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OPENSEQ.org
PxPl
Genes: A B A+B
Length: 327 89 414
Sequences: 4903 91 67
Seq/Len: 14.99 1.02 0.16
MirrorTree (Pazo et al. 2001) 0.19
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.00 0.00
2 0.04 0.00 0.00
5 0.06 0.00 0.00
10 0.07 0.00 0.00
20 0.08 0.00 0.00
100 0.12 0.00 0.01
∞ 0.19 0.03 0.16
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
308_S 16_Y 1.96 0.52 0.01
292_V 56_E 1.64 0.35 0.00
103_I 58_R 1.64 0.34 0.00
255_L 25_K 1.53 0.29 0.00
256_L 76_E 1.52 0.28 0.00
317_I 39_L 1.44 0.25 0.00
169_P 50_E 1.39 0.23 0.00
248_H 18_I 1.28 0.19 0.00
255_L 70_R 1.28 0.19 0.00
66_V 50_E 1.27 0.18 0.00
31_Y 16_Y 1.26 0.18 0.00
270_A 58_R 1.26 0.18 0.00
137_S 84_F 1.24 0.17 0.00
264_D 76_E 1.22 0.17 0.00
228_S 7_L 1.22 0.17 0.00
307_C 68_L 1.21 0.16 0.00
69_A 16_Y 1.18 0.16 0.00
285_I 60_L 1.17 0.15 0.00
19_Y 5_N 1.17 0.15 0.00
274_S 27_L 1.16 0.15 0.00
104_R 72_A 1.15 0.15 0.00
265_Q 23_D 1.15 0.15 0.00
221_L 85_K 1.14 0.14 0.00
124_F 72_A 1.12 0.14 0.00
267_K 77_Y 1.12 0.14 0.00
235_I 77_Y 1.11 0.14 0.00
212_Y 36_L 1.11 0.14 0.00
264_D 18_I 1.11 0.14 0.00
161_L 14_L 1.10 0.13 0.00
160_A 16_Y 1.10 0.13 0.00
5_H 3_S 1.08 0.13 0.00
179_Q 28_F 1.07 0.13 0.00
241_R 3_S 1.07 0.13 0.00
104_R 84_F 1.07 0.12 0.00
289_K 2_A 1.06 0.12 0.00
271_M 85_K 1.06 0.12 0.00
282_Q 46_G 1.06 0.12 0.00
154_Y 56_E 1.06 0.12 0.00
306_L 16_Y 1.06 0.12 0.00
322_R 40_V 1.06 0.12 0.00
214_Y 36_L 1.05 0.12 0.00
178_K 50_E 1.05 0.12 0.00
204_A 84_F 1.05 0.12 0.00
66_V 29_A 1.05 0.12 0.00
177_L 58_R 1.05 0.12 0.00
45_M 58_R 1.05 0.12 0.00
169_P 65_L 1.05 0.12 0.00
115_C 3_S 1.04 0.12 0.00
103_I 52_I 1.04 0.12 0.00
211_L 14_L 1.04 0.12 0.00
93_R 52_I 1.03 0.12 0.00
326_L 56_E 1.03 0.12 0.00
195_A 39_L 1.03 0.12 0.00
266_T 72_A 1.02 0.11 0.00
245_I 52_I 1.01 0.11 0.00
305_L 79_Q 1.00 0.11 0.00
95_Q 52_I 1.00 0.11 0.00
20_N 17_Q 0.99 0.11 0.00
168_V 58_R 0.99 0.11 0.00
227_G 79_Q 0.99 0.11 0.00
198_I 51_P 0.99 0.11 0.00
185_V 60_L 0.99 0.11 0.00
249_S 12_F 0.99 0.11 0.00
84_R 76_E 0.98 0.10 0.00
94_K 16_Y 0.98 0.10 0.00
66_V 12_F 0.98 0.10 0.00
120_I 81_Q 0.97 0.10 0.00
260_C 62_D 0.97 0.10 0.00
254_A 61_V 0.97 0.10 0.00
31_Y 81_Q 0.97 0.10 0.00
270_A 44_A 0.97 0.10 0.00
288_V 24_S 0.96 0.10 0.00
28_S 28_F 0.96 0.10 0.00
254_A 18_I 0.95 0.10 0.00
65_G 69_R 0.95 0.10 0.00
178_K 41_A 0.95 0.10 0.00
64_D 85_K 0.94 0.10 0.00
319_L 77_Y 0.94 0.10 0.00
100_D 85_K 0.93 0.10 0.00
69_A 29_A 0.93 0.09 0.00
154_Y 23_D 0.92 0.09 0.00
22_I 51_P 0.92 0.09 0.00
285_I 53_G 0.92 0.09 0.00
93_R 85_K 0.91 0.09 0.00
106_H 7_L 0.91 0.09 0.00
80_G 17_Q 0.91 0.09 0.00
125_L 68_L 0.90 0.09 0.00
63_E 58_R 0.90 0.09 0.00
22_I 18_I 0.90 0.09 0.00
265_Q 7_L 0.90 0.09 0.00
292_V 55_N 0.90 0.09 0.00
113_Q 25_K 0.90 0.09 0.00
160_A 27_L 0.90 0.09 0.00
22_I 36_L 0.90 0.09 0.00
258_M 18_I 0.90 0.09 0.00
306_L 55_N 0.90 0.09 0.00
5_H 46_G 0.89 0.09 0.00
73_S 57_A 0.89 0.09 0.00
20_N 84_F 0.89 0.09 0.00
230_I 3_S 0.89 0.09 0.00
295_I 58_R 0.89 0.09 0.00
154_Y 2_A 0.89 0.09 0.00
246_I 22_G 0.89 0.09 0.00
246_I 81_Q 0.88 0.09 0.00
242_A 79_Q 0.88 0.09 0.00
285_I 59_M 0.88 0.09 0.00
180_K 58_R 0.88 0.09 0.00
211_L 5_N 0.88 0.08 0.00
247_I 84_F 0.87 0.08 0.00
20_N 2_A 0.87 0.08 0.00
110_L 50_E 0.87 0.08 0.00
70_Q 46_G 0.86 0.08 0.00
305_L 56_E 0.86 0.08 0.00
316_S 64_R 0.86 0.08 0.00
279_I 29_A 0.86 0.08 0.00
104_R 11_T 0.86 0.08 0.00
292_V 64_R 0.86 0.08 0.00
90_Q 61_V 0.86 0.08 0.00
70_Q 83_V 0.86 0.08 0.00
316_S 54_R 0.86 0.08 0.00
313_S 25_K 0.86 0.08 0.00
306_L 18_I 0.85 0.08 0.00
135_S 39_L 0.85 0.08 0.00
276_S 84_F 0.85 0.08 0.00
46_Q 81_Q 0.85 0.08 0.00
299_L 40_V 0.85 0.08 0.00
213_D 1_M 0.85 0.08 0.00
126_A 27_L 0.85 0.08 0.00
206_T 28_F 0.85 0.08 0.00
151_E 27_L 0.85 0.08 0.00
209_L 27_L 0.85 0.08 0.00
16_T 3_S 0.85 0.08 0.00
221_L 46_G 0.84 0.08 0.00
163_V 64_R 0.84 0.08 0.00
269_E 46_G 0.84 0.08 0.00
11_D 50_E 0.84 0.08 0.00
125_L 14_L 0.84 0.08 0.00
104_R 50_E 0.84 0.08 0.00
317_I 77_Y 0.84 0.08 0.00
157_L 77_Y 0.83 0.08 0.00
280_C 86_Q 0.83 0.08 0.00
14_A 64_R 0.83 0.08 0.00
95_Q 59_M 0.82 0.08 0.00
143_P 65_L 0.82 0.08 0.00
177_L 7_L 0.82 0.07 0.00
279_I 51_P 0.82 0.07 0.00
312_I 36_L 0.82 0.07 0.00
69_A 11_T 0.82 0.07 0.00
275_A 47_T 0.82 0.07 0.00
306_L 53_G 0.82 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)
ID Seq/Len Name Options I_Prob Status
2836 0.15 PxPl Δgene:(0, ∞) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
2835 0 PxPl Δgene:(0, ∞) A:(1E-20, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) Killed - Shared
2833 0.16 PxPl Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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