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OPENSEQ.org
yC_bB
Genes: A B A+B
Length: 548 392 926
Sequences: 1547 3152 564
Seq/Len: 2.82 8.04 0.61
MirrorTree (Pazo et al. 2001) 0.48
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 0.08 0.02 0.00
2 0.08 0.02 0.00
5 0.08 0.04 0.00
10 0.08 0.05 0.00
20 0.08 0.05 0.01
100 0.08 0.07 0.04
∞ 0.08 0.13 0.60
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
351_V 274_S 1.27 0.44 0.00
332_W 73_Y 1.21 0.39 0.00
165_F 64_H 1.17 0.36 0.00
359_I 135_N 1.15 0.35 0.00
511_S 78_A 1.14 0.34 0.00
392_A 131_V 1.13 0.33 0.00
511_S 285_S 1.11 0.32 0.00
390_I 140_T 1.11 0.32 0.00
351_V 74_A 1.10 0.31 0.00
186_K 85_N 1.09 0.30 0.00
511_S 185_V 1.08 0.30 0.00
61_I 372_V 1.06 0.28 0.00
185_E 92_I 1.05 0.28 0.00
140_L 155_P 1.04 0.27 0.00
298_G 307_A 1.03 0.27 0.00
403_R 47_A 1.01 0.25 0.00
407_E 306_M 1.01 0.25 0.00
31_P 84_L 1.00 0.25 0.00
370_Y 356_F 0.97 0.23 0.00
427_L 380_I 0.95 0.22 0.00
517_Y 245_S 0.95 0.22 0.00
79_V 146_K 0.95 0.22 0.00
296_Q 274_S 0.95 0.22 0.00
79_V 39_E 0.95 0.22 0.00
474_T 297_Y 0.94 0.21 0.00
393_M 178_D 0.94 0.21 0.00
469_I 320_S 0.94 0.21 0.00
226_P 157_V 0.92 0.20 0.00
382_K 355_R 0.92 0.20 0.00
50_Q 69_D 0.91 0.20 0.00
157_A 124_I 0.90 0.19 0.00
29_P 178_D 0.90 0.19 0.00
523_V 219_V 0.89 0.19 0.00
469_I 72_V 0.89 0.19 0.00
350_F 380_I 0.89 0.19 0.00
150_P 81_V 0.89 0.18 0.00
417_V 149_G 0.88 0.18 0.00
174_V 140_T 0.88 0.18 0.00
511_S 370_E 0.87 0.18 0.00
149_V 182_K 0.87 0.18 0.00
396_R 83_A 0.87 0.18 0.00
54_A 122_V 0.87 0.17 0.00
360_I 304_R 0.87 0.17 0.00
382_K 133_A 0.87 0.17 0.00
357_S 64_H 0.87 0.17 0.00
87_Y 271_D 0.86 0.17 0.00
49_D 69_D 0.86 0.17 0.00
350_F 368_Q 0.85 0.17 0.00
492_Q 348_W 0.85 0.17 0.00
174_V 8_L 0.84 0.16 0.00
174_V 255_N 0.84 0.16 0.00
31_P 335_G 0.84 0.16 0.00
444_V 175_N 0.84 0.16 0.00
396_R 88_D 0.84 0.16 0.00
11_A 47_A 0.84 0.16 0.00
470_L 44_P 0.84 0.16 0.00
405_S 51_S 0.83 0.16 0.00
386_L 178_D 0.83 0.16 0.00
428_I 312_G 0.83 0.16 0.00
105_Q 178_D 0.83 0.16 0.00
386_L 201_T 0.83 0.16 0.00
480_K 120_G 0.83 0.16 0.00
401_K 193_S 0.83 0.16 0.00
270_G 308_L 0.83 0.16 0.00
180_V 91_E 0.83 0.16 0.00
144_Q 135_N 0.82 0.16 0.00
390_I 298_L 0.82 0.15 0.00
162_T 207_A 0.82 0.15 0.00
451_F 244_L 0.82 0.15 0.00
366_R 352_E 0.82 0.15 0.00
169_R 85_N 0.82 0.15 0.00
164_T 313_G 0.82 0.15 0.00
58_G 115_V 0.82 0.15 0.00
180_V 177_A 0.82 0.15 0.00
404_I 175_N 0.82 0.15 0.00
448_Q 85_N 0.81 0.15 0.00
377_Y 89_G 0.80 0.15 0.00
421_G 247_V 0.80 0.14 0.00
180_V 297_Y 0.80 0.14 0.00
407_E 83_A 0.80 0.14 0.00
469_I 253_V 0.80 0.14 0.00
261_A 133_A 0.80 0.14 0.00
522_L 14_V 0.80 0.14 0.00
511_S 341_D 0.80 0.14 0.00
61_I 353_D 0.79 0.14 0.00
466_I 121_H 0.79 0.14 0.00
389_K 162_V 0.79 0.14 0.00
310_G 317_W 0.79 0.14 0.00
477_F 177_A 0.79 0.14 0.00
466_I 142_A 0.78 0.14 0.00
475_M 265_G 0.78 0.14 0.00
375_A 367_F 0.78 0.14 0.00
286_I 196_G 0.78 0.14 0.00
86_A 223_Q 0.78 0.14 0.00
261_A 244_L 0.78 0.14 0.00
365_V 52_V 0.78 0.14 0.00
117_R 72_V 0.78 0.14 0.00
376_Q 205_G 0.78 0.14 0.00
459_S 147_V 0.78 0.14 0.00
533_R 281_R 0.78 0.14 0.00
465_Y 18_S 0.77 0.14 0.00
371_P 271_D 0.77 0.14 0.00
370_Y 297_Y 0.77 0.14 0.00
466_I 228_W 0.77 0.14 0.00
469_I 249_T 0.77 0.14 0.00
469_I 290_I 0.77 0.13 0.00
448_Q 96_S 0.77 0.13 0.00
357_S 193_S 0.77 0.13 0.00
6_N 178_D 0.77 0.13 0.00
335_F 97_L 0.77 0.13 0.00
397_L 311_D 0.77 0.13 0.00
54_A 19_G 0.77 0.13 0.00
227_D 66_A 0.77 0.13 0.00
286_I 133_A 0.77 0.13 0.00
413_K 76_D 0.76 0.13 0.00
61_I 240_E 0.76 0.13 0.00
4_Q 262_A 0.76 0.13 0.00
494_I 198_S 0.76 0.13 0.00
17_F 297_Y 0.76 0.13 0.00
35_Q 137_S 0.76 0.13 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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