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OPENSEQ.org
PIGA_DPM2 (A, 32-420)
Genes: A B A+B
Length: 389 84 455
Sequences: 36990 397 118
Seq/Len: 95.09 4.73 0.26
MirrorTree (Pazo et al. 2001) 0.12
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 0.12 0.01 0.00
2 0.17 0.01 0.00
5 0.23 0.01 0.00
10 0.27 0.01 0.00
20 0.28 0.01 0.01
100 0.32 0.01 0.06
∞ 0.36 0.02 0.25
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
242_E 56_A 1.25 0.24 0.00
232_G 54_P 1.20 0.22 0.00
333_F 49_Y 1.18 0.21 0.00
294_G 45_L 1.17 0.21 0.00
288_V 15_A 1.16 0.20 0.00
309_L 53_I 1.16 0.20 0.00
230_I 29_I 1.13 0.19 0.00
131_V 53_I 1.11 0.18 0.00
131_V 60_L 1.10 0.18 0.00
169_P 57_A 1.09 0.18 0.00
109_F 35_D 1.07 0.17 0.00
86_F 45_L 1.06 0.16 0.00
295_L 15_A 1.05 0.16 0.00
58_V 36_S 1.04 0.16 0.00
222_K 71_Y 1.04 0.16 0.00
159_E 61_L 1.04 0.16 0.00
232_G 27_W 1.03 0.15 0.00
232_G 32_P 1.03 0.15 0.00
229_I 46_P 1.02 0.15 0.00
82_L 50_A 1.02 0.15 0.00
194_S 49_Y 1.01 0.15 0.00
344_E 26_A 1.01 0.15 0.00
229_I 49_Y 1.01 0.15 0.00
119_V 19_I 1.00 0.14 0.00
202_R 27_W 1.00 0.14 0.00
202_R 32_P 1.00 0.14 0.00
252_R 69_I 0.99 0.14 0.00
246_R 45_L 0.99 0.14 0.00
352_T 38_H 0.98 0.14 0.00
118_T 17_S 0.98 0.14 0.00
208_G 70_S 0.97 0.14 0.00
207_K 27_W 0.97 0.13 0.00
207_K 32_P 0.97 0.13 0.00
202_R 54_P 0.96 0.13 0.00
270_Q 69_I 0.96 0.13 0.00
33_G 27_W 0.96 0.13 0.00
33_G 32_P 0.96 0.13 0.00
239_I 19_I 0.95 0.13 0.00
253_V 24_Y 0.95 0.13 0.00
351_K 51_V 0.94 0.13 0.00
226_L 53_I 0.94 0.13 0.00
29_L 27_W 0.94 0.13 0.00
29_L 32_P 0.94 0.13 0.00
288_V 62_L 0.94 0.12 0.00
311_E 15_A 0.94 0.12 0.00
197_I 29_I 0.94 0.12 0.00
195_I 59_L 0.93 0.12 0.00
150_I 45_L 0.93 0.12 0.00
277_T 20_I 0.93 0.12 0.00
61_L 46_P 0.92 0.12 0.00
39_V 61_L 0.91 0.12 0.00
224_P 71_Y 0.91 0.12 0.00
182_T 51_V 0.91 0.12 0.00
207_K 54_P 0.91 0.12 0.00
249_L 53_I 0.91 0.12 0.00
241_E 62_L 0.90 0.12 0.00
253_V 67_L 0.90 0.12 0.00
229_I 55_L 0.90 0.12 0.00
17_G 27_W 0.90 0.11 0.00
17_G 32_P 0.90 0.11 0.00
258_A 22_T 0.89 0.11 0.00
197_I 66_G 0.88 0.11 0.00
17_G 54_P 0.88 0.11 0.00
197_I 16_V 0.88 0.11 0.00
268_L 78_R 0.88 0.11 0.00
130_D 26_A 0.88 0.11 0.00
164_R 70_S 0.87 0.11 0.00
179_V 40_I 0.87 0.11 0.00
281_E 27_W 0.87 0.11 0.00
281_E 32_P 0.87 0.11 0.00
326_E 50_A 0.86 0.10 0.00
195_I 70_S 0.86 0.10 0.00
166_A 51_V 0.85 0.10 0.00
152_C 19_I 0.85 0.10 0.00
253_V 19_I 0.85 0.10 0.00
249_L 47_R 0.85 0.10 0.00
221_Q 18_L 0.85 0.10 0.00
185_T 55_L 0.84 0.10 0.00
61_L 63_L 0.84 0.10 0.00
197_I 53_I 0.83 0.10 0.00
339_T 65_V 0.83 0.10 0.00
322_K 39_V 0.82 0.10 0.00
64_K 49_Y 0.82 0.10 0.00
167_L 66_G 0.82 0.10 0.00
229_I 30_L 0.82 0.10 0.00
371_S 43_Y 0.82 0.10 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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