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OPENSEQ.org
cI_B_G
Genes: A B A+B
Length: 613 100 708
Sequences: 2092 1241 1231
Seq/Len: 3.41 12.41 1.74
MirrorTree (Pazo et al. 2001) 0.74
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 1.52
2 0.00 0.00 1.54
5 0.00 0.00 1.60
10 0.00 0.00 1.65
20 0.00 0.00 1.69
100 0.00 0.01 1.71
∞ 0.01 0.02 1.73
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
298_A 66_I 1.08 0.56 0.00
407_M 47_V 0.98 0.46 0.00
598_M 89_N 0.94 0.42 0.00
89_L 46_F 0.91 0.39 0.00
234_P 40_N 0.91 0.38 0.00
16_V 65_A 0.89 0.37 0.00
188_L 19_L 0.88 0.35 0.00
151_Y 80_L 0.87 0.35 0.00
355_A 35_L 0.87 0.34 0.00
263_V 62_Y 0.86 0.34 0.00
104_S 63_I 0.85 0.33 0.00
322_A 3_P 0.85 0.33 0.00
220_L 26_R 0.85 0.33 0.00
138_L 45_A 0.85 0.33 0.00
458_I 38_M 0.85 0.33 0.00
355_A 98_M 0.84 0.32 0.00
495_I 13_I 0.84 0.32 0.00
188_L 60_V 0.84 0.32 0.00
351_S 17_L 0.82 0.30 0.00
234_P 83_L 0.82 0.30 0.00
39_G 41_A 0.80 0.28 0.00
459_V 47_V 0.79 0.28 0.00
140_Y 65_A 0.79 0.27 0.00
99_I 45_A 0.78 0.27 0.00
15_F 97_E 0.78 0.26 0.00
140_Y 81_L 0.78 0.26 0.00
231_A 46_F 0.78 0.26 0.00
176_V 63_I 0.77 0.26 0.00
85_S 34_G 0.76 0.25 0.00
411_H 89_N 0.76 0.25 0.00
128_V 37_I 0.76 0.25 0.00
348_A 25_R 0.76 0.25 0.00
316_I 74_S 0.76 0.24 0.00
98_L 23_V 0.75 0.24 0.00
403_L 17_L 0.75 0.24 0.00
231_A 82_Q 0.74 0.24 0.00
308_L 78_A 0.74 0.23 0.00
79_L 65_A 0.74 0.23 0.00
135_N 21_G 0.74 0.23 0.00
189_Y 63_I 0.74 0.23 0.00
39_G 89_N 0.73 0.23 0.00
306_R 92_I 0.72 0.22 0.00
169_K 78_A 0.72 0.22 0.00
575_L 35_L 0.72 0.22 0.00
336_M 92_I 0.71 0.21 0.00
434_F 16_V 0.71 0.21 0.00
224_G 35_L 0.71 0.21 0.00
134_D 42_S 0.71 0.21 0.00
218_A 17_L 0.71 0.21 0.00
389_L 77_L 0.70 0.21 0.00
436_V 79_L 0.70 0.21 0.00
136_L 20_T 0.70 0.20 0.00
193_G 41_A 0.69 0.20 0.00
75_I 80_L 0.69 0.20 0.00
132_L 73_A 0.69 0.20 0.00
116_F 77_L 0.69 0.20 0.00
306_R 78_A 0.69 0.20 0.00
136_L 32_L 0.69 0.20 0.00
436_V 97_E 0.69 0.20 0.00
270_H 40_N 0.69 0.20 0.00
269_T 32_L 0.68 0.19 0.00
600_I 35_L 0.68 0.19 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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