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OPENSEQ.org
PhyR_NepR_Coev
Genes: A B A+B
Length: 266 61 308
Sequences: 3488 133 98
Seq/Len: 13.11 2.18 0.32
MirrorTree (Pazo et al. 2001) 0.57
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 0.02 0.00 0.27
2 0.03 0.00 0.29
5 0.03 0.00 0.30
10 0.04 0.00 0.30
20 0.05 0.00 0.30
100 0.08 0.00 0.31
∞ 0.15 0.00 0.32
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
208_I 41_E 1.67 0.55 0.00
206_K 46_E 1.58 0.48 0.00
116_I 47_F 1.53 0.46 0.00
22_T 20_A 1.42 0.38 0.00
20_A 47_F 1.42 0.38 0.00
14_I 50_I 1.30 0.31 0.00
125_E 32_R 1.29 0.30 0.00
117_L 28_G 1.29 0.30 0.00
42_G 35_F 1.29 0.30 0.00
155_D 27_I 1.26 0.28 0.00
172_A 46_E 1.22 0.26 0.00
242_F 28_G 1.22 0.26 0.00
57_Y 57_P 1.20 0.25 0.00
154_A 54_A 1.18 0.24 0.00
251_I 55_E 1.17 0.23 0.00
189_V 41_E 1.12 0.21 0.00
53_R 32_R 1.07 0.19 0.00
226_L 41_E 1.06 0.19 0.00
180_A 45_D 1.06 0.19 0.00
43_E 53_K 1.05 0.18 0.00
141_T 38_V 1.05 0.18 0.00
191_A 54_A 1.04 0.18 0.00
103_T 53_K 1.04 0.18 0.00
141_T 30_K 1.03 0.17 0.00
52_P 24_Q 1.03 0.17 0.00
137_A 34_M 1.02 0.17 0.00
32_V 54_A 1.01 0.17 0.00
249_A 28_G 1.01 0.17 0.00
57_Y 48_L 1.01 0.17 0.00
167_V 48_L 0.99 0.16 0.00
166_D 53_K 0.99 0.16 0.00
22_T 52_R 0.98 0.16 0.00
226_L 51_L 0.98 0.16 0.00
141_T 28_G 0.98 0.16 0.00
31_Y 48_L 0.97 0.15 0.00
98_Q 55_E 0.96 0.15 0.00
57_Y 20_A 0.96 0.15 0.00
151_V 35_F 0.96 0.15 0.00
235_T 46_E 0.94 0.14 0.00
136_D 24_Q 0.94 0.14 0.00
105_L 47_F 0.93 0.14 0.00
159_L 19_E 0.93 0.14 0.00
144_L 58_A 0.92 0.14 0.00
54_V 32_R 0.92 0.14 0.00
255_L 28_G 0.91 0.13 0.00
40_A 54_A 0.91 0.13 0.00
100_F 30_K 0.91 0.13 0.00
235_T 41_E 0.90 0.13 0.00
181_V 34_M 0.89 0.12 0.00
104_A 28_G 0.88 0.12 0.00
50_L 35_F 0.88 0.12 0.00
235_T 40_N 0.87 0.12 0.00
244_P 33_Q 0.87 0.12 0.00
111_T 49_A 0.87 0.12 0.00
24_D 50_I 0.87 0.12 0.00
247_V 43_V 0.86 0.12 0.00
95_R 18_D 0.85 0.11 0.00
214_V 38_V 0.85 0.11 0.00
141_T 47_F 0.84 0.11 0.00
225_R 31_L 0.84 0.11 0.00
159_L 30_K 0.84 0.11 0.00
252_G 23_R 0.84 0.11 0.00
242_F 30_K 0.84 0.11 0.00
122_G 47_F 0.84 0.11 0.00
8_A 55_E 0.83 0.11 0.00
7_L 54_A 0.83 0.11 0.00
168_T 22_L 0.82 0.11 0.00
53_R 53_K 0.82 0.11 0.00
167_V 31_L 0.82 0.11 0.00
5_A 39_V 0.82 0.11 0.00
93_A 28_G 0.82 0.11 0.00
183_R 22_L 0.82 0.10 0.00
246_T 46_E 0.82 0.10 0.00
128_I 16_A 0.81 0.10 0.00
159_L 34_M 0.81 0.10 0.00
14_I 35_F 0.81 0.10 0.00
4_L 55_E 0.81 0.10 0.00
189_V 27_I 0.81 0.10 0.00
117_L 30_K 0.81 0.10 0.00
35_A 26_A 0.81 0.10 0.00
107_G 27_I 0.81 0.10 0.00
145_I 29_V 0.81 0.10 0.00
10_H 48_L 0.81 0.10 0.00
26_A 43_V 0.80 0.10 0.00
107_G 28_G 0.80 0.10 0.00
151_V 33_Q 0.79 0.10 0.00
155_D 25_Q 0.79 0.10 0.00
141_T 55_E 0.79 0.10 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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