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OPENSEQ.org
L3-L15
Genes: A B A+B
Length: 209 144 352
Sequences: 2524 2737 1638
Seq/Len: 12.08 19.01 4.65
MirrorTree (Pazo et al. 2001) 0.78
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 0.02
20 0.00 0.00 4.64
100 0.00 0.00 5.33
∞ 0.00 0.00 5.75
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
131_D 64_F 0.86 0.61 0.00
143_P 8_P 0.83 0.57 0.00
158_G 33_R 0.77 0.48 0.00
92_V 77_I 0.73 0.42 0.00
181_D 29_K 0.69 0.37 0.00
72_G 108_A 0.69 0.37 0.00
131_D 47_R 0.69 0.37 0.00
193_V 89_V 0.69 0.37 0.00
193_V 10_E 0.68 0.36 0.00
155_V 50_F 0.67 0.35 0.00
27_I 90_V 0.67 0.35 0.00
153_G 23_I 0.67 0.34 0.00
125_W 64_F 0.66 0.34 0.00
29_V 99_N 0.65 0.32 0.00
97_S 117_T 0.65 0.32 0.00
96_I 86_E 0.64 0.32 0.00
188_L 1_M 0.64 0.32 0.00
40_L 122_V 0.64 0.31 0.00
202_I 24_G 0.63 0.30 0.00
155_V 84_K 0.63 0.30 0.00
36_Q 42_S 0.62 0.29 0.00
109_V 83_A 0.61 0.28 0.00
83_R 87_G 0.60 0.27 0.00
193_V 31_G 0.60 0.27 0.00
18_D 96_K 0.60 0.26 0.00
19_G 25_S 0.59 0.26 0.00
32_N 106_E 0.59 0.26 0.00
61_T 101_I 0.59 0.26 0.00
154_K 58_Y 0.58 0.25 0.00
165_M 86_E 0.58 0.25 0.00
147_G 36_K 0.58 0.25 0.00
189_V 7_S 0.58 0.25 0.00
80_W 64_F 0.58 0.24 0.00
182_A 128_T 0.58 0.24 0.00
129_T 143_E 0.58 0.24 0.00
153_G 33_R 0.58 0.24 0.00
54_A 142_I 0.58 0.24 0.00
157_K 142_I 0.57 0.24 0.00
109_V 59_R 0.57 0.24 0.00
95_S 7_S 0.57 0.23 0.00
150_Q 4_N 0.56 0.23 0.00
26_V 122_V 0.56 0.22 0.00
129_T 111_I 0.56 0.22 0.00
164_Q 7_S 0.55 0.22 0.00
149_N 36_K 0.55 0.22 0.00
111_G 77_I 0.55 0.22 0.00
193_V 119_P 0.55 0.22 0.00
13_R 32_G 0.55 0.21 0.00
119_A 45_G 0.55 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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