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OPENSEQ.org
trps
Genes: A B A+B
Length: 268 397 609
Sequences: 2736 5696 1903
Seq/Len: 10.21 14.35 3.12
MirrorTree (Pazo et al. 2001) 0.69
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 0.08 0.03 2.59
2 0.08 0.03 2.69
5 0.08 0.03 2.74
10 0.08 0.04 2.84
20 0.08 0.04 2.86
100 0.08 0.06 2.88
∞ 0.09 0.18 3.13
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
58_L 174_L 2.69 1.00 1.00
108_N 275_R 2.54 1.00 1.00
103_A 278_I 2.05 1.00 0.99
107_F 283_K 1.53 0.96 0.91
79_A 291_D 1.39 0.93 0.85
78_P 291_D 1.29 0.89 0.79
65_Q 172_E 1.28 0.89 0.78
77_T 291_D 1.23 0.86 0.74
107_F 278_I 1.15 0.81 0.67
180_A 182_E 0.99 0.64 0.48
58_L 197_Y 0.97 0.62 0.46
79_A 290_E 0.96 0.62 0.46
157_N 181_Y 0.88 0.51 0.36
33_S 60_T 0.85 0.48 0.32
54_F 294_I 0.82 0.44 0.29
95_I 183_T 0.81 0.43 0.28
258_F 258_G 0.81 0.43 0.28
255_L 126_L 0.75 0.36 0.22
156_P 197_Y 0.75 0.35 0.21
65_Q 175_R 0.75 0.35 0.21
116_A 368_K 0.75 0.35 0.21
238_V 174_L 0.75 0.35 0.21
43_A 314_A 0.74 0.35 0.21
107_F 282_M 0.74 0.34 0.20
162_L 90_Q 0.73 0.34 0.20
198_A 330_D 0.73 0.33 0.20
58_L 170_C 0.73 0.33 0.19
59_A 85_A 0.72 0.32 0.19
37_I 327_I 0.72 0.32 0.18
179_R 280_F 0.71 0.31 0.18
43_A 375_N 0.71 0.30 0.17
155_P 181_Y 0.70 0.30 0.17
51_G 148_R 0.69 0.29 0.17
138_P 283_K 0.69 0.29 0.16
100_L 175_R 0.69 0.29 0.16
129_A 282_M 0.68 0.28 0.15
180_A 179_G 0.67 0.27 0.15
215_S 340_C 0.67 0.27 0.15
174_T 157_I 0.67 0.27 0.14
131_V 59_L 0.67 0.27 0.14
67_A 317_N 0.66 0.26 0.14
185_A 179_G 0.66 0.26 0.14
180_A 123_S 0.66 0.26 0.14
154_C 340_C 0.66 0.25 0.14
19_F 197_Y 0.65 0.25 0.13
58_L 279_Y 0.65 0.25 0.13
33_S 150_R 0.65 0.25 0.13
158_A 91_V 0.65 0.25 0.13
131_V 294_I 0.65 0.25 0.13
127_L 60_T 0.65 0.25 0.13
50_L 171_N 0.65 0.25 0.13
81_C 88_T 0.65 0.25 0.13
157_N 178_S 0.64 0.24 0.13
77_T 323_D 0.64 0.24 0.13
51_G 279_Y 0.64 0.24 0.12
156_P 172_E 0.63 0.23 0.12
123_V 53_A 0.63 0.23 0.12
36_I 133_Y 0.63 0.23 0.12
223_A 258_G 0.63 0.23 0.12
40_L 346_I 0.63 0.23 0.12
54_F 192_A 0.63 0.23 0.12
100_L 197_Y 0.63 0.23 0.12
108_N 132_I 0.62 0.23 0.12
221_K 207_M 0.62 0.23 0.12
125_S 90_Q 0.62 0.22 0.11
40_L 284_A 0.62 0.22 0.11
89_R 98_A 0.62 0.22 0.11
62_P 243_D 0.61 0.21 0.11
54_F 210_E 0.61 0.21 0.10
79_A 200_I 0.61 0.21 0.10
227_G 121_L 0.61 0.21 0.10
131_V 244_F 0.60 0.21 0.10
238_V 372_L 0.60 0.21 0.10
231_A 243_D 0.60 0.20 0.10
236_A 223_L 0.59 0.20 0.10
151_I 74_Y 0.59 0.20 0.10
4_Y 174_L 0.59 0.20 0.10
20_V 180_S 0.59 0.20 0.10
227_G 83_G 0.59 0.20 0.10
180_A 181_Y 0.59 0.20 0.10
12_K 213_K 0.59 0.20 0.10
230_G 290_E 0.59 0.20 0.09
80_Q 291_D 0.59 0.19 0.09
54_F 388_H 0.59 0.19 0.09
51_G 286_M 0.58 0.19 0.09
238_V 312_Q 0.58 0.19 0.09
158_A 264_T 0.58 0.19 0.09
22_F 258_G 0.58 0.19 0.09
107_F 276_V 0.58 0.19 0.09
166_I 139_V 0.58 0.19 0.09
152_F 88_T 0.57 0.18 0.09
174_T 100_R 0.57 0.18 0.09
48_L 242_A 0.57 0.18 0.09
169_Y 258_G 0.57 0.18 0.08
108_N 213_K 0.57 0.18 0.08
230_G 258_G 0.57 0.18 0.08
212_F 255_V 0.56 0.18 0.08
215_S 355_L 0.56 0.18 0.08
147_N 127_G 0.56 0.18 0.08
71_A 174_L 0.56 0.18 0.08
70_R 321_R 0.56 0.17 0.08
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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