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OPENSEQ.org
PcrA vs YerB
Genes: A B A+B
Length: 739 331 949
Sequences: 3698 512 132
Seq/Len: 5 1.55 0.14
MirrorTree (Pazo et al. 2001) 0.53
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 0.09 0.02 0.00
2 0.09 0.02 0.00
5 0.09 0.02 0.00
10 0.09 0.02 0.01
20 0.09 0.02 0.01
100 0.10 0.02 0.02
∞ 0.16 0.03 0.12
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
558_D 314_I 1.64 0.32 0.00
237_K 86_F 1.62 0.31 0.00
149_S 250_I 1.31 0.18 0.00
316_D 56_V 1.30 0.18 0.00
353_D 131_Q 1.23 0.16 0.00
100_L 314_I 1.21 0.15 0.00
94_S 295_R 1.21 0.15 0.00
356_I 307_F 1.18 0.14 0.00
274_Y 101_V 1.17 0.14 0.00
239_L 165_S 1.12 0.13 0.00
40_V 96_E 1.11 0.13 0.00
74_E 140_M 1.11 0.13 0.00
235_L 158_P 1.10 0.12 0.00
161_F 124_W 1.10 0.12 0.00
220_I 51_P 1.08 0.12 0.00
18_E 205_V 1.08 0.12 0.00
35_S 189_F 1.07 0.12 0.00
598_M 101_V 1.07 0.12 0.00
220_I 111_L 1.07 0.12 0.00
351_L 51_P 1.05 0.11 0.00
515_F 112_S 1.05 0.11 0.00
376_L 233_G 1.04 0.11 0.00
289_T 112_S 1.04 0.11 0.00
337_A 304_W 1.03 0.11 0.00
221_H 115_F 1.02 0.11 0.00
70_R 287_T 1.02 0.10 0.00
171_Q 307_F 1.01 0.10 0.00
217_F 75_I 1.01 0.10 0.00
587_P 72_D 1.01 0.10 0.00
62_I 314_I 1.00 0.10 0.00
395_I 250_I 1.00 0.10 0.00
338_G 41_K 1.00 0.10 0.00
74_E 120_V 1.00 0.10 0.00
578_L 161_N 1.00 0.10 0.00
185_L 277_L 0.99 0.10 0.00
94_S 280_Q 0.99 0.10 0.00
64_F 74_V 0.99 0.10 0.00
371_L 49_R 0.99 0.10 0.00
94_S 62_A 0.98 0.10 0.00
228_T 276_G 0.98 0.10 0.00
578_L 287_T 0.98 0.10 0.00
436_I 205_V 0.98 0.10 0.00
159_E 73_I 0.97 0.10 0.00
223_D 105_R 0.97 0.10 0.00
373_K 189_F 0.97 0.10 0.00
534_F 80_E 0.97 0.10 0.00
294_R 96_E 0.96 0.10 0.00
608_G 161_N 0.96 0.09 0.00
261_G 63_R 0.96 0.09 0.00
68_A 90_F 0.96 0.09 0.00
340_I 202_N 0.96 0.09 0.00
356_I 90_F 0.95 0.09 0.00
581_L 141_N 0.95 0.09 0.00
353_D 84_T 0.95 0.09 0.00
618_L 139_Y 0.95 0.09 0.00
336_V 162_S 0.94 0.09 0.00
336_V 299_V 0.94 0.09 0.00
190_L 90_F 0.94 0.09 0.00
337_A 302_G 0.93 0.09 0.00
264_I 51_P 0.93 0.09 0.00
255_S 235_I 0.93 0.09 0.00
220_I 90_F 0.92 0.09 0.00
584_G 160_H 0.92 0.09 0.00
317_E 307_F 0.92 0.09 0.00
574_P 188_L 0.92 0.09 0.00
205_R 314_I 0.92 0.09 0.00
286_Y 238_D 0.91 0.09 0.00
614_Q 141_N 0.91 0.09 0.00
430_I 124_W 0.91 0.09 0.00
392_I 163_Y 0.91 0.09 0.00
28_L 72_D 0.91 0.09 0.00
369_E 235_I 0.90 0.08 0.00
581_L 98_V 0.90 0.08 0.00
578_L 119_F 0.89 0.08 0.00
295_A 119_F 0.89 0.08 0.00
331_G 244_P 0.89 0.08 0.00
441_F 297_V 0.89 0.08 0.00
500_E 84_T 0.89 0.08 0.00
76_V 205_V 0.89 0.08 0.00
223_D 289_W 0.89 0.08 0.00
580_G 264_G 0.89 0.08 0.00
534_F 65_Q 0.88 0.08 0.00
482_E 276_G 0.88 0.08 0.00
291_R 124_W 0.88 0.08 0.00
223_D 85_R 0.88 0.08 0.00
223_D 102_R 0.88 0.08 0.00
223_D 103_S 0.88 0.08 0.00
94_S 60_P 0.88 0.08 0.00
159_E 193_D 0.88 0.08 0.00
234_M 75_I 0.88 0.08 0.00
20_V 307_F 0.88 0.08 0.00
641_E 101_V 0.88 0.08 0.00
359_R 302_G 0.88 0.08 0.00
185_L 283_N 0.87 0.08 0.00
161_F 141_N 0.87 0.08 0.00
608_G 159_P 0.87 0.08 0.00
392_I 111_L 0.87 0.08 0.00
510_E 291_Q 0.87 0.08 0.00
32_G 37_L 0.86 0.08 0.00
211_E 116_D 0.86 0.08 0.00
352_S 293_N 0.86 0.08 0.00
432_S 250_I 0.86 0.08 0.00
441_F 119_F 0.86 0.08 0.00
261_G 72_D 0.86 0.08 0.00
568_A 146_D 0.86 0.08 0.00
41_L 101_V 0.86 0.08 0.00
153_N 122_H 0.86 0.08 0.00
356_I 255_A 0.86 0.08 0.00
466_Q 90_F 0.86 0.08 0.00
512_I 86_F 0.85 0.08 0.00
522_F 242_G 0.85 0.08 0.00
100_L 227_Y 0.85 0.08 0.00
617_Y 241_T 0.85 0.07 0.00
575_V 314_I 0.85 0.07 0.00
371_L 286_E 0.85 0.07 0.00
513_D 126_P 0.85 0.07 0.00
229_N 306_P 0.85 0.07 0.00
185_L 49_R 0.85 0.07 0.00
39_R 116_D 0.85 0.07 0.00
222_V 243_K 0.85 0.07 0.00
54_V 66_S 0.85 0.07 0.00
73_K 219_N 0.84 0.07 0.00
386_F 111_L 0.84 0.07 0.00
216_K 74_V 0.84 0.07 0.00
279_V 61_K 0.84 0.07 0.00
397_A 277_L 0.84 0.07 0.00
118_T 66_S 0.84 0.07 0.00
255_S 225_E 0.83 0.07 0.00
353_D 56_V 0.83 0.07 0.00
49_M 88_A 0.83 0.07 0.00
370_T 280_Q 0.83 0.07 0.00
562_L 54_V 0.82 0.07 0.00
600_E 163_Y 0.82 0.07 0.00
29_L 255_A 0.82 0.07 0.00
142_R 87_L 0.82 0.07 0.00
221_H 74_V 0.82 0.07 0.00
223_D 71_A 0.82 0.07 0.00
425_T 220_Y 0.82 0.07 0.00
378_Y 50_R 0.82 0.07 0.00
402_V 305_L 0.82 0.07 0.00
236_V 317_V 0.81 0.07 0.00
473_N 193_D 0.81 0.07 0.00
461_L 97_T 0.81 0.07 0.00
493_Y 188_L 0.81 0.07 0.00
276_N 73_I 0.81 0.07 0.00
132_R 98_V 0.81 0.07 0.00
432_S 86_F 0.81 0.07 0.00
317_E 118_I 0.81 0.07 0.00
581_L 19_S 0.81 0.07 0.00
579_M 218_Y 0.81 0.07 0.00
121_Q 279_F 0.80 0.07 0.00
352_S 198_N 0.80 0.07 0.00
223_D 282_G 0.80 0.07 0.00
366_V 239_R 0.80 0.07 0.00
211_E 224_A 0.80 0.07 0.00
366_V 287_T 0.80 0.07 0.00
191_D 310_G 0.80 0.07 0.00
297_N 244_P 0.80 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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