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OPENSEQ.org
5K98
Genes: A B A+B
Length: 340 88 407
Sequences: 1875 22435 267
Seq/Len: 5.51 254.94 0.66
MirrorTree (Pazo et al. 2001) 0.75
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 0.01 0.06 0.62
2 0.02 0.07 0.65
5 0.03 0.09 0.72
10 0.04 0.11 0.77
20 0.05 0.12 0.91
100 0.07 0.18 1.42
∞ 0.12 0.23 2.64
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
181_F 59_K 1.35 0.52 0.00
16_L 41_T 1.22 0.42 0.00
294_D 66_L 1.22 0.42 0.00
58_F 64_L 1.16 0.37 0.00
94_G 28_Q 1.12 0.34 0.00
156_C 16_A 1.10 0.33 0.00
331_G 83_Q 1.09 0.32 0.00
38_A 36_G 1.08 0.31 0.00
137_P 48_N 1.07 0.30 0.00
216_S 76_A 1.06 0.30 0.00
46_P 37_I 1.05 0.29 0.00
280_V 75_N 1.05 0.29 0.00
59_N 35_I 1.03 0.28 0.00
92_E 44_N 1.03 0.28 0.00
295_F 17_M 1.03 0.28 0.00
192_R 18_K 1.02 0.27 0.00
274_F 41_T 1.01 0.26 0.00
26_F 20_V 1.00 0.26 0.00
59_N 58_F 1.00 0.26 0.00
61_F 60_I 1.00 0.26 0.00
275_L 27_T 1.00 0.26 0.00
153_E 44_N 0.98 0.24 0.00
66_P 21_R 0.98 0.24 0.00
99_G 21_R 0.98 0.24 0.00
80_H 31_L 0.98 0.24 0.00
141_I 41_T 0.97 0.24 0.00
21_N 42_I 0.97 0.24 0.00
226_R 70_L 0.95 0.23 0.00
137_P 61_L 0.95 0.23 0.00
87_F 64_L 0.95 0.23 0.00
256_L 78_P 0.95 0.23 0.00
118_E 45_F 0.95 0.23 0.00
171_G 42_I 0.94 0.22 0.00
35_S 70_L 0.93 0.22 0.00
274_F 42_I 0.93 0.21 0.00
140_M 21_R 0.93 0.21 0.00
142_R 21_R 0.93 0.21 0.00
216_S 24_N 0.92 0.21 0.00
12_R 30_E 0.92 0.21 0.00
196_M 54_L 0.91 0.21 0.00
41_L 32_A 0.91 0.21 0.00
75_I 39_Q 0.91 0.20 0.00
131_A 55_T 0.90 0.20 0.00
229_P 21_R 0.90 0.20 0.00
216_S 47_N 0.90 0.20 0.00
279_K 65_E 0.89 0.20 0.00
211_H 21_R 0.89 0.20 0.00
232_D 21_R 0.89 0.20 0.00
231_Y 46_E 0.89 0.19 0.00
256_L 18_K 0.89 0.19 0.00
149_I 58_F 0.89 0.19 0.00
291_I 31_L 0.88 0.19 0.00
133_K 18_K 0.88 0.19 0.00
270_Y 15_N 0.88 0.19 0.00
161_L 22_Q 0.88 0.19 0.00
219_I 27_T 0.88 0.19 0.00
63_N 41_T 0.88 0.19 0.00
316_E 17_M 0.88 0.19 0.00
207_A 41_T 0.87 0.19 0.00
182_L 37_I 0.87 0.19 0.00
152_Q 37_I 0.87 0.18 0.00
233_I 41_T 0.87 0.18 0.00
201_F 8_Y 0.86 0.18 0.00
171_G 71_C 0.86 0.18 0.00
141_I 49_P 0.86 0.18 0.00
33_L 51_N 0.86 0.18 0.00
214_N 21_R 0.86 0.18 0.00
156_C 50_D 0.86 0.18 0.00
54_S 13_L 0.86 0.18 0.00
81_A 10_P 0.85 0.17 0.00
293_S 65_E 0.85 0.17 0.00
212_A 40_A 0.84 0.17 0.00
212_A 68_M 0.84 0.17 0.00
234_I 39_Q 0.84 0.17 0.00
85_Q 22_Q 0.84 0.17 0.00
289_H 11_T 0.84 0.17 0.00
275_L 47_N 0.83 0.17 0.00
184_G 58_F 0.83 0.17 0.00
59_N 43_S 0.83 0.16 0.00
199_Q 42_I 0.82 0.16 0.00
252_L 16_A 0.82 0.16 0.00
74_R 45_F 0.82 0.16 0.00
183_M 67_S 0.82 0.16 0.00
22_G 30_E 0.82 0.16 0.00
194_D 35_I 0.82 0.16 0.00
106_E 77_S 0.81 0.16 0.00
292_L 16_A 0.81 0.16 0.00
41_L 64_L 0.81 0.16 0.00
185_S 26_W 0.81 0.15 0.00
26_F 24_N 0.80 0.15 0.00
180_A 27_T 0.80 0.15 0.00
87_F 65_E 0.80 0.15 0.00
32_W 39_Q 0.80 0.15 0.00
151_P 52_T 0.80 0.15 0.00
45_L 65_E 0.79 0.15 0.00
103_L 28_Q 0.79 0.15 0.00
21_N 65_E 0.79 0.15 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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