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OPENSEQ.org
EnvZOmpR
Genes: A B A+B
Length: 450 239 670
Sequences: 2251 32166 1019
Seq/Len: 5 134.59 1.52
MirrorTree (Pazo et al. 2001) 0.57
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 0.00 0.01 1.28
2 0.00 0.02 1.29
5 0.00 0.04 1.33
10 0.00 0.06 1.40
20 0.01 0.09 1.48
100 0.01 0.19 2.03
∞ 0.12 0.24 2.92
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
250_T 16_L 2.38 1.00 0.98
254_L 19_L 1.58 0.90 0.80
258_M 23_Y 1.49 0.86 0.73
266_L 22_R 1.13 0.58 0.38
93_A 185_L 1.12 0.56 0.36
437_P 82_V 1.11 0.56 0.35
179_I 13_D 1.10 0.55 0.35
185_P 95_L 1.09 0.54 0.34
280_I 204_Q 1.09 0.54 0.34
346_V 80_I 1.08 0.53 0.33
272_K 15_R 1.08 0.52 0.32
170_L 181_S 1.05 0.50 0.30
246_R 203_V 1.05 0.49 0.29
80_I 24_L 1.04 0.48 0.28
258_M 13_D 1.02 0.47 0.27
249_L 223_Q 1.00 0.44 0.24
273_D 15_R 0.99 0.43 0.24
234_R 67_C 0.98 0.43 0.23
265_Y 18_A 0.98 0.43 0.23
122_V 126_E 0.97 0.42 0.22
218_R 53_V 0.96 0.41 0.21
257_E 108_N 0.96 0.40 0.21
228_K 205_I 0.93 0.37 0.19
276_E 152_M 0.92 0.36 0.18
277_C 37_A 0.92 0.36 0.18
101_W 185_L 0.92 0.36 0.18
249_L 178_E 0.91 0.36 0.18
344_M 79_I 0.91 0.36 0.17
402_T 53_V 0.89 0.34 0.16
164_T 144_K 0.89 0.34 0.16
189_L 140_F 0.89 0.33 0.16
280_I 168_V 0.88 0.33 0.16
137_T 103_I 0.88 0.33 0.15
164_T 222_I 0.88 0.33 0.15
257_E 88_E 0.88 0.32 0.15
251_R 13_D 0.88 0.32 0.15
416_H 51_L 0.87 0.32 0.15
80_I 39_Q 0.87 0.32 0.14
331_K 29_F 0.87 0.32 0.14
381_E 17_R 0.86 0.31 0.14
346_V 180_L 0.86 0.31 0.14
340_A 111_E 0.86 0.31 0.14
151_E 7_I 0.86 0.31 0.14
327_S 79_I 0.86 0.31 0.14
392_R 226_W 0.86 0.30 0.14
356_I 166_F 0.85 0.30 0.14
422_L 150_R 0.84 0.29 0.13
241_V 87_E 0.84 0.29 0.13
192_A 11_D 0.84 0.29 0.13
249_L 206_S 0.84 0.29 0.13
165_L 166_F 0.83 0.29 0.12
356_I 222_I 0.83 0.28 0.12
80_I 170_K 0.83 0.28 0.12
346_V 77_M 0.82 0.28 0.12
379_A 176_P 0.82 0.27 0.12
394_D 203_V 0.82 0.27 0.12
227_V 203_V 0.81 0.27 0.11
395_S 193_E 0.81 0.27 0.11
434_A 134_E 0.81 0.26 0.11
249_L 207_R 0.80 0.26 0.11
288_L 213_E 0.80 0.26 0.11
417_N 85_K 0.80 0.26 0.11
273_D 164_G 0.80 0.26 0.11
415_N 79_I 0.80 0.26 0.11
192_A 119_V 0.79 0.25 0.10
306_G 159_M 0.79 0.25 0.10
255_A 19_L 0.79 0.25 0.10
235_T 13_D 0.79 0.25 0.10
143_I 31_V 0.79 0.25 0.10
186_L 34_V 0.79 0.25 0.10
260_S 20_L 0.79 0.25 0.10
400_S 28_G 0.78 0.24 0.10
73_P 113_L 0.78 0.24 0.10
167_I 81_M 0.78 0.24 0.10
233_D 9_V 0.78 0.24 0.10
413_V 43_L 0.77 0.24 0.09
268_E 9_V 0.77 0.24 0.09
256_T 29_F 0.77 0.23 0.09
226_G 205_I 0.77 0.23 0.09
186_L 11_D 0.77 0.23 0.09
413_V 76_P 0.76 0.23 0.09
314_G 68_R 0.76 0.23 0.09
255_A 15_R 0.76 0.23 0.09
167_I 168_V 0.76 0.23 0.09
186_L 43_L 0.76 0.23 0.09
332_M 13_D 0.76 0.23 0.09
147_V 21_E 0.76 0.23 0.09
437_P 10_V 0.76 0.23 0.09
339_R 207_R 0.76 0.23 0.09
175_A 20_L 0.75 0.22 0.09
352_G 10_V 0.75 0.22 0.09
333_H 176_P 0.75 0.22 0.08
423_G 214_E 0.75 0.22 0.08
120_T 38_E 0.75 0.22 0.08
342_A 60_G 0.75 0.22 0.08
88_L 77_M 0.74 0.21 0.08
171_A 4_N 0.74 0.21 0.08
330_V 124_A 0.73 0.21 0.08
322_A 205_I 0.73 0.21 0.08
126_V 61_E 0.73 0.21 0.08
386_L 103_I 0.73 0.21 0.08
434_A 80_I 0.73 0.21 0.08
220_F 200_S 0.73 0.21 0.07
125_E 60_G 0.73 0.21 0.07
147_V 185_L 0.73 0.20 0.07
24_F 9_V 0.73 0.20 0.07
230_L 37_A 0.73 0.20 0.07
190_E 223_Q 0.73 0.20 0.07
338_K 20_L 0.72 0.20 0.07
122_V 159_M 0.72 0.20 0.07
185_P 44_L 0.72 0.20 0.07
379_A 39_Q 0.72 0.20 0.07
259_M 65_S 0.72 0.20 0.07
286_D 205_I 0.72 0.20 0.07
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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