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OPENSEQ.org
tolB_pal
Genes: A B A+B
Length: 430 173 588
Sequences: 1116 1521 793
Seq/Len: 2.6 8.79 1.35
MirrorTree (Pazo et al. 2001) 0.79
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 0.07 0.01 1.26
2 0.07 0.01 1.27
5 0.07 0.01 1.31
10 0.07 0.01 1.31
20 0.07 0.02 1.32
100 0.07 0.03 1.32
∞ 0.08 0.10 1.44
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
261_A 150_K 1.63 0.90 0.33
335_Q 114_T 1.35 0.74 0.16
404_V 21_A 1.34 0.74 0.16
238_Q 146_V 1.32 0.72 0.15
247_G 119_I 1.30 0.70 0.14
423_F 115_P 1.29 0.69 0.13
272_V 83_D 1.28 0.69 0.13
298_D 145_I 1.22 0.63 0.11
405_S 91_H 1.20 0.61 0.10
248_A 164_S 1.18 0.59 0.09
170_V 77_K 1.14 0.55 0.08
291_T 129_V 1.13 0.54 0.08
325_Q 164_S 1.12 0.54 0.08
200_Q 152_K 1.12 0.53 0.08
14_L 128_A 1.09 0.50 0.07
124_A 15_P 1.08 0.49 0.07
391_Y 129_V 1.08 0.49 0.07
262_L 168_R 1.07 0.48 0.07
81_G 71_V 1.07 0.48 0.07
203_M 119_I 1.05 0.46 0.06
382_L 108_H 1.04 0.45 0.06
104_V 19_I 1.03 0.44 0.06
314_V 139_S 1.02 0.43 0.06
256_S 102_K 1.02 0.43 0.06
303_A 75_L 1.02 0.43 0.05
297_P 19_I 1.02 0.43 0.05
283_V 165_K 1.02 0.43 0.05
399_S 115_P 1.00 0.41 0.05
172_Q 115_P 1.00 0.41 0.05
269_N 123_E 1.00 0.41 0.05
167_I 148_Y 0.99 0.40 0.05
112_Y 148_Y 0.98 0.40 0.05
169_Y 173_Y 0.98 0.39 0.05
27_I 128_A 0.97 0.39 0.04
114_V 18_A 0.97 0.39 0.04
202_L 172_V 0.97 0.38 0.04
239_V 134_Q 0.97 0.38 0.04
152_V 158_H 0.97 0.38 0.04
347_V 20_A 0.96 0.38 0.04
420_Q 103_V 0.95 0.37 0.04
43_Q 104_T 0.95 0.36 0.04
288_S 138_V 0.94 0.35 0.04
236_V 130_K 0.93 0.34 0.04
55_G 109_A 0.93 0.34 0.04
366_G 92_A 0.92 0.34 0.04
389_V 104_T 0.92 0.34 0.04
372_S 98_N 0.92 0.34 0.04
141_L 141_D 0.92 0.33 0.04
214_L 55_E 0.92 0.33 0.04
71_L 169_A 0.91 0.33 0.04
115_A 163_Y 0.91 0.33 0.04
195_V 80_I 0.91 0.33 0.04
326_R 123_E 0.91 0.33 0.04
368_V 150_K 0.91 0.32 0.04
366_G 162_A 0.90 0.32 0.03
154_E 74_D 0.90 0.32 0.03
241_S 155_V 0.90 0.32 0.03
360_K 165_K 0.89 0.31 0.03
103_Q 155_V 0.89 0.31 0.03
10_G 148_Y 0.89 0.31 0.03
263_S 123_E 0.89 0.31 0.03
401_L 138_V 0.89 0.31 0.03
295_W 123_E 0.88 0.30 0.03
382_L 132_Y 0.88 0.30 0.03
218_T 127_N 0.88 0.30 0.03
41_P 105_V 0.88 0.30 0.03
403_L 115_P 0.88 0.30 0.03
274_D 128_A 0.88 0.30 0.03
389_V 7_L 0.88 0.30 0.03
165_T 143_I 0.87 0.30 0.03
235_A 160_E 0.87 0.30 0.03
70_P 170_V 0.87 0.30 0.03
154_E 76_D 0.87 0.29 0.03
61_D 158_H 0.87 0.29 0.03
267_S 145_I 0.87 0.29 0.03
375_F 163_Y 0.87 0.29 0.03
248_A 139_S 0.87 0.29 0.03
236_V 129_V 0.86 0.29 0.03
110_G 20_A 0.86 0.29 0.03
110_G 143_I 0.86 0.29 0.03
260_F 108_H 0.86 0.29 0.03
27_I 159_D 0.86 0.29 0.03
257_K 154_A 0.86 0.28 0.03
193_F 99_P 0.85 0.28 0.03
127_T 83_D 0.85 0.28 0.03
174_N 164_S 0.85 0.28 0.03
427_S 132_Y 0.85 0.28 0.03
382_L 71_V 0.85 0.28 0.03
394_S 161_A 0.85 0.28 0.03
282_Q 71_V 0.85 0.27 0.03
101_V 72_Y 0.85 0.27 0.03
201_P 173_Y 0.84 0.27 0.03
245_H 119_I 0.84 0.27 0.03
19_L 128_A 0.84 0.27 0.03
268_L 172_V 0.84 0.27 0.03
114_V 51_N 0.84 0.27 0.03
430_L 27_N 0.84 0.27 0.03
239_V 148_Y 0.84 0.27 0.03
226_L 72_Y 0.84 0.27 0.03
267_S 123_E 0.84 0.27 0.03
189_G 112_R 0.84 0.27 0.03
229_Q 129_V 0.83 0.27 0.03
424_P 123_E 0.83 0.27 0.03
52_E 169_A 0.83 0.26 0.03
342_D 91_H 0.83 0.26 0.03
288_S 163_Y 0.83 0.26 0.03
54_I 95_L 0.83 0.26 0.03
358_I 106_E 0.83 0.26 0.03
362_D 158_H 0.82 0.26 0.03
340_S 165_K 0.82 0.26 0.03
106_P 138_V 0.82 0.26 0.03
191_N 71_V 0.82 0.26 0.03
288_S 131_M 0.82 0.26 0.03
95_G 163_Y 0.82 0.26 0.03
94_L 145_I 0.82 0.26 0.02
112_Y 16_V 0.82 0.26 0.02
402_N 138_V 0.81 0.25 0.02
25_I 150_K 0.81 0.25 0.02
231_L 52_M 0.81 0.25 0.02
305_T 91_H 0.81 0.25 0.02
25_I 104_T 0.81 0.25 0.02
259_A 140_A 0.81 0.25 0.02
142_R 151_E 0.81 0.24 0.02
73_R 26_K 0.81 0.24 0.02
121_T 143_I 0.81 0.24 0.02
24_R 21_A 0.81 0.24 0.02
201_P 119_I 0.81 0.24 0.02
121_T 47_G 0.80 0.24 0.02
65_S 90_A 0.80 0.24 0.02
315_Y 115_P 0.80 0.24 0.02
161_G 87_M 0.80 0.24 0.02
156_L 55_E 0.80 0.24 0.02
374_T 154_A 0.80 0.24 0.02
401_L 109_A 0.80 0.24 0.02
414_L 128_A 0.80 0.24 0.02
29_S 21_A 0.80 0.23 0.02
45_A 143_I 0.79 0.23 0.02
39_V 51_N 0.79 0.23 0.02
328_T 101_Y 0.79 0.23 0.02
214_L 131_M 0.79 0.23 0.02
335_Q 123_E 0.79 0.23 0.02
57_I 38_G 0.79 0.23 0.02
160_K 159_D 0.79 0.23 0.02
286_G 74_D 0.79 0.23 0.02
136_V 80_I 0.79 0.23 0.02
265_T 127_N 0.79 0.23 0.02
222_G 142_Q 0.79 0.23 0.02
170_V 98_N 0.78 0.23 0.02
281_R 141_D 0.78 0.23 0.02
214_L 159_D 0.78 0.23 0.02
96_I 86_Q 0.78 0.23 0.02
188_D 151_E 0.78 0.22 0.02
420_Q 123_E 0.78 0.22 0.02
291_T 116_E 0.78 0.22 0.02
61_D 103_V 0.78 0.22 0.02
239_V 93_N 0.78 0.22 0.02
169_Y 138_V 0.77 0.22 0.02
170_V 146_V 0.77 0.22 0.02
270_L 131_M 0.77 0.22 0.02
54_I 43_M 0.77 0.22 0.02
251_F 140_A 0.77 0.22 0.02
65_S 79_D 0.77 0.22 0.02
242_F 144_S 0.77 0.22 0.02
375_F 158_H 0.77 0.22 0.02
16_A 10_L 0.77 0.22 0.02
13_I 93_N 0.77 0.22 0.02
25_I 72_Y 0.77 0.22 0.02
37_I 104_T 0.77 0.22 0.02
269_N 131_M 0.77 0.22 0.02
146_H 129_V 0.77 0.21 0.02
157_T 132_Y 0.77 0.21 0.02
190_Y 162_A 0.77 0.21 0.02
180_Y 152_K 0.77 0.21 0.02
347_V 150_K 0.76 0.21 0.02
402_N 92_A 0.76 0.21 0.02
311_R 43_M 0.76 0.21 0.02
295_W 97_S 0.76 0.21 0.02
382_L 109_A 0.76 0.21 0.02
320_N 34_E 0.76 0.21 0.02
389_V 140_A 0.76 0.21 0.02
383_A 139_S 0.76 0.21 0.02
26_V 74_D 0.76 0.21 0.02
203_M 123_E 0.76 0.21 0.02
204_S 75_L 0.76 0.21 0.02
18_V 100_S 0.76 0.21 0.02
170_V 33_S 0.76 0.21 0.02
95_G 162_A 0.76 0.21 0.02
247_G 123_E 0.76 0.21 0.02
230_T 159_D 0.76 0.21 0.02
299_S 151_E 0.76 0.21 0.02
393_S 18_A 0.76 0.21 0.02
161_G 112_R 0.76 0.21 0.02
372_S 92_A 0.76 0.21 0.02
425_A 132_Y 0.75 0.21 0.02
393_S 158_H 0.75 0.21 0.02
372_S 33_S 0.75 0.21 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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