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OPENSEQ.org
2qi9_A_F
Genes: A B A+B
Length: 326 245 544
Sequences: 6627 11128 4972
Seq/Len: 20.33 45.42 9.14
MirrorTree (Pazo et al. 2001) 0.46
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 0.36 0.03 6.48
2 0.37 0.04 8.16
5 0.37 0.05 8.52
10 0.37 0.09 8.64
20 0.38 0.12 8.71
100 0.39 0.16 8.80
∞ 0.43 0.25 9.05
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
302_E 179_S 1.05 0.94 0.07
54_Q 78_S 0.99 0.91 0.06
35_E 49_N 0.96 0.89 0.05
47_R 184_L 0.75 0.66 0.03
36_Q 185_A 0.71 0.60 0.02
191_S 16_A 0.69 0.56 0.02
158_A 182_Q 0.69 0.56 0.02
293_V 37_Q 0.66 0.52 0.02
55_I 184_L 0.63 0.47 0.02
47_R 57_K 0.62 0.45 0.01
56_R 51_E 0.62 0.45 0.01
87_E 158_V 0.60 0.41 0.01
259_V 91_I 0.60 0.41 0.01
307_V 47_G 0.57 0.37 0.01
195_L 109_D 0.57 0.36 0.01
48_G 60_L 0.57 0.36 0.01
127_I 132_K 0.56 0.34 0.01
276_L 57_K 0.56 0.34 0.01
312_L 172_R 0.56 0.34 0.01
44_F 241_L 0.55 0.34 0.01
146_L 11_A 0.55 0.34 0.01
165_Y 19_A 0.55 0.33 0.01
47_R 212_K 0.54 0.31 0.01
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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