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OPENSEQ.org
TagA_vs_TssA
Genes: A B A+B
Length: 455 532 938
Sequences: 154 386 127
Seq/Len: 0.34 0.73 0.14
MirrorTree (Pazo et al. 2001) 0.78
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 0.00 0.01
2 0.00 0.00 0.05
5 0.00 0.00 0.09
10 0.00 0.00 0.12
20 0.00 0.00 0.13
100 0.01 0.01 0.13
∞ 0.05 0.03 0.14
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
317_P 338_I 1.50 0.25 0.00
15_S 42_A 1.26 0.17 0.00
449_L 518_I 1.19 0.15 0.00
387_G 441_L 1.18 0.14 0.00
319_Y 291_Y 1.18 0.14 0.00
197_V 513_A 1.17 0.14 0.00
428_S 80_T 1.16 0.14 0.00
30_T 55_M 1.14 0.13 0.00
26_I 142_I 1.10 0.12 0.00
365_W 285_A 1.08 0.12 0.00
316_P 118_F 1.06 0.12 0.00
410_I 414_E 1.06 0.11 0.00
431_Q 87_V 1.06 0.11 0.00
76_L 235_V 1.05 0.11 0.00
12_D 62_L 1.05 0.11 0.00
247_L 397_D 1.04 0.11 0.00
264_P 396_G 1.03 0.11 0.00
359_E 521_A 1.03 0.11 0.00
81_A 168_E 1.02 0.11 0.00
84_V 431_S 1.02 0.11 0.00
254_P 499_S 1.02 0.11 0.00
210_Y 478_L 1.02 0.10 0.00
403_M 227_Q 1.02 0.10 0.00
71_T 270_A 1.01 0.10 0.00
252_A 161_A 1.00 0.10 0.00
53_N 317_D 1.00 0.10 0.00
83_I 61_K 1.00 0.10 0.00
410_I 369_L 0.99 0.10 0.00
331_L 171_F 0.99 0.10 0.00
58_Q 440_L 0.99 0.10 0.00
9_T 478_L 0.98 0.10 0.00
237_P 77_L 0.98 0.10 0.00
386_R 265_L 0.98 0.10 0.00
131_L 431_S 0.98 0.10 0.00
349_Q 421_S 0.97 0.10 0.00
87_T 500_D 0.97 0.10 0.00
376_A 417_E 0.97 0.10 0.00
311_R 118_F 0.97 0.10 0.00
84_V 510_H 0.97 0.10 0.00
193_D 338_I 0.97 0.10 0.00
42_V 201_V 0.96 0.10 0.00
365_W 292_L 0.96 0.09 0.00
186_P 155_A 0.96 0.09 0.00
70_T 521_A 0.95 0.09 0.00
56_E 119_G 0.95 0.09 0.00
111_N 148_L 0.95 0.09 0.00
242_V 82_T 0.95 0.09 0.00
14_R 62_L 0.94 0.09 0.00
332_R 118_F 0.94 0.09 0.00
28_K 433_R 0.94 0.09 0.00
76_L 454_L 0.93 0.09 0.00
195_P 510_H 0.93 0.09 0.00
66_A 415_G 0.93 0.09 0.00
159_P 259_H 0.93 0.09 0.00
163_V 172_T 0.93 0.09 0.00
195_P 380_G 0.93 0.09 0.00
23_R 469_L 0.93 0.09 0.00
59_T 425_A 0.92 0.09 0.00
135_E 493_K 0.92 0.09 0.00
382_L 360_G 0.92 0.09 0.00
108_G 167_A 0.92 0.09 0.00
197_V 168_E 0.92 0.09 0.00
251_V 468_R 0.92 0.09 0.00
197_V 510_H 0.92 0.09 0.00
69_H 167_A 0.91 0.09 0.00
63_Y 180_L 0.91 0.09 0.00
373_Q 324_Q 0.91 0.09 0.00
14_R 423_L 0.91 0.08 0.00
44_T 492_M 0.91 0.08 0.00
104_E 59_V 0.90 0.08 0.00
49_L 190_R 0.90 0.08 0.00
197_V 167_A 0.90 0.08 0.00
26_I 414_E 0.90 0.08 0.00
397_T 172_T 0.90 0.08 0.00
38_D 214_S 0.90 0.08 0.00
101_A 445_V 0.90 0.08 0.00
236_K 509_E 0.90 0.08 0.00
195_P 170_T 0.90 0.08 0.00
195_P 513_A 0.89 0.08 0.00
255_G 255_K 0.89 0.08 0.00
250_S 168_E 0.89 0.08 0.00
375_L 440_L 0.89 0.08 0.00
72_G 419_A 0.89 0.08 0.00
45_L 417_E 0.89 0.08 0.00
309_I 274_T 0.89 0.08 0.00
426_N 434_S 0.88 0.08 0.00
141_L 513_A 0.88 0.08 0.00
410_I 518_I 0.88 0.08 0.00
143_D 435_N 0.88 0.08 0.00
109_L 280_G 0.88 0.08 0.00
159_P 329_T 0.88 0.08 0.00
306_G 172_T 0.88 0.08 0.00
38_D 80_T 0.88 0.08 0.00
349_Q 493_K 0.88 0.08 0.00
321_L 55_M 0.88 0.08 0.00
180_S 387_P 0.88 0.08 0.00
365_W 282_D 0.88 0.08 0.00
316_P 398_N 0.88 0.08 0.00
289_S 262_L 0.87 0.08 0.00
22_L 186_A 0.87 0.08 0.00
153_S 435_N 0.87 0.08 0.00
397_T 453_D 0.87 0.08 0.00
370_T 421_S 0.87 0.08 0.00
47_L 417_E 0.87 0.08 0.00
379_L 403_L 0.87 0.08 0.00
81_A 132_A 0.87 0.08 0.00
395_L 440_L 0.86 0.08 0.00
112_H 450_G 0.86 0.08 0.00
385_Q 306_M 0.86 0.08 0.00
260_T 391_I 0.86 0.08 0.00
260_T 140_A 0.86 0.08 0.00
72_G 352_L 0.86 0.08 0.00
34_R 406_E 0.86 0.08 0.00
22_L 441_L 0.86 0.08 0.00
69_H 120_E 0.85 0.08 0.00
368_G 282_D 0.85 0.08 0.00
48_R 488_K 0.85 0.08 0.00
449_L 167_A 0.85 0.08 0.00
188_Q 464_E 0.85 0.08 0.00
157_A 509_E 0.85 0.07 0.00
311_R 521_A 0.85 0.07 0.00
276_P 273_R 0.84 0.07 0.00
209_V 469_L 0.84 0.07 0.00
308_Q 469_L 0.84 0.07 0.00
254_P 336_A 0.84 0.07 0.00
299_S 509_E 0.84 0.07 0.00
7_L 237_A 0.84 0.07 0.00
444_S 42_A 0.84 0.07 0.00
446_Y 440_L 0.83 0.07 0.00
137_F 277_A 0.83 0.07 0.00
370_T 142_I 0.83 0.07 0.00
404_Q 284_R 0.83 0.07 0.00
188_Q 394_A 0.83 0.07 0.00
248_A 219_A 0.83 0.07 0.00
18_D 316_L 0.83 0.07 0.00
21_A 332_E 0.83 0.07 0.00
445_R 471_L 0.83 0.07 0.00
197_V 308_A 0.83 0.07 0.00
82_L 88_A 0.83 0.07 0.00
386_R 302_Q 0.83 0.07 0.00
196_D 380_G 0.83 0.07 0.00
45_L 299_L 0.83 0.07 0.00
195_P 384_A 0.83 0.07 0.00
245_A 435_N 0.83 0.07 0.00
424_N 185_Q 0.82 0.07 0.00
242_V 155_A 0.82 0.07 0.00
251_V 120_E 0.82 0.07 0.00
195_P 332_E 0.82 0.07 0.00
385_Q 173_D 0.82 0.07 0.00
409_H 318_L 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)
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