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OPENSEQ.org
bama_tolc
Genes: A B A+B
Length: 810 428 1158
Sequences: 1555 14142 1257
Seq/Len: 1.92 33.04 1.09
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 0.39
∞ 0.04 0.21 1.02
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
61_N 362_Y 1.00 0.36 0.00
443_G 130_K 0.88 0.26 0.00
75_V 189_Y 0.86 0.25 0.00
256_V 310_V 0.84 0.23 0.00
235_Y 335_N 0.84 0.23 0.00
256_V 379_L 0.83 0.23 0.00
621_I 63_N 0.83 0.23 0.00
457_G 348_V 0.82 0.22 0.00
268_L 312_A 0.82 0.22 0.00
513_V 39_L 0.81 0.22 0.00
741_M 154_V 0.81 0.21 0.00
235_Y 371_D 0.81 0.21 0.00
791_F 253_S 0.81 0.21 0.00
67_F 105_L 0.80 0.21 0.00
50_T 69_L 0.78 0.20 0.00
652_F 399_N 0.78 0.20 0.00
621_I 23_D 0.78 0.20 0.00
516_G 233_A 0.78 0.19 0.00
260_I 286_L 0.78 0.19 0.00
35_Q 345_K 0.77 0.19 0.00
303_K 137_L 0.77 0.19 0.00
483_V 400_I 0.77 0.19 0.00
352_I 11_R 0.77 0.19 0.00
432_Y 221_L 0.77 0.19 0.00
444_V 188_N 0.76 0.19 0.00
406_P 116_V 0.76 0.18 0.00
169_F 8_Q 0.76 0.18 0.00
265_Q 330_S 0.76 0.18 0.00
394_F 26_A 0.76 0.18 0.00
287_L 145_N 0.75 0.18 0.00
94_I 146_V 0.75 0.18 0.00
526_R 327_V 0.74 0.17 0.00
382_V 389_A 0.73 0.17 0.00
752_S 172_R 0.72 0.17 0.00
281_S 292_I 0.72 0.16 0.00
258_V 155_Q 0.72 0.16 0.00
74_D 10_A 0.72 0.16 0.00
54_V 179_V 0.72 0.16 0.00
791_F 42_L 0.71 0.16 0.00
352_I 311_G 0.71 0.16 0.00
512_D 134_Y 0.71 0.16 0.00
180_I 109_T 0.71 0.16 0.00
416_Y 94_Q 0.71 0.16 0.00
519_I 130_K 0.70 0.15 0.00
308_I 315_Q 0.70 0.15 0.00
576_W 389_A 0.70 0.15 0.00
529_L 388_N 0.70 0.15 0.00
271_V 76_F 0.70 0.15 0.00
151_V 200_N 0.70 0.15 0.00
226_L 239_Q 0.69 0.15 0.00
611_V 178_A 0.69 0.15 0.00
489_L 36_S 0.69 0.15 0.00
31_F 39_L 0.69 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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