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OPENSEQ.org
1wbj
Genes: A B A+B
Length: 268 397 655
Sequences: 4521 12017 2756
Seq/Len: 16.87 30.27 4.21
MirrorTree (Pazo et al. 2001) 0.65
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 3.81
2 0.00 0.00 3.94
5 0.00 0.00 4.00
10 0.00 0.01 4.12
20 0.00 0.01 4.14
100 0.00 0.07 4.23
∞ 0.00 0.13 4.60
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
108_N 275_R 2.89 1.00 1.00
58_L 174_L 2.20 1.00 0.99
135_E 8_Y 2.18 1.00 0.99
103_A 278_I 1.92 1.00 0.98
107_F 283_K 1.66 0.99 0.96
79_A 291_D 1.54 0.98 0.93
77_T 291_D 1.42 0.97 0.89
78_P 291_D 1.40 0.96 0.89
107_F 278_I 1.33 0.95 0.85
65_Q 172_E 1.27 0.93 0.81
134_E 22_M 1.25 0.92 0.80
180_S 182_E 1.19 0.89 0.76
58_L 18_P 1.17 0.88 0.74
79_A 290_A 1.11 0.84 0.68
137_A 6_N 0.87 0.59 0.40
157_N 20_I 0.85 0.57 0.38
157_N 181_Y 0.82 0.53 0.34
54_F 294_I 0.74 0.41 0.25
159_D 23_P 0.73 0.40 0.24
58_L 197_Y 0.69 0.35 0.20
58_L 279_Y 0.69 0.34 0.19
227_G 83_G 0.68 0.34 0.19
177_L 20_I 0.67 0.32 0.18
40_L 284_A 0.66 0.32 0.17
58_L 170_C 0.65 0.30 0.16
180_S 20_I 0.64 0.30 0.16
163_L 23_P 0.64 0.29 0.15
134_E 26_N 0.64 0.29 0.15
215_S 339_L 0.62 0.27 0.14
174_T 157_I 0.62 0.27 0.14
180_S 123_S 0.62 0.27 0.14
83_E 43_A 0.61 0.26 0.13
65_Q 161_S 0.59 0.24 0.12
43_A 309_V 0.58 0.23 0.11
108_N 288_Q 0.58 0.23 0.11
185_A 179_G 0.58 0.23 0.11
173_Y 200_I 0.57 0.22 0.11
89_R 98_A 0.57 0.22 0.10
155_P 181_Y 0.57 0.22 0.10
129_A 18_P 0.57 0.22 0.10
12_N 213_K 0.56 0.21 0.10
138_P 283_K 0.56 0.21 0.10
59_A 85_A 0.56 0.21 0.10
215_S 340_C 0.55 0.20 0.10
107_F 282_M 0.55 0.20 0.10
33_S 60_T 0.55 0.20 0.09
198_E 330_D 0.54 0.19 0.09
108_N 18_P 0.54 0.19 0.09
177_L 258_G 0.54 0.19 0.09
68_N 258_G 0.53 0.19 0.09
135_E 191_A 0.53 0.19 0.09
131_V 59_L 0.53 0.19 0.08
241_I 122_A 0.53 0.18 0.08
154_C 151_L 0.52 0.18 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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