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OPENSEQ.org
3pnl_ab
Genes: A B A+B
Length: 356 211 530
Sequences: 1710 2044 850
Seq/Len: 4.8 9.69 1.6
MirrorTree (Pazo et al. 2001) 0.71
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 0.01 0.02 1.44
2 0.07 0.05 1.47
5 0.09 0.05 1.50
10 0.10 0.05 1.50
20 0.10 0.05 1.50
100 0.11 0.06 1.51
∞ 0.14 0.09 1.52
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
119_L 90_I 1.43 0.84 0.11
122_D 90_I 1.32 0.77 0.08
118_E 91_R 1.15 0.62 0.05
114_E 121_R 1.12 0.58 0.04
79_T 80_A 1.03 0.49 0.03
201_K 29_G 1.01 0.47 0.03
83_P 39_H 0.99 0.45 0.03
107_T 182_Y 0.99 0.45 0.03
10_D 140_E 0.94 0.40 0.02
211_M 43_M 0.94 0.40 0.02
126_K 165_S 0.94 0.40 0.02
203_S 32_R 0.93 0.39 0.02
79_T 73_L 0.92 0.38 0.02
118_E 121_R 0.92 0.38 0.02
79_T 34_I 0.91 0.37 0.02
151_A 37_A 0.91 0.37 0.02
76_E 73_L 0.90 0.35 0.02
114_E 123_K 0.89 0.34 0.02
97_E 118_V 0.88 0.34 0.02
137_A 193_P 0.86 0.32 0.02
122_D 94_Q 0.85 0.31 0.02
296_V 200_F 0.85 0.31 0.02
72_A 81_S 0.84 0.30 0.02
83_P 197_S 0.83 0.30 0.02
84_D 75_S 0.82 0.28 0.01
83_P 131_M 0.81 0.28 0.01
111_L 61_D 0.80 0.27 0.01
57_E 79_G 0.80 0.26 0.01
34_Y 13_L 0.79 0.26 0.01
79_T 45_R 0.79 0.26 0.01
60_H 182_Y 0.78 0.25 0.01
203_S 135_W 0.78 0.25 0.01
79_T 77_V 0.78 0.25 0.01
70_S 163_A 0.77 0.25 0.01
71_G 92_A 0.77 0.24 0.01
235_V 207_L 0.76 0.23 0.01
79_T 42_N 0.74 0.22 0.01
114_E 80_A 0.74 0.22 0.01
57_E 39_H 0.74 0.22 0.01
60_H 81_S 0.73 0.22 0.01
57_E 78_G 0.73 0.22 0.01
104_K 81_S 0.73 0.22 0.01
104_K 182_Y 0.73 0.22 0.01
146_G 182_Y 0.73 0.21 0.01
239_F 29_G 0.73 0.21 0.01
291_S 39_H 0.72 0.21 0.01
208_D 185_E 0.72 0.21 0.01
88_E 125_E 0.72 0.20 0.01
76_E 45_R 0.71 0.20 0.01
63_Y 81_S 0.71 0.20 0.01
291_S 83_P 0.71 0.20 0.01
100_L 9_I 0.71 0.20 0.01
73_C 37_A 0.71 0.20 0.01
119_L 75_S 0.70 0.20 0.01
111_L 142_L 0.70 0.20 0.01
330_I 49_K 0.70 0.19 0.01
351_A 79_G 0.69 0.19 0.01
57_E 83_P 0.69 0.19 0.01
153_T 182_Y 0.69 0.19 0.01
239_F 103_T 0.69 0.18 0.01
228_F 9_I 0.69 0.18 0.01
79_T 198_V 0.69 0.18 0.01
104_K 42_N 0.69 0.18 0.01
21_K 18_D 0.68 0.18 0.01
221_P 87_T 0.68 0.18 0.01
350_P 107_L 0.68 0.18 0.01
146_G 181_S 0.68 0.18 0.01
157_E 42_N 0.68 0.18 0.01
22_A 93_A 0.68 0.18 0.01
348_H 147_E 0.68 0.18 0.01
104_K 177_K 0.68 0.18 0.01
199_A 41_L 0.68 0.18 0.01
320_C 71_M 0.67 0.18 0.01
49_L 72_T 0.67 0.18 0.01
113_F 122_G 0.67 0.17 0.01
154_V 13_L 0.67 0.17 0.01
230_S 187_S 0.67 0.17 0.01
186_S 33_E 0.67 0.17 0.01
124_G 94_Q 0.66 0.17 0.01
308_G 161_S 0.66 0.17 0.01
111_L 32_R 0.66 0.17 0.01
153_T 79_G 0.66 0.17 0.01
57_E 81_S 0.65 0.17 0.01
48_L 43_M 0.65 0.17 0.01
91_M 154_V 0.65 0.16 0.01
145_A 28_T 0.65 0.16 0.01
7_D 109_Q 0.65 0.16 0.01
79_T 197_S 0.65 0.16 0.01
153_T 81_S 0.65 0.16 0.01
50_S 180_A 0.65 0.16 0.01
348_H 207_L 0.65 0.16 0.01
274_S 101_S 0.65 0.16 0.01
71_G 20_F 0.65 0.16 0.01
137_A 73_L 0.64 0.16 0.01
175_E 112_R 0.64 0.16 0.01
71_G 63_G 0.64 0.16 0.01
242_L 206_A 0.64 0.16 0.01
323_L 181_S 0.64 0.16 0.01
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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