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OPENSEQ.org
PopN - PscB (A, 40-270) (B, 5-125)
Genes: A B A+B
Length: 231 121 348
Sequences: 200 741 151
Seq/Len: 0.87 6.12 0.43
MirrorTree (Pazo et al. 2001) 0.50
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 0.00 0.02 0.10
2 0.00 0.05 0.14
5 0.00 0.09 0.18
10 0.00 0.12 0.21
20 0.00 0.13 0.34
100 0.01 0.17 0.38
∞ 0.07 0.21 0.43
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
72_S 92_L 1.66 0.63 0.00
153_L 39_L 1.46 0.49 0.00
87_I 78_I 1.34 0.40 0.00
76_L 5_A 1.33 0.40 0.00
166_G 88_L 1.31 0.38 0.00
217_M 56_Q 1.25 0.34 0.00
194_L 107_A 1.16 0.28 0.00
123_D 106_L 1.16 0.28 0.00
195_S 47_H 1.16 0.28 0.00
88_S 9_G 1.16 0.28 0.00
129_I 78_I 1.15 0.27 0.00
123_D 85_R 1.14 0.27 0.00
62_I 45_L 1.11 0.25 0.00
177_R 86_L 1.09 0.24 0.00
170_A 72_R 1.09 0.24 0.00
223_L 1_L 1.08 0.24 0.00
146_G 113_L 1.08 0.23 0.00
58_L 26_D 1.03 0.21 0.00
195_S 27_G 1.02 0.20 0.00
166_G 3_G 1.02 0.20 0.00
151_Q 32_L 1.01 0.20 0.00
122_A 47_H 0.99 0.19 0.00
198_L 65_S 0.99 0.19 0.00
80_L 9_G 0.98 0.19 0.00
195_S 66_R 0.98 0.19 0.00
178_F 81_D 0.98 0.18 0.00
154_R 112_L 0.97 0.18 0.00
201_Q 39_L 0.97 0.18 0.00
78_A 25_I 0.97 0.18 0.00
206_D 39_L 0.96 0.18 0.00
171_W 120_L 0.96 0.18 0.00
210_L 88_L 0.96 0.18 0.00
86_E 45_L 0.96 0.18 0.00
47_K 26_D 0.95 0.17 0.00
220_L 102_L 0.95 0.17 0.00
176_A 102_L 0.95 0.17 0.00
174_I 116_L 0.94 0.17 0.00
200_S 104_R 0.94 0.17 0.00
160_A 121_E 0.93 0.16 0.00
208_V 69_S 0.92 0.16 0.00
28_L 32_L 0.92 0.16 0.00
87_I 10_Q 0.91 0.16 0.00
128_E 20_S 0.91 0.16 0.00
153_L 36_G 0.91 0.16 0.00
183_L 64_L 0.90 0.15 0.00
187_V 8_L 0.90 0.15 0.00
131_L 60_L 0.89 0.15 0.00
118_L 30_V 0.89 0.15 0.00
189_F 73_R 0.89 0.15 0.00
40_A 116_L 0.89 0.15 0.00
153_L 106_L 0.89 0.15 0.00
200_S 85_R 0.89 0.15 0.00
102_A 37_D 0.88 0.15 0.00
107_A 19_G 0.88 0.15 0.00
104_R 41_L 0.88 0.15 0.00
75_Q 79_V 0.88 0.14 0.00
23_L 88_L 0.87 0.14 0.00
153_L 108_A 0.87 0.14 0.00
26_R 60_L 0.87 0.14 0.00
51_D 45_L 0.87 0.14 0.00
175_Q 79_V 0.87 0.14 0.00
163_D 30_V 0.87 0.14 0.00
199_D 106_L 0.86 0.14 0.00
118_L 1_L 0.86 0.14 0.00
19_A 72_R 0.86 0.14 0.00
22_S 92_L 0.86 0.14 0.00
155_D 27_G 0.86 0.14 0.00
97_A 16_D 0.85 0.14 0.00
195_S 106_L 0.85 0.14 0.00
37_E 64_L 0.85 0.14 0.00
155_D 106_L 0.85 0.14 0.00
228_E 21_Y 0.84 0.13 0.00
125_Q 6_T 0.84 0.13 0.00
206_D 40_L 0.84 0.13 0.00
118_L 101_R 0.83 0.13 0.00
209_K 104_R 0.83 0.13 0.00
168_S 106_L 0.83 0.13 0.00
72_S 15_A 0.83 0.13 0.00
195_S 49_P 0.83 0.13 0.00
198_L 29_S 0.82 0.13 0.00
118_L 102_L 0.82 0.13 0.00
148_G 51_D 0.82 0.13 0.00
179_A 40_L 0.82 0.12 0.00
82_G 45_L 0.82 0.12 0.00
174_I 57_Q 0.82 0.12 0.00
71_S 38_D 0.81 0.12 0.00
185_R 83_D 0.81 0.12 0.00
27_R 48_A 0.81 0.12 0.00
168_S 76_Q 0.81 0.12 0.00
80_L 32_L 0.81 0.12 0.00
126_G 93_G 0.81 0.12 0.00
86_E 64_L 0.81 0.12 0.00
88_S 98_D 0.81 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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