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OPENSEQ.org
L4-L15
Genes: A B A+B
Length: 201 144 340
Sequences: 2818 2737 1804
Seq/Len: 14.02 19.01 5.31
MirrorTree (Pazo et al. 2001) 0.82
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 0.01
5 0.00 0.00 0.03
10 0.00 0.00 0.05
20 0.00 0.00 5.23
100 0.00 0.00 5.92
∞ 0.00 0.00 6.30
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
33_V 13_K 2.06 1.00 0.99
184_D 2_R 1.96 1.00 0.98
26_A 9_A 1.02 0.82 0.59
29_H 8_P 0.93 0.73 0.47
26_A 8_P 0.90 0.70 0.45
182_A 3_L 0.88 0.68 0.42
29_H 13_K 0.86 0.65 0.39
25_E 5_T 0.83 0.61 0.36
122_E 129_K 0.77 0.52 0.28
49_R 42_S 0.76 0.50 0.27
79_R 23_I 0.72 0.45 0.23
85_F 42_S 0.71 0.43 0.22
77_I 29_K 0.70 0.42 0.21
30_Q 9_A 0.68 0.40 0.19
77_I 40_S 0.68 0.39 0.19
32_V 6_L 0.68 0.39 0.19
30_Q 13_K 0.65 0.36 0.17
85_F 47_R 0.65 0.36 0.17
97_N 92_L 0.65 0.35 0.17
60_W 57_L 0.65 0.35 0.16
125_S 31_G 0.64 0.34 0.16
86_A 74_T 0.63 0.33 0.15
114_R 96_K 0.62 0.32 0.15
121_V 137_A 0.62 0.32 0.14
64_G 43_G 0.62 0.31 0.14
28_V 5_T 0.62 0.31 0.14
19_F 24_G 0.61 0.31 0.14
85_F 44_G 0.60 0.29 0.13
129_P 40_S 0.60 0.29 0.13
36_A 70_K 0.59 0.28 0.12
113_V 110_V 0.59 0.28 0.12
29_H 9_A 0.58 0.27 0.12
33_V 8_P 0.58 0.27 0.11
72_S 58_Y 0.57 0.26 0.11
112_L 1_M 0.57 0.26 0.11
61_R 128_T 0.57 0.26 0.11
153_L 24_G 0.57 0.26 0.11
139_K 97_A 0.57 0.26 0.11
61_R 79_L 0.57 0.25 0.11
169_V 136_E 0.57 0.25 0.11
132_K 77_I 0.56 0.25 0.10
112_L 5_T 0.56 0.24 0.10
121_V 106_E 0.56 0.24 0.10
198_E 143_E 0.55 0.24 0.10
117_R 2_R 0.55 0.23 0.09
67_R 55_M 0.55 0.23 0.09
88_R 105_I 0.54 0.23 0.09
50_A 24_G 0.54 0.23 0.09
118_L 86_E 0.54 0.23 0.09
97_N 4_N 0.54 0.22 0.09
27_L 92_L 0.54 0.22 0.09
42_G 50_F 0.54 0.22 0.09
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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