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OPENSEQ.org
EttA-vs-S4
Genes: A B A+B
Length: 555 206 732
Sequences: 8126 1236 676
Seq/Len: 14.64 6 0.92
MirrorTree (Pazo et al. 2001) 0.22
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 0.01 0.09 0.00
2 0.01 0.09 0.00
5 0.01 0.09 0.01
10 0.01 0.09 0.01
20 0.02 0.09 0.03
100 0.06 0.09 0.17
∞ 0.17 0.09 0.89
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
22_L 206_K 1.16 0.46 0.00
406_E 148_K 1.03 0.34 0.00
215_I 68_L 0.99 0.32 0.00
68_D 81_R 0.98 0.31 0.00
213_V 118_V 0.92 0.26 0.00
490_F 200_I 0.91 0.25 0.00
17_P 133_A 0.89 0.24 0.00
295_E 145_I 0.88 0.24 0.00
211_T 88_E 0.88 0.23 0.00
240_W 144_S 0.87 0.23 0.00
38_L 139_P 0.86 0.23 0.00
195_A 51_Y 0.85 0.21 0.00
436_V 88_E 0.84 0.21 0.00
71_I 16_G 0.84 0.21 0.00
343_S 203_L 0.83 0.20 0.00
442_V 172_E 0.83 0.20 0.00
323_V 19_L 0.81 0.19 0.00
29_F 105_M 0.81 0.19 0.00
389_A 187_E 0.81 0.19 0.00
428_V 197_E 0.80 0.18 0.00
465_M 181_T 0.78 0.18 0.00
329_L 37_A 0.77 0.17 0.00
338_L 7_P 0.76 0.17 0.00
99_N 135_Y 0.76 0.17 0.00
489_E 135_Y 0.76 0.17 0.00
240_W 179_E 0.76 0.17 0.00
468_L 143_V 0.76 0.16 0.00
329_L 88_E 0.75 0.16 0.00
62_E 81_R 0.75 0.16 0.00
99_N 51_Y 0.74 0.16 0.00
338_L 190_D 0.74 0.16 0.00
37_V 200_I 0.74 0.15 0.00
339_I 67_V 0.74 0.15 0.00
22_L 54_Q 0.73 0.15 0.00
228_W 101_V 0.73 0.15 0.00
428_V 87_G 0.73 0.15 0.00
245_S 52_G 0.73 0.15 0.00
352_V 145_I 0.73 0.15 0.00
467_L 147_E 0.73 0.15 0.00
15_V 89_N 0.72 0.15 0.00
512_L 92_A 0.72 0.15 0.00
328_N 128_R 0.72 0.15 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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