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OPENSEQ.org
13
Genes: A B A+B
Length: 252 266 484
Sequences: 2590 71907 269
Seq/Len: 10.28 270.33 0.56
MirrorTree (Pazo et al. 2001) 0.17
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 0.12 0.09 0.05
2 0.12 0.10 0.08
5 0.13 0.13 0.14
10 0.13 0.15 0.27
20 0.14 0.18 0.52
100 0.15 0.26 1.99
∞ 0.22 0.29 3.77
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
206_V 24_V 1.40 0.52 0.00
138_L 100_E 1.05 0.26 0.00
13_G 169_L 1.04 0.26 0.00
165_I 6_I 1.03 0.25 0.00
147_C 24_V 1.02 0.24 0.00
170_I 209_S 1.01 0.24 0.00
221_S 26_F 0.99 0.23 0.00
95_G 24_V 0.99 0.23 0.00
30_L 168_V 0.98 0.22 0.00
194_G 211_L 0.96 0.21 0.00
150_V 240_M 0.96 0.21 0.00
90_S 64_I 0.96 0.21 0.00
29_T 100_E 0.94 0.20 0.00
164_G 24_V 0.93 0.20 0.00
122_A 28_I 0.91 0.18 0.00
35_R 24_V 0.91 0.18 0.00
233_A 25_S 0.89 0.18 0.00
55_F 51_M 0.89 0.18 0.00
93_V 51_M 0.89 0.18 0.00
88_I 62_V 0.88 0.17 0.00
192_V 22_K 0.88 0.17 0.00
183_I 212_V 0.88 0.17 0.00
167_I 24_V 0.88 0.17 0.00
194_G 59_K 0.87 0.17 0.00
193_F 148_R 0.87 0.17 0.00
188_I 102_V 0.86 0.16 0.00
240_F 242_H 0.85 0.16 0.00
183_I 36_V 0.85 0.16 0.00
72_I 48_L 0.85 0.16 0.00
10_I 230_L 0.85 0.16 0.00
89_T 36_V 0.85 0.16 0.00
138_L 10_D 0.84 0.15 0.00
153_A 123_Q 0.84 0.15 0.00
224_V 100_E 0.84 0.15 0.00
188_I 191_R 0.84 0.15 0.00
70_R 169_L 0.84 0.15 0.00
138_L 35_G 0.83 0.15 0.00
8_V 186_V 0.82 0.15 0.00
124_P 213_V 0.82 0.15 0.00
206_V 25_S 0.82 0.15 0.00
180_P 243_E 0.82 0.15 0.00
164_G 242_H 0.81 0.14 0.00
230_I 94_D 0.81 0.14 0.00
153_A 42_T 0.81 0.14 0.00
192_V 45_S 0.81 0.14 0.00
236_V 220_I 0.81 0.14 0.00
80_F 246_T 0.80 0.14 0.00
189_K 173_E 0.80 0.14 0.00
196_I 194_H 0.80 0.14 0.00
126_D 230_L 0.80 0.14 0.00
142_F 126_A 0.79 0.14 0.00
200_I 98_V 0.79 0.14 0.00
31_Q 36_V 0.79 0.13 0.00
153_A 230_L 0.79 0.13 0.00
179_R 218_S 0.79 0.13 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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