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OPENSEQ.org
1BKD
Genes: A B A+B
Length: 166 245 398
Sequences: 11837 13492 331
Seq/Len: 71.31 55.07 0.83
MirrorTree (Pazo et al. 2001) 0.08
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 0.05 0.18 0.09
2 0.06 0.20 0.13
5 0.08 0.21 0.28
10 0.10 0.22 0.48
20 0.13 0.23 0.81
100 0.23 0.25 1.96
∞ 0.28 0.28 2.35
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
20_T 53_V 1.09 0.38 0.00
113_L 68_A 1.07 0.35 0.00
8_V 192_M 0.97 0.28 0.00
159_L 237_W 0.91 0.24 0.00
128_R 46_L 0.88 0.22 0.00
26_N 139_T 0.81 0.18 0.00
17_S 199_L 0.79 0.17 0.00
125_V 88_V 0.79 0.17 0.00
80_C 223_S 0.75 0.15 0.00
113_L 141_W 0.75 0.15 0.00
17_S 146_Y 0.74 0.15 0.00
126_E 16_I 0.73 0.14 0.00
91_E 48_N 0.73 0.14 0.00
34_P 236_N 0.73 0.14 0.00
28_F 197_G 0.73 0.14 0.00
127_S 33_L 0.72 0.14 0.00
21_I 88_V 0.71 0.14 0.00
35_T 69_G 0.71 0.13 0.00
51_C 190_S 0.70 0.13 0.00
145_S 108_L 0.69 0.13 0.00
111_M 112_A 0.69 0.13 0.00
155_A 51_W 0.68 0.12 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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