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OPENSEQ.org
L6-L15
Genes: A B A+B
Length: 177 144 320
Sequences: 2962 2737 2232
Seq/Len: 16.73 19.01 6.97
MirrorTree (Pazo et al. 2001) 0.86
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 0.01
2 0.00 0.00 0.04
5 0.00 0.00 6.42
10 0.00 0.00 6.92
20 0.00 0.00 6.95
100 0.00 0.00 6.98
∞ 0.00 0.00 7.26
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
67_T 134_A 0.92 0.79 0.01
137_D 24_G 0.81 0.66 0.01
85_K 132_R 0.73 0.54 0.01
44_K 97_A 0.66 0.44 0.01
158_K 55_M 0.64 0.41 0.00
176_K 35_H 0.64 0.40 0.00
95_R 39_K 0.62 0.38 0.00
151_Y 109_K 0.61 0.36 0.00
71_L 40_S 0.58 0.32 0.00
60_D 99_N 0.58 0.32 0.00
95_R 137_A 0.57 0.31 0.00
89_L 74_T 0.57 0.31 0.00
25_T 10_E 0.56 0.29 0.00
89_L 33_R 0.54 0.27 0.00
63_A 55_M 0.54 0.27 0.00
21_G 33_R 0.54 0.26 0.00
158_K 108_A 0.54 0.26 0.00
176_K 29_K 0.54 0.26 0.00
152_R 40_S 0.51 0.23 0.00
34_T 97_A 0.51 0.23 0.00
60_D 113_A 0.51 0.23 0.00
124_E 135_I 0.51 0.23 0.00
106_S 19_L 0.50 0.22 0.00
151_Y 13_K 0.50 0.22 0.00
128_Q 71_A 0.49 0.21 0.00
119_A 19_L 0.49 0.21 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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