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OPENSEQ.org
bama_tolc_gonor
Genes: A B A+B
Length: 792 428 1157
Sequences: 1555 14142 1251
Seq/Len: 1.96 33.04 1.08
MirrorTree (Pazo et al. 2001) 0.33
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 0.02 0.00 0.00
2 0.02 0.00 0.00
5 0.02 0.02 0.01
10 0.02 0.04 0.03
20 0.02 0.07 0.09
100 0.02 0.14 0.40
∞ 0.04 0.21 1.03
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
60_A 362_Y 0.97 0.33 0.00
179_I 109_T 0.89 0.27 0.00
621_L 63_N 0.89 0.27 0.00
443_G 130_K 0.87 0.25 0.00
234_Y 371_D 0.85 0.24 0.00
257_I 155_Q 0.84 0.24 0.00
150_I 200_N 0.84 0.23 0.00
515_V 39_L 0.84 0.23 0.00
621_L 23_D 0.83 0.23 0.00
352_I 11_R 0.82 0.22 0.00
514_G 134_Y 0.81 0.22 0.00
96_L 2_N 0.81 0.21 0.00
234_Y 335_N 0.81 0.21 0.00
150_I 396_N 0.81 0.21 0.00
457_A 348_V 0.81 0.21 0.00
444_V 188_N 0.80 0.21 0.00
168_I 8_Q 0.80 0.21 0.00
773_L 42_L 0.80 0.20 0.00
287_L 145_N 0.79 0.20 0.00
255_I 310_V 0.79 0.20 0.00
267_W 312_A 0.79 0.20 0.00
382_L 389_A 0.78 0.20 0.00
714_A 154_V 0.78 0.20 0.00
725_A 172_R 0.78 0.19 0.00
66_Y 105_L 0.77 0.19 0.00
773_L 352_Q 0.77 0.19 0.00
483_V 400_I 0.77 0.19 0.00
394_Y 26_A 0.75 0.18 0.00
518_G 233_A 0.75 0.18 0.00
352_I 135_R 0.74 0.17 0.00
34_Q 345_K 0.74 0.17 0.00
49_V 69_L 0.74 0.17 0.00
489_I 36_S 0.74 0.17 0.00
255_I 379_L 0.73 0.17 0.00
129_L 355_L 0.73 0.17 0.00
432_W 221_L 0.73 0.17 0.00
264_R 330_S 0.72 0.16 0.00
178_D 305_A 0.72 0.16 0.00
652_Y 249_D 0.72 0.16 0.00
283_E 292_I 0.72 0.16 0.00
651_F 399_N 0.72 0.16 0.00
303_A 137_L 0.72 0.16 0.00
225_V 239_Q 0.72 0.16 0.00
765_M 113_Y 0.72 0.16 0.00
96_L 178_A 0.71 0.16 0.00
267_W 45_G 0.71 0.16 0.00
718_W 305_A 0.70 0.15 0.00
88_I 132_A 0.70 0.15 0.00
489_I 241_Q 0.69 0.15 0.00
216_Q 362_Y 0.69 0.15 0.00
341_I 359_E 0.69 0.15 0.00
308_I 315_Q 0.69 0.15 0.00
458_L 282_N 0.69 0.14 0.00
576_W 389_A 0.69 0.14 0.00
53_Y 179_V 0.68 0.14 0.00
442_A 76_F 0.68 0.14 0.00
654_G 182_L 0.68 0.14 0.00
271_S 42_L 0.68 0.14 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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