 0.01 0.02 0.66
5 0.01 0.03 0.75
10 0.01 0.04 0.82
20 0.01 0.05 0.88
100 0.03 0.10 1.24
∞ 0.08 0.21 2.46
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
120_V 337_L 1.36 0.63 0.00
85_R 307_L 1.32 0.60 0.00
53_K 25_V 1.31 0.59 0.00
63_A 366_E 1.25 0.54 0.00
119_L 213_K 1.21 0.51 0.00
62_I 213_K 1.16 0.45 0.00
203_K 114_I 1.16 0.45 0.00
71_C 44_L 1.15 0.44 0.00
71_C 186_E 1.14 0.44 0.00
89_V 308_E 1.14 0.44 0.00
80_A 310_G 1.13 0.43 0.00
68_P 175_I 1.13 0.43 0.00
208_V 327_S 1.10 0.40 0.00
50_V 156_E 1.09 0.39 0.00
101_P 338_L 1.08 0.39 0.00
55_K 57_V 1.06 0.36 0.00
114_K 44_L 1.05 0.36 0.00
171_E 177_K 1.03 0.35 0.00
42_C 322_E 1.02 0.34 0.00
69_A 33_A 1.02 0.34 0.00
14_I 193_A 0.99 0.31 0.00
6_V 168_I 0.99 0.31 0.00
173_L 112_V 0.99 0.31 0.00
153_V 56_L 0.97 0.30 0.00
68_P 197_I 0.95 0.28 0.00
143_D 137_M 0.95 0.28 0.00
203_K 186_E 0.94 0.28 0.00
78_A 135_S 0.94 0.28 0.00
138_T 337_L 0.94 0.27 0.00
68_P 186_E 0.94 0.27 0.00
192_Y 19_F 0.93 0.27 0.00
68_P 232_L 0.93 0.27 0.00
224_V 177_K 0.93 0.27 0.00
109_A 238_K 0.93 0.26 0.00
238_K 54_V 0.92 0.26 0.00
102_L 307_L 0.92 0.26 0.00
134_T 226_G 0.92 0.26 0.00
79_L 210_L 0.92 0.26 0.00
71_C 48_H 0.91 0.25 0.00
89_V 368_I 0.91 0.25 0.00
38_M 249_V 0.90 0.24 0.00
38_M 164_S 0.89 0.24 0.00
246_V 370_N 0.89 0.24 0.00
47_E 41_L 0.88 0.24 0.00
236_G 338_L 0.88 0.23 0.00
143_D 279_V 0.88 0.23 0.00
65_S 17_E 0.88 0.23 0.00
171_E 367_S 0.87 0.23 0.00
145_P 58_E 0.87 0.23 0.00
100_G 211_Y 0.87 0.23 0.00
172_T 275_L 0.86 0.22 0.00
46_V 242_P 0.86 0.22 0.00
152_Q 372_L 0.86 0.22 0.00
237_V 51_D 0.86 0.22 0.00
131_C 278_V 0.86 0.22 0.00
181_V 43_Q 0.85 0.21 0.00
111_L 305_P 0.85 0.21 0.00
112_A 197_I 0.84 0.21 0.00
173_L 207_A 0.84 0.21 0.00
92_P 45_A 0.84 0.21 0.00
71_C 54_V 0.84 0.21 0.00
157_G 304_R 0.83 0.20 0.00
65_S 56_L 0.83 0.20 0.00
139_A 168_I 0.83 0.20 0.00
14_I 75_P 0.83 0.20 0.00
220_S 212_K 0.83 0.20 0.00
173_L 115_L 0.83 0.20 0.00
153_V 143_A 0.82 0.20 0.00
89_V 26_V 0.82 0.20 0.00
26_R 152_Y 0.82 0.19 0.00
238_K 297_W 0.81 0.19 0.00
49_A 56_L 0.81 0.19 0.00
71_C 86_K 0.81 0.19 0.00
131_C 322_E 0.81 0.19 0.00
152_Q 97_T 0.81 0.19 0.00
227_V 55_C 0.80 0.19 0.00
63_A 33_A 0.80 0.19 0.00
85_R 200_E 0.80 0.19 0.00
63_A 278_V 0.80 0.18 0.00
52_L 106_E 0.80 0.18 0.00
135_G 275_L 0.80 0.18 0.00
65_S 120_M 0.80 0.18 0.00
196_P 355_H 0.80 0.18 0.00
176_K 128_V 0.79 0.18 0.00
226_S 108_Y 0.79 0.18 0.00
111_L 181_P 0.79 0.18 0.00
121_L 303_I 0.79 0.18 0.00
4_L 56_L 0.79 0.18 0.00
144_W 56_L 0.79 0.18 0.00
247_A 313_I 0.79 0.18 0.00
249_L 104_L 0.79 0.18 0.00
29_V 288_L 0.79 0.18 0.00
231_P 119_P 0.79 0.18 0.00
160_L 337_L 0.78 0.18 0.00
121_L 168_I 0.78 0.18 0.00
131_C 211_Y 0.78 0.18 0.00
224_V 166_K 0.78 0.18 0.00
173_L 345_F 0.78 0.18 0.00
6_V 60_A 0.78 0.18 0.00
165_E 252_P 0.78 0.17 0.00
237_V 184_T 0.78 0.17 0.00
33_G 363_L 0.78 0.17 0.00
7_L 345_F 0.78 0.17 0.00
160_L 178_D 0.78 0.17 0.00
203_K 274_A 0.77 0.17 0.00
119_L 365_A 0.77 0.17 0.00
122_L 199_A 0.77 0.17 0.00
10_V 263_L 0.77 0.17 0.00
42_C 93_N 0.77 0.17 0.00
157_G 51_D 0.77 0.17 0.00
238_K 175_I 0.77 0.17 0.00
29_V 336_G 0.77 0.17 0.00
129_D 341_C 0.77 0.17 0.00
9_A 82_F 0.77 0.17 0.00
53_K 310_G 0.77 0.17 0.00
74_T 93_N 0.77 0.17 0.00
110_K 128_V 0.76 0.17 0.00
38_M 308_E 0.76 0.17 0.00
157_G 303_I 0.76 0.17 0.00
179_A 344_G 0.76 0.17 0.00
79_L 56_L 0.76 0.17 0.00
166_I 56_L 0.76 0.17 0.00
101_P 51_D 0.76 0.16 0.00
97_E 211_Y 0.76 0.16 0.00
174_R 292_R 0.76 0.16 0.00
32_D 157_V 0.76 0.16 0.00
238_K 42_K 0.75 0.16 0.00
113_E 30_A 0.75 0.16 0.00
76_R 273_V 0.75 0.16 0.00
66_C 185_F 0.75 0.16 0.00
65_S 337_L 0.75 0.16 0.00
23_K 27_I 0.75 0.16 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)
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