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AM

Genes: A B A+B
Length: 451 169 588
Sequences: 7707 1254 307
Seq/Len: 17.09 7.42 0.52
MirrorTree (Pazo et al. 2001) 0.65
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 0.03 0.00 0.04
2 0.03 0.00 0.35
5 0.03 0.00 0.42
10 0.04 0.00 0.45
20 0.04 0.00 0.50
100 0.08 0.00 0.63
0.18 0.03 1.30
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
132_L 96_S 1.37 0.47 0.00
64_A 53_I 1.36 0.47 0.00
348_I 85_K 1.35 0.46 0.00
36_H 119_S 1.33 0.44 0.00
258_V 18_I 1.30 0.42 0.00
266_I 103_K 1.29 0.41 0.00
56_E 133_I 1.28 0.41 0.00
124_E 80_I 1.26 0.39 0.00
268_G 57_S 1.26 0.39 0.00
18_L 130_T 1.25 0.39 0.00
245_G 98_S 1.25 0.38 0.00
4_Y 123_T 1.23 0.37 0.00
426_A 82_Q 1.22 0.36 0.00
284_S 116_S 1.21 0.35 0.00
73_V 70_P 1.20 0.34 0.00
332_I 84_T 1.19 0.34 0.00
349_Q 97_D 1.19 0.34 0.00
178_I 39_F 1.18 0.33 0.00
344_L 113_V 1.18 0.33 0.00
351_A 60_S 1.17 0.33 0.00
29_Y 56_D 1.16 0.32 0.00
403_M 55_M 1.14 0.31 0.00
28_R 44_G 1.13 0.30 0.00
14_A 43_T 1.12 0.29 0.00
179_A 38_V 1.10 0.28 0.00
47_V 65_I 1.10 0.28 0.00
392_V 124_V 1.09 0.27 0.00
71_A 118_V 1.08 0.27 0.00
239_L 141_L 1.07 0.26 0.00
134_D 130_T 1.07 0.26 0.00
53_V 69_I 1.05 0.25 0.00
291_G 130_T 1.04 0.25 0.00
30_G 71_N 1.04 0.24 0.00
220_S 66_N 1.03 0.24 0.00
426_A 20_S 1.03 0.24 0.00
357_T 57_S 1.02 0.23 0.00
298_Q 124_V 1.01 0.23 0.00
435_F 90_A 1.01 0.23 0.00
380_V 78_A 1.01 0.23 0.00
298_Q 56_D 1.00 0.22 0.00
158_A 32_R 1.00 0.22 0.00
265_F 63_L 0.99 0.22 0.00
426_A 38_V 0.99 0.22 0.00
127_N 85_K 0.99 0.22 0.00
201_D 18_I 0.99 0.22 0.00
31_G 28_M 0.99 0.22 0.00
282_I 29_A 0.99 0.21 0.00
257_I 86_I 0.98 0.21 0.00
332_I 133_I 0.98 0.21 0.00
357_T 28_M 0.98 0.21 0.00
30_G 66_N 0.98 0.21 0.00
179_A 133_I 0.97 0.21 0.00
420_V 71_N 0.97 0.20 0.00
31_G 123_T 0.97 0.20 0.00
259_D 65_I 0.96 0.20 0.00
306_T 40_E 0.96 0.20 0.00
248_I 79_M 0.96 0.20 0.00
360_S 57_S 0.95 0.20 0.00
323_N 31_R 0.95 0.20 0.00
45_V 96_S 0.95 0.20 0.00
249_I 50_E 0.95 0.20 0.00
48_G 84_T 0.95 0.20 0.00
235_S 79_M 0.95 0.19 0.00
426_A 28_M 0.94 0.19 0.00
420_V 118_V 0.94 0.19 0.00
344_L 96_S 0.93 0.18 0.00
190_L 123_T 0.92 0.18 0.00
409_I 67_V 0.92 0.18 0.00
217_K 146_S 0.92 0.18 0.00
148_I 87_A 0.92 0.18 0.00
115_G 96_S 0.92 0.18 0.00
176_L 124_V 0.92 0.18 0.00
48_G 133_I 0.91 0.18 0.00
282_I 146_S 0.91 0.18 0.00
314_V 101_I 0.91 0.18 0.00
24_F 130_T 0.91 0.17 0.00
220_S 72_T 0.91 0.17 0.00
178_I 156_E 0.91 0.17 0.00
269_Q 157_H 0.90 0.17 0.00
323_N 101_I 0.90 0.17 0.00
345_L 158_W 0.90 0.17 0.00
428_T 123_T 0.90 0.17 0.00
218_C 20_S 0.90 0.17 0.00
424_V 69_I 0.90 0.17 0.00
108_D 152_E 0.89 0.17 0.00
195_F 112_A 0.89 0.17 0.00
418_P 85_K 0.89 0.17 0.00
49_R 97_D 0.89 0.17 0.00
317_M 63_L 0.89 0.17 0.00
220_S 118_V 0.89 0.17 0.00
21_E 112_A 0.89 0.17 0.00
227_A 135_V 0.88 0.17 0.00
323_N 23_K 0.88 0.17 0.00
265_F 38_V 0.88 0.17 0.00
73_V 33_I 0.88 0.16 0.00
235_S 89_A 0.88 0.16 0.00
178_I 59_I 0.88 0.16 0.00
235_S 70_P 0.88 0.16 0.00
422_V 152_E 0.88 0.16 0.00
184_N 160_G 0.88 0.16 0.00
379_R 46_Q 0.88 0.16 0.00
38_K 133_I 0.87 0.16 0.00
68_S 44_G 0.87 0.16 0.00
47_V 91_S 0.87 0.16 0.00
292_F 24_A 0.87 0.16 0.00
301_I 92_Y 0.87 0.16 0.00
191_A 102_S 0.87 0.16 0.00
58_L 130_T 0.87 0.16 0.00
206_G 33_I 0.86 0.16 0.00
58_L 66_N 0.86 0.16 0.00
28_R 57_S 0.86 0.16 0.00
145_G 43_T 0.86 0.16 0.00
239_L 103_K 0.86 0.15 0.00
378_V 21_V 0.86 0.15 0.00
57_M 66_N 0.86 0.15 0.00
98_M 38_V 0.86 0.15 0.00
245_G 115_I 0.86 0.15 0.00
47_V 40_E 0.85 0.15 0.00
47_V 146_S 0.85 0.15 0.00
83_G 82_Q 0.85 0.15 0.00
432_A 28_M 0.85 0.15 0.00
205_I 80_I 0.85 0.15 0.00
221_T 66_N 0.85 0.15 0.00
47_V 58_N 0.85 0.15 0.00
267_I 157_H 0.85 0.15 0.00
268_G 29_A 0.84 0.15 0.00
360_S 25_V 0.84 0.15 0.00
87_L 72_T 0.84 0.15 0.00
248_I 99_P 0.84 0.15 0.00
413_P 51_T 0.84 0.15 0.00
269_Q 39_F 0.84 0.15 0.00
176_L 37_I 0.84 0.15 0.00
422_V 45_L 0.84 0.15 0.00
249_I 33_I 0.84 0.15 0.00
351_A 39_F 0.83 0.14 0.00
435_F 28_M 0.83 0.14 0.00
44_R 85_K 0.83 0.14 0.00
180_L 140_K 0.83 0.14 0.00
250_A 92_Y 0.83 0.14 0.00
134_D 123_T 0.82 0.14 0.00
306_T 52_G 0.82 0.14 0.00
4_Y 92_Y 0.82 0.14 0.00
344_L 119_S 0.82 0.14 0.00
290_L 87_A 0.82 0.14 0.00
187_T 33_I 0.82 0.14 0.00
290_L 135_V 0.82 0.14 0.00
84_V 72_T 0.82 0.14 0.00
155_F 28_M 0.82 0.14 0.00
320_G 18_I 0.82 0.14 0.00
391_D 118_V 0.82 0.14 0.00
184_N 14_E 0.82 0.14 0.00
351_A 21_V 0.82 0.14 0.00
284_S 39_F 0.82 0.14 0.00
88_T 40_E 0.81 0.14 0.00
88_T 91_S 0.81 0.14 0.00
10_V 118_V 0.81 0.14 0.00
195_F 21_V 0.81 0.14 0.00
28_R 130_T 0.81 0.14 0.00
13_V 143_R 0.81 0.13 0.00
221_T 72_T 0.81 0.13 0.00
432_A 38_V 0.81 0.13 0.00
296_L 130_T 0.81 0.13 0.00
394_E 60_S 0.81 0.13 0.00
46_L 151_E 0.80 0.13 0.00
122_S 144_D 0.80 0.13 0.00
365_A 20_S 0.80 0.13 0.00
346_T 121_A 0.80 0.13 0.00
34_L 18_I 0.80 0.13 0.00
31_G 112_A 0.80 0.13 0.00
182_G 91_S 0.80 0.13 0.00
196_G 124_V 0.80 0.13 0.00
401_V 15_E 0.80 0.13 0.00
87_L 66_N 0.80 0.13 0.00
241_F 63_L 0.80 0.13 0.00
131_A 57_S 0.79 0.13 0.00
413_P 43_T 0.79 0.13 0.00
299_E 16_K 0.79 0.13 0.00
264_M 30_K 0.79 0.13 0.00
162_L 90_A 0.79 0.13 0.00
196_G 112_A 0.79 0.13 0.00
305_K 145_I 0.79 0.13 0.00
307_K 61_Q 0.79 0.13 0.00
22_L 66_N 0.79 0.13 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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