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OPENSEQ.org
N-B
Genes: A B A+B
Length: 314 807 1095
Sequences: 10396 1607 571
Seq/Len: 33.11 1.99 0.52
MirrorTree (Pazo et al. 2001) 0.12
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 0.08 0.00 0.00
2 0.09 0.00 0.00
5 0.10 0.01 0.00
10 0.11 0.01 0.01
20 0.12 0.01 0.02
100 0.14 0.01 0.09
∞ 0.20 0.04 0.51
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
14_V 296_Y 1.24 0.38 0.00
262_T 365_L 1.19 0.34 0.00
102_F 240_I 1.18 0.34 0.00
79_N 169_F 1.09 0.27 0.00
263_L 471_L 1.08 0.27 0.00
90_A 612_Y 1.06 0.26 0.00
241_T 80_D 1.02 0.23 0.00
208_L 229_Y 1.02 0.23 0.00
143_V 792_S 1.01 0.23 0.00
236_A 256_I 1.00 0.22 0.00
247_L 584_D 1.00 0.22 0.00
244_A 780_L 0.98 0.21 0.00
139_D 625_L 0.97 0.20 0.00
208_L 537_T 0.97 0.20 0.00
255_S 89_K 0.95 0.19 0.00
259_L 672_I 0.94 0.19 0.00
16_I 97_I 0.93 0.19 0.00
70_A 226_L 0.93 0.19 0.00
297_A 88_V 0.92 0.18 0.00
177_T 511_L 0.92 0.18 0.00
17_I 25_I 0.92 0.18 0.00
266_T 785_A 0.91 0.18 0.00
237_A 341_V 0.91 0.18 0.00
145_I 341_V 0.89 0.17 0.00
236_A 108_E 0.88 0.16 0.00
195_G 513_S 0.88 0.16 0.00
14_V 614_K 0.87 0.16 0.00
256_G 64_R 0.86 0.15 0.00
97_Q 799_F 0.86 0.15 0.00
199_A 419_K 0.86 0.15 0.00
145_I 632_V 0.85 0.15 0.00
59_A 69_T 0.84 0.15 0.00
296_N 112_Q 0.84 0.15 0.00
216_Y 245_V 0.84 0.15 0.00
113_T 484_S 0.83 0.14 0.00
208_L 632_V 0.83 0.14 0.00
61_T 86_V 0.83 0.14 0.00
218_Y 414_V 0.83 0.14 0.00
250_R 515_L 0.83 0.14 0.00
14_V 414_V 0.82 0.14 0.00
146_T 374_G 0.82 0.14 0.00
204_A 260_L 0.81 0.14 0.00
26_S 592_Q 0.81 0.14 0.00
209_T 559_V 0.81 0.14 0.00
263_L 766_S 0.81 0.14 0.00
259_L 127_R 0.81 0.14 0.00
264_L 110_L 0.81 0.14 0.00
8_T 338_H 0.80 0.13 0.00
145_I 365_L 0.79 0.13 0.00
101_I 190_T 0.79 0.13 0.00
296_N 639_A 0.79 0.13 0.00
86_N 426_F 0.79 0.13 0.00
72_Y 341_V 0.78 0.13 0.00
22_A 769_V 0.78 0.13 0.00
241_T 757_Y 0.78 0.13 0.00
12_N 710_T 0.77 0.12 0.00
65_L 603_V 0.77 0.12 0.00
241_T 599_L 0.77 0.12 0.00
250_R 444_V 0.77 0.12 0.00
32_N 394_F 0.77 0.12 0.00
71_L 16_M 0.76 0.12 0.00
28_I 252_K 0.76 0.12 0.00
175_A 436_S 0.76 0.12 0.00
37_S 169_F 0.76 0.12 0.00
247_L 290_F 0.76 0.12 0.00
298_A 26_V 0.75 0.12 0.00
237_A 282_N 0.75 0.12 0.00
53_G 332_S 0.75 0.12 0.00
88_A 579_G 0.75 0.12 0.00
209_T 511_L 0.75 0.11 0.00
175_A 68_A 0.74 0.11 0.00
101_I 394_F 0.74 0.11 0.00
169_L 208_V 0.74 0.11 0.00
247_L 598_S 0.74 0.11 0.00
16_I 23_G 0.74 0.11 0.00
174_L 64_R 0.74 0.11 0.00
295_L 66_L 0.73 0.11 0.00
177_T 526_N 0.73 0.11 0.00
143_V 511_L 0.73 0.11 0.00
267_A 271_T 0.73 0.11 0.00
106_Y 622_Y 0.73 0.11 0.00
61_T 286_K 0.73 0.11 0.00
132_L 528_G 0.73 0.11 0.00
237_A 194_L 0.73 0.11 0.00
244_A 710_T 0.73 0.11 0.00
247_L 418_V 0.73 0.11 0.00
90_A 622_Y 0.73 0.11 0.00
177_T 320_P 0.73 0.11 0.00
145_I 427_N 0.73 0.11 0.00
197_F 265_R 0.72 0.11 0.00
68_D 559_V 0.72 0.11 0.00
37_S 189_S 0.72 0.11 0.00
179_I 469_V 0.72 0.11 0.00
208_L 337_L 0.72 0.11 0.00
143_V 193_L 0.72 0.11 0.00
141_L 265_R 0.72 0.11 0.00
259_L 110_L 0.72 0.11 0.00
269_Y 785_A 0.72 0.10 0.00
41_S 49_H 0.72 0.10 0.00
141_L 152_K 0.71 0.10 0.00
247_L 735_A 0.71 0.10 0.00
21_L 599_L 0.71 0.10 0.00
149_N 560_T 0.71 0.10 0.00
13_K 378_N 0.71 0.10 0.00
241_T 327_E 0.70 0.10 0.00
237_A 478_F 0.70 0.10 0.00
135_V 803_I 0.70 0.10 0.00
14_V 26_V 0.70 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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