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OPENSEQ.org
2OT3_l_u_Apdb 2OT3_r_u_Apdb
Genes: A B A+B
Length: 165 245 403
Sequences: 11607 581 59
Seq/Len: 70.35 2.37 0.15
MirrorTree (Pazo et al. 2001) 0.19
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 0.01
2 0.06 0.04 0.02
5 0.08 0.04 0.05
10 0.10 0.04 0.08
20 0.13 0.04 0.14
100 0.23 0.04 0.40
∞ 0.28 0.06 0.74
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
101_L 181_Y 1.64 0.33 0.00
153_I 181_Y 1.49 0.26 0.00
87_D 111_V 1.37 0.21 0.00
101_L 136_I 1.32 0.20 0.00
131_A 136_I 1.23 0.16 0.00
20_V 111_V 1.21 0.16 0.00
18_S 181_Y 1.19 0.15 0.00
81_L 23_I 1.17 0.15 0.00
58_D 173_D 1.13 0.14 0.00
120_L 158_I 1.13 0.14 0.00
129_Q 181_Y 1.12 0.13 0.00
26_N 99_L 1.11 0.13 0.00
38_A 142_R 1.10 0.13 0.00
119_D 144_P 1.09 0.12 0.00
95_K 181_Y 1.08 0.12 0.00
48_G 136_I 1.08 0.12 0.00
131_A 135_D 1.07 0.12 0.00
19_L 198_I 1.07 0.12 0.00
46_N 40_S 1.06 0.12 0.00
48_G 141_K 1.05 0.12 0.00
20_V 104_R 1.04 0.11 0.00
112_C 241_D 1.02 0.11 0.00
160_L 197_Y 1.01 0.11 0.00
87_D 158_I 1.01 0.11 0.00
135_A 136_I 1.01 0.11 0.00
94_V 158_I 1.01 0.11 0.00
148_K 75_I 1.01 0.11 0.00
78_G 70_E 1.00 0.11 0.00
115_G 174_D 1.00 0.11 0.00
116_N 216_T 1.00 0.10 0.00
45_L 139_D 0.99 0.10 0.00
117_K 181_Y 0.99 0.10 0.00
147_A 172_A 0.99 0.10 0.00
120_L 225_I 0.97 0.10 0.00
14_V 184_L 0.97 0.10 0.00
16_K 98_D 0.97 0.10 0.00
61_G 173_D 0.96 0.10 0.00
155_E 244_S 0.96 0.10 0.00
120_L 185_K 0.95 0.10 0.00
63_E 43_E 0.95 0.10 0.00
102_R 136_I 0.94 0.09 0.00
56_I 216_T 0.94 0.09 0.00
15_G 191_L 0.94 0.09 0.00
50_K 197_Y 0.94 0.09 0.00
80_I 238_E 0.93 0.09 0.00
10_G 191_L 0.93 0.09 0.00
18_S 166_K 0.93 0.09 0.00
5_K 59_Q 0.92 0.09 0.00
101_L 170_A 0.92 0.09 0.00
10_G 98_D 0.92 0.09 0.00
23_Y 41_I 0.92 0.09 0.00
50_K 216_T 0.92 0.09 0.00
127_S 146_D 0.91 0.09 0.00
52_V 118_P 0.90 0.09 0.00
50_K 194_N 0.90 0.09 0.00
131_A 160_N 0.90 0.09 0.00
131_A 238_E 0.90 0.09 0.00
19_L 158_I 0.90 0.09 0.00
16_K 191_L 0.90 0.09 0.00
147_A 184_L 0.89 0.09 0.00
158_L 148_L 0.89 0.08 0.00
18_S 71_K 0.88 0.08 0.00
16_K 172_A 0.88 0.08 0.00
151_K 155_S 0.88 0.08 0.00
20_V 73_D 0.88 0.08 0.00
80_I 129_V 0.87 0.08 0.00
58_D 172_A 0.87 0.08 0.00
26_N 40_S 0.87 0.08 0.00
63_E 222_V 0.87 0.08 0.00
75_D 198_I 0.86 0.08 0.00
147_A 216_T 0.86 0.08 0.00
131_A 164_I 0.86 0.08 0.00
56_I 184_L 0.86 0.08 0.00
4_F 198_I 0.85 0.08 0.00
15_G 98_D 0.85 0.08 0.00
35_T 173_D 0.85 0.08 0.00
5_K 187_N 0.85 0.08 0.00
147_A 142_R 0.85 0.08 0.00
94_V 36_K 0.85 0.08 0.00
61_G 94_D 0.85 0.08 0.00
86_T 132_A 0.84 0.08 0.00
68_L 175_F 0.84 0.08 0.00
94_V 185_K 0.84 0.08 0.00
153_I 207_L 0.84 0.08 0.00
85_I 67_E 0.84 0.08 0.00
94_V 63_K 0.84 0.08 0.00
99_K 151_I 0.84 0.08 0.00
9_L 22_E 0.84 0.08 0.00
91_F 184_L 0.83 0.07 0.00
79_A 125_E 0.83 0.07 0.00
60_A 177_P 0.83 0.07 0.00
52_V 162_I 0.83 0.07 0.00
113_I 101_I 0.83 0.07 0.00
118_I 211_D 0.82 0.07 0.00
148_K 151_I 0.82 0.07 0.00
20_V 17_H 0.82 0.07 0.00
58_D 210_E 0.82 0.07 0.00
17_T 98_D 0.82 0.07 0.00
148_K 97_K 0.82 0.07 0.00
115_G 173_D 0.82 0.07 0.00
86_T 216_T 0.82 0.07 0.00
10_G 172_A 0.81 0.07 0.00
113_I 136_I 0.81 0.07 0.00
117_K 172_A 0.81 0.07 0.00
140_A 229_D 0.81 0.07 0.00
92_Q 46_E 0.81 0.07 0.00
117_K 177_P 0.81 0.07 0.00
148_K 169_P 0.81 0.07 0.00
130_E 226_E 0.81 0.07 0.00
9_L 164_I 0.81 0.07 0.00
58_D 177_P 0.81 0.07 0.00
6_V 141_K 0.81 0.07 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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