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OPENSEQ.org
L1-vs-TsaD
Genes: A B A+B
Length: 234 337 559
Sequences: 3196 3839 1495
Seq/Len: 13.66 11.39 2.67
MirrorTree (Pazo et al. 2001) 0.45
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 0.09 0.07 0.00
2 0.09 0.07 0.00
5 0.09 0.08 0.01
10 0.09 0.08 0.03
20 0.09 0.08 0.09
100 0.09 0.08 0.53
∞ 0.10 0.11 2.62
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
134_R 216_T 0.84 0.42 0.00
216_T 24_L 0.83 0.41 0.00
126_Q 31_S 0.82 0.40 0.00
153_V 29_L 0.81 0.39 0.00
224_V 289_E 0.77 0.34 0.00
63_T 211_F 0.76 0.33 0.00
186_K 241_D 0.76 0.33 0.00
153_V 226_G 0.75 0.32 0.00
104_I 243_V 0.75 0.32 0.00
11_I 142_L 0.74 0.31 0.00
203_Q 197_F 0.74 0.31 0.00
19_K 17_I 0.74 0.31 0.00
124_V 214_L 0.74 0.30 0.00
203_Q 48_S 0.73 0.30 0.00
72_S 290_V 0.72 0.29 0.00
209_I 102_W 0.71 0.28 0.00
209_I 62_A 0.71 0.28 0.00
23_I 171_K 0.70 0.27 0.00
142_V 130_F 0.70 0.27 0.00
120_A 46_L 0.69 0.26 0.00
67_H 222_I 0.69 0.26 0.00
167_K 186_M 0.68 0.25 0.00
45_A 128_F 0.68 0.25 0.00
192_L 183_L 0.67 0.25 0.00
163_Y 195_F 0.67 0.24 0.00
165_N 120_M 0.67 0.24 0.00
74_R 214_L 0.67 0.24 0.00
97_M 242_A 0.67 0.24 0.00
68_G 211_F 0.64 0.22 0.00
114_V 24_L 0.64 0.22 0.00
124_V 245_D 0.64 0.21 0.00
226_Q 61_A 0.64 0.21 0.00
76_A 134_L 0.64 0.21 0.00
170_I 130_F 0.64 0.21 0.00
212_V 116_L 0.63 0.21 0.00
10_V 76_V 0.63 0.21 0.00
46_V 104_V 0.63 0.21 0.00
129_Q 306_A 0.63 0.21 0.00
217_T 140_T 0.63 0.21 0.00
142_V 117_L 0.63 0.21 0.00
67_H 72_D 0.62 0.20 0.00
42_V 282_M 0.62 0.20 0.00
55_S 116_L 0.62 0.20 0.00
54_K 156_E 0.61 0.19 0.00
120_A 106_A 0.60 0.19 0.00
18_T 3_V 0.60 0.19 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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