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OPENSEQ.org
MurGRodA
Genes: A B A+B
Length: 393 363 718
Sequences: 3562 10854 1282
Seq/Len: 9.06 29.9 1.79
MirrorTree (Pazo et al. 2001) 0.68
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 0.01 0.08 1.63
2 0.01 0.09 1.65
5 0.01 0.11 1.66
10 0.02 0.11 1.67
20 0.02 0.11 1.70
100 0.05 0.13 1.99
∞ 0.14 0.20 2.76
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
176_F 136_K 1.18 0.68 0.01
334_I 40_N 1.00 0.50 0.01
330_Y 278_L 0.98 0.46 0.01
312_L 86_S 0.96 0.44 0.00
168_A 57_I 0.94 0.42 0.00
157_V 232_M 0.94 0.42 0.00
86_I 90_E 0.93 0.41 0.00
352_T 17_A 0.92 0.41 0.00
104_S 165_A 0.91 0.39 0.00
282_I 189_V 0.90 0.38 0.00
19_I 17_A 0.90 0.38 0.00
364_S 130_T 0.88 0.37 0.00
50_V 340_E 0.87 0.35 0.00
86_I 86_S 0.87 0.35 0.00
359_V 267_A 0.87 0.35 0.00
190_K 340_E 0.86 0.34 0.00
26_I 325_L 0.85 0.34 0.00
116_S 160_T 0.85 0.33 0.00
341_N 281_P 0.85 0.33 0.00
354_I 99_T 0.85 0.33 0.00
372_G 350_A 0.83 0.32 0.00
364_S 119_I 0.83 0.31 0.00
102_A 116_I 0.82 0.31 0.00
324_S 3_I 0.82 0.31 0.00
113_I 203_R 0.82 0.30 0.00
299_V 273_A 0.82 0.30 0.00
272_V 108_V 0.82 0.30 0.00
292_F 59_I 0.81 0.30 0.00
376_V 341_R 0.81 0.29 0.00
334_I 46_I 0.80 0.29 0.00
334_I 88_L 0.80 0.29 0.00
365_S 120_V 0.80 0.29 0.00
126_M 38_T 0.79 0.28 0.00
70_L 315_E 0.79 0.28 0.00
366_T 33_F 0.79 0.28 0.00
352_T 222_I 0.78 0.27 0.00
225_Y 17_A 0.78 0.27 0.00
161_G 53_P 0.78 0.27 0.00
164_L 358_L 0.78 0.27 0.00
104_S 11_G 0.78 0.27 0.00
352_T 188_T 0.78 0.27 0.00
62_L 133_F 0.78 0.27 0.00
335_V 281_P 0.78 0.27 0.00
312_L 316_L 0.78 0.27 0.00
118_F 283_V 0.77 0.26 0.00
25_I 317_S 0.77 0.26 0.00
61_V 86_S 0.77 0.26 0.00
305_L 156_K 0.77 0.26 0.00
202_L 205_V 0.77 0.26 0.00
183_F 168_V 0.77 0.26 0.00
293_I 78_L 0.77 0.26 0.00
257_I 250_L 0.76 0.26 0.00
107_R 5_I 0.76 0.25 0.00
65_F 327_R 0.76 0.25 0.00
189_W 120_V 0.76 0.25 0.00
284_S 281_P 0.75 0.25 0.00
358_F 192_F 0.75 0.25 0.00
302_F 41_G 0.75 0.25 0.00
286_I 345_L 0.75 0.25 0.00
376_V 273_A 0.75 0.24 0.00
78_F 189_V 0.74 0.24 0.00
161_G 233_N 0.74 0.24 0.00
355_P 49_R 0.73 0.23 0.00
351_V 188_T 0.73 0.23 0.00
316_I 310_V 0.73 0.23 0.00
256_A 321_L 0.73 0.23 0.00
344_M 287_S 0.73 0.23 0.00
86_I 82_K 0.73 0.23 0.00
300_I 356_S 0.72 0.22 0.00
86_I 78_L 0.72 0.22 0.00
87_I 52_I 0.72 0.22 0.00
200_I 86_S 0.72 0.22 0.00
245_N 328_I 0.72 0.22 0.00
340_Q 247_K 0.72 0.22 0.00
118_F 76_R 0.71 0.22 0.00
119_M 3_I 0.71 0.22 0.00
245_N 120_V 0.71 0.22 0.00
69_Q 205_V 0.71 0.22 0.00
307_Y 79_K 0.71 0.21 0.00
309_L 273_A 0.71 0.21 0.00
374_G 6_S 0.71 0.21 0.00
298_V 248_P 0.70 0.21 0.00
166_Q 291_T 0.70 0.21 0.00
371_I 59_I 0.70 0.21 0.00
60_T 352_A 0.70 0.21 0.00
173_I 196_R 0.70 0.20 0.00
222_I 114_M 0.70 0.20 0.00
351_V 292_A 0.70 0.20 0.00
354_I 257_L 0.69 0.20 0.00
255_M 222_I 0.69 0.20 0.00
79_I 360_E 0.69 0.20 0.00
104_S 290_V 0.69 0.20 0.00
302_F 277_A 0.69 0.20 0.00
308_R 222_I 0.69 0.20 0.00
78_F 169_V 0.69 0.20 0.00
257_I 70_N 0.69 0.20 0.00
60_T 53_P 0.69 0.20 0.00
65_F 265_A 0.69 0.20 0.00
334_I 280_I 0.69 0.20 0.00
364_S 31_V 0.69 0.20 0.00
253_A 219_V 0.69 0.20 0.00
327_C 102_Y 0.69 0.20 0.00
21_G 3_I 0.69 0.20 0.00
108_I 353_R 0.69 0.20 0.00
106_F 171_I 0.69 0.20 0.00
375_I 247_K 0.69 0.20 0.00
270_L 218_Q 0.69 0.20 0.00
355_P 15_Y 0.68 0.20 0.00
185_S 14_I 0.68 0.20 0.00
120_K 311_L 0.68 0.19 0.00
122_G 120_V 0.68 0.19 0.00
292_F 234_E 0.68 0.19 0.00
182_V 142_A 0.68 0.19 0.00
47_Q 102_Y 0.68 0.19 0.00
308_R 105_G 0.68 0.19 0.00
373_F 287_S 0.68 0.19 0.00
329_G 160_T 0.68 0.19 0.00
157_V 203_R 0.68 0.19 0.00
185_S 42_L 0.68 0.19 0.00
61_V 158_V 0.67 0.19 0.00
102_A 289_Y 0.67 0.19 0.00
272_V 290_V 0.67 0.19 0.00
358_F 31_V 0.67 0.19 0.00
284_S 218_Q 0.67 0.19 0.00
36_Q 142_A 0.67 0.19 0.00
265_N 46_I 0.67 0.19 0.00
48_Q 42_L 0.67 0.19 0.00
373_F 141_V 0.67 0.19 0.00
351_V 7_G 0.67 0.19 0.00
170_T 52_I 0.67 0.19 0.00
305_L 250_L 0.67 0.18 0.00
339_F 116_I 0.67 0.18 0.00
343_G 299_A 0.67 0.18 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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