May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
PIGA_DPM2
Genes: A B A+B
Length: 420 84 469
Sequences: 31707 397 102
Seq/Len: 75.49 4.73 0.22
MirrorTree (Pazo et al. 2001) 0.15
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 0.11 0.01 0.00
2 0.15 0.01 0.00
5 0.20 0.01 0.00
10 0.24 0.01 0.00
20 0.25 0.01 0.01
100 0.29 0.01 0.05
∞ 0.33 0.02 0.20
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
149_T 17_S 1.30 0.24 0.00
260_I 49_Y 1.21 0.20 0.00
383_T 38_H 1.18 0.19 0.00
283_R 69_I 1.17 0.19 0.00
340_L 53_I 1.12 0.17 0.00
364_F 49_Y 1.11 0.17 0.00
375_E 26_A 1.09 0.16 0.00
332_R 71_Y 1.08 0.15 0.00
415_R 50_A 1.07 0.15 0.00
261_I 29_I 1.07 0.15 0.00
225_S 49_Y 1.06 0.15 0.00
92_L 46_P 1.05 0.14 0.00
104_T 45_L 1.04 0.14 0.00
226_I 59_L 1.03 0.14 0.00
263_G 27_W 1.03 0.14 0.00
263_G 32_P 1.03 0.14 0.00
263_G 54_P 1.03 0.14 0.00
210_V 40_I 1.02 0.14 0.00
231_V 16_V 1.02 0.14 0.00
213_T 51_V 1.01 0.14 0.00
332_R 72_V 1.01 0.13 0.00
233_R 27_W 1.01 0.13 0.00
233_R 32_P 1.01 0.13 0.00
233_R 54_P 1.01 0.13 0.00
302_G 50_A 1.01 0.13 0.00
213_T 47_R 1.00 0.13 0.00
343_N 57_A 1.00 0.13 0.00
238_K 27_W 1.00 0.13 0.00
238_K 32_P 1.00 0.13 0.00
238_K 54_P 1.00 0.13 0.00
165_V 49_Y 1.00 0.13 0.00
301_Q 69_I 0.98 0.12 0.00
34_N 57_A 0.97 0.12 0.00
319_V 62_L 0.96 0.12 0.00
272_E 62_L 0.96 0.12 0.00
342_E 15_A 0.95 0.12 0.00
353_K 55_L 0.95 0.12 0.00
312_E 27_W 0.95 0.12 0.00
312_E 32_P 0.95 0.12 0.00
312_E 54_P 0.95 0.12 0.00
250_L 42_K 0.95 0.12 0.00
359_L 25_T 0.94 0.11 0.00
382_K 53_I 0.93 0.11 0.00
341_P 16_V 0.93 0.11 0.00
48_G 27_W 0.92 0.11 0.00
48_G 32_P 0.92 0.11 0.00
48_G 54_P 0.92 0.11 0.00
325_G 45_L 0.91 0.11 0.00
68_I 51_V 0.91 0.11 0.00
60_L 27_W 0.90 0.10 0.00
60_L 32_P 0.90 0.10 0.00
60_L 54_P 0.90 0.10 0.00
319_V 15_A 0.90 0.10 0.00
139_L 19_I 0.90 0.10 0.00
260_I 78_R 0.89 0.10 0.00
181_I 15_A 0.89 0.10 0.00
65_H 51_V 0.88 0.10 0.00
273_E 56_A 0.88 0.10 0.00
92_L 63_L 0.88 0.10 0.00
117_F 45_L 0.87 0.10 0.00
257_L 53_I 0.87 0.10 0.00
398_Y 61_L 0.87 0.10 0.00
110_L 30_L 0.87 0.10 0.00
393_R 26_A 0.86 0.10 0.00
326_L 15_A 0.86 0.10 0.00
113_L 50_A 0.86 0.10 0.00
300_V 64_F 0.86 0.10 0.00
319_V 50_A 0.85 0.09 0.00
382_K 51_V 0.84 0.09 0.00
253_K 71_Y 0.84 0.09 0.00
140_F 35_D 0.84 0.09 0.00
154_H 71_Y 0.84 0.09 0.00
317_A 43_Y 0.84 0.09 0.00
249_E 53_I 0.84 0.09 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)
Page generated in 0.0927 seconds.