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OPENSEQ.org
L2-L5
Genes: A B A+B
Length: 273 179 452
Sequences: 2103 2198 1621
Seq/Len: 7.7 12.28 3.59
MirrorTree (Pazo et al. 2001) 0.90
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 0.19
10 0.00 0.00 3.46
20 0.00 0.00 3.59
100 0.00 0.00 3.68
∞ 0.00 0.00 3.83
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
269_R 111_I 1.23 0.89 0.21
165_V 24_S 0.88 0.56 0.07
263_T 157_T 0.80 0.45 0.05
15_H 61_S 0.79 0.44 0.05
116_I 13_V 0.78 0.42 0.05
210_A 79_I 0.76 0.40 0.04
123_A 47_K 0.75 0.39 0.04
126_P 148_R 0.74 0.38 0.04
253_K 47_K 0.73 0.37 0.04
224_A 32_E 0.73 0.36 0.04
12_G 45_A 0.73 0.36 0.04
34_L 85_I 0.72 0.35 0.04
39_K 168_A 0.72 0.35 0.04
154_L 162_S 0.70 0.32 0.03
149_G 82_G 0.69 0.31 0.03
152_G 5_H 0.68 0.30 0.03
137_V 38_M 0.67 0.30 0.03
24_L 5_H 0.67 0.29 0.03
41_G 153_D 0.67 0.29 0.03
213_W 45_A 0.66 0.29 0.03
65_V 50_L 0.66 0.28 0.03
144_V 156_I 0.66 0.28 0.03
176_L 106_I 0.66 0.28 0.03
201_M 47_K 0.65 0.27 0.03
239_N 28_V 0.64 0.27 0.03
123_A 35_T 0.64 0.27 0.03
243_H 136_I 0.64 0.26 0.03
180_E 113_D 0.63 0.26 0.03
2_A 58_A 0.63 0.26 0.03
266_F 44_I 0.63 0.25 0.03
252_T 117_L 0.63 0.25 0.03
149_G 177_F 0.63 0.25 0.03
101_R 71_R 0.63 0.25 0.03
213_W 179_K 0.63 0.25 0.03
210_A 83_Y 0.63 0.25 0.03
243_H 98_E 0.63 0.25 0.03
90_N 155_T 0.62 0.24 0.02
177_R 174_D 0.62 0.24 0.02
176_L 149_V 0.62 0.24 0.02
269_R 81_Q 0.61 0.23 0.02
143_N 46_D 0.61 0.23 0.02
245_V 72_K 0.61 0.23 0.02
148_P 50_L 0.60 0.22 0.02
145_E 151_G 0.59 0.22 0.02
6_C 24_S 0.59 0.21 0.02
12_G 19_E 0.59 0.21 0.02
265_K 119_A 0.59 0.21 0.02
202_L 24_S 0.59 0.21 0.02
262_R 179_K 0.59 0.21 0.02
204_V 129_S 0.58 0.21 0.02
167_R 178_R 0.58 0.21 0.02
232_H 143_Y 0.58 0.21 0.02
90_N 132_V 0.58 0.21 0.02
88_S 55_A 0.58 0.21 0.02
61_A 30_R 0.58 0.21 0.02
173_T 10_D 0.58 0.20 0.02
210_A 35_T 0.57 0.20 0.02
266_F 46_D 0.57 0.20 0.02
228_V 47_K 0.57 0.20 0.02
259_S 94_E 0.57 0.20 0.02
108_K 108_V 0.57 0.20 0.02
94_V 10_D 0.57 0.20 0.02
4_V 106_I 0.57 0.20 0.02
174_L 166_G 0.57 0.20 0.02
17_V 137_I 0.57 0.20 0.02
39_K 71_R 0.57 0.20 0.02
175_R 179_K 0.57 0.20 0.02
224_A 12_V 0.57 0.20 0.02
253_K 46_D 0.57 0.20 0.02
19_V 46_D 0.56 0.19 0.02
129_T 56_D 0.56 0.19 0.02
76_A 119_A 0.56 0.19 0.02
17_V 46_D 0.56 0.19 0.02
253_K 153_D 0.56 0.19 0.02
173_T 167_R 0.55 0.18 0.02
164_I 156_I 0.55 0.18 0.02
41_G 98_E 0.55 0.18 0.02
169_G 24_S 0.55 0.18 0.02
27_G 47_K 0.55 0.18 0.02
168_D 57_L 0.55 0.18 0.02
184_V 172_A 0.55 0.18 0.02
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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