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OPENSEQ.org
1r8s_A_B
Genes: A B A+B
Length: 180 195 355
Sequences: 12105 1218 157
Seq/Len: 67.25 6.25 0.44
MirrorTree (Pazo et al. 2001) 0.05
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 0.05 0.04 0.03
2 0.06 0.04 0.05
5 0.07 0.05 0.11
10 0.09 0.05 0.22
20 0.12 0.05 0.42
100 0.22 0.07 1.14
∞ 0.28 0.10 1.88
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
30_T 75_V 1.39 0.44 0.00
83_N 156_K 1.36 0.42 0.00
157_T 167_R 1.25 0.34 0.00
91_V 181_R 1.24 0.33 0.00
22_V 83_H 1.23 0.33 0.00
159_A 87_D 1.20 0.31 0.00
141_K 64_Y 1.18 0.30 0.00
99_V 64_Y 1.16 0.28 0.00
60_I 163_V 1.14 0.27 0.00
94_N 189_N 1.05 0.23 0.00
131_N 79_F 1.05 0.22 0.00
123_F 130_S 1.03 0.21 0.00
139_T 184_Y 0.96 0.18 0.00
138_I 189_N 0.95 0.17 0.00
62_F 107_A 0.95 0.17 0.00
76_L 30_I 0.94 0.17 0.00
22_V 78_A 0.93 0.17 0.00
30_T 146_T 0.91 0.16 0.00
122_V 83_H 0.91 0.16 0.00
30_T 15_M 0.89 0.15 0.00
176_L 148_L 0.89 0.15 0.00
174_N 176_P 0.89 0.15 0.00
44_T 151_P 0.88 0.15 0.00
124_A 121_Y 0.88 0.15 0.00
138_I 75_V 0.88 0.15 0.00
142_L 184_Y 0.87 0.15 0.00
118_A 194_I 0.87 0.14 0.00
81_F 184_Y 0.87 0.14 0.00
121_L 188_R 0.87 0.14 0.00
170_D 87_D 0.86 0.14 0.00
140_D 50_L 0.86 0.14 0.00
35_K 127_V 0.86 0.14 0.00
87_L 97_F 0.85 0.14 0.00
19_I 158_G 0.85 0.14 0.00
91_V 138_S 0.84 0.14 0.00
102_A 140_S 0.84 0.13 0.00
81_F 75_V 0.84 0.13 0.00
27_A 30_I 0.84 0.13 0.00
55_V 39_L 0.83 0.13 0.00
30_T 60_A 0.83 0.13 0.00
165_L 86_T 0.83 0.13 0.00
98_R 85_F 0.83 0.13 0.00
149_H 138_S 0.82 0.13 0.00
122_V 60_A 0.82 0.13 0.00
140_D 139_Y 0.81 0.12 0.00
19_I 46_I 0.80 0.12 0.00
20_L 90_L 0.80 0.12 0.00
56_E 114_M 0.80 0.12 0.00
89_F 114_M 0.79 0.12 0.00
121_L 84_E 0.79 0.12 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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