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OPENSEQ.org
L15-L16
Genes: A B A+B
Length: 144 136 277
Sequences: 2737 1796 1559
Seq/Len: 19.01 13.21 5.63
MirrorTree (Pazo et al. 2001) 0.67
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.00 0.66
20 0.00 0.00 5.57
100 0.00 0.00 5.73
∞ 0.00 0.00 6.34
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
128_T 28_F 0.96 0.78 0.01
70_K 80_V 0.87 0.68 0.01
33_R 76_K 0.85 0.65 0.01
116_V 130_F 0.84 0.65 0.01
24_G 109_P 0.80 0.59 0.01
109_K 75_E 0.79 0.57 0.01
40_S 84_K 0.78 0.56 0.01
97_A 9_F 0.76 0.52 0.01
48_R 74_T 0.75 0.51 0.01
31_G 7_T 0.73 0.48 0.01
39_K 97_Q 0.72 0.46 0.01
84_K 32_G 0.70 0.44 0.01
3_L 80_V 0.70 0.43 0.01
8_P 71_K 0.69 0.43 0.01
13_K 84_K 0.69 0.43 0.01
61_L 105_M 0.69 0.42 0.01
85_V 111_E 0.65 0.37 0.01
7_S 3_Q 0.65 0.36 0.01
76_E 33_L 0.64 0.36 0.01
138_A 102_L 0.64 0.35 0.01
108_A 84_K 0.64 0.35 0.01
64_F 84_K 0.63 0.34 0.01
131_A 6_R 0.63 0.34 0.01
134_A 80_V 0.63 0.34 0.01
134_A 44_R 0.62 0.33 0.01
13_K 102_L 0.62 0.33 0.01
40_S 60_Q 0.62 0.32 0.01
88_G 13_H 0.61 0.32 0.01
24_G 77_P 0.61 0.32 0.01
66_F 92_W 0.61 0.31 0.01
85_V 67_V 0.61 0.31 0.01
25_S 34_K 0.61 0.31 0.01
58_Y 3_Q 0.60 0.30 0.01
58_Y 70_D 0.60 0.30 0.01
31_G 82_M 0.59 0.29 0.01
101_I 93_V 0.59 0.29 0.01
137_A 37_G 0.59 0.29 0.01
47_R 34_K 0.59 0.28 0.01
100_I 121_A 0.58 0.28 0.01
17_K 126_I 0.58 0.28 0.01
110_V 22_Q 0.58 0.28 0.01
5_T 63_I 0.58 0.28 0.01
122_V 93_V 0.58 0.27 0.01
97_A 42_T 0.57 0.27 0.01
64_F 14_K 0.57 0.27 0.01
4_N 80_V 0.57 0.27 0.01
33_R 133_K 0.57 0.26 0.01
51_E 81_R 0.57 0.26 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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