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OPENSEQ.org
MurG-RodA (Bs)
Genes: A B A+B
Length: 363 393 718
Sequences: 10854 3562 1280
Seq/Len: 29.9 9.06 1.78
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 0.08 0.01 1.63
2 0.09 0.01 1.65
5 0.11 0.01 1.66
10 0.11 0.02 1.68
20 0.11 0.02 1.69
100 0.13 0.05 1.99
∞ 0.20 0.14 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
136_K 176_F 1.20 0.69 0.01
86_S 312_L 0.99 0.48 0.01
40_N 334_I 0.98 0.47 0.01
278_L 330_Y 0.98 0.46 0.01
86_S 86_I 0.96 0.45 0.01
57_I 168_A 0.94 0.42 0.01
17_A 352_T 0.93 0.41 0.01
165_A 104_S 0.91 0.40 0.01
17_A 19_I 0.89 0.38 0.00
130_T 364_S 0.89 0.37 0.00
53_P 161_G 0.89 0.37 0.00
120_V 365_S 0.88 0.36 0.00
189_V 282_I 0.87 0.35 0.00
267_A 359_V 0.87 0.35 0.00
116_I 102_A 0.86 0.34 0.00
160_T 116_S 0.86 0.34 0.00
99_T 354_I 0.85 0.33 0.00
203_R 113_I 0.85 0.33 0.00
281_P 341_N 0.84 0.33 0.00
340_E 190_K 0.84 0.32 0.00
340_E 50_V 0.84 0.32 0.00
232_M 157_V 0.84 0.32 0.00
119_I 364_S 0.84 0.32 0.00
341_R 376_V 0.84 0.32 0.00
273_A 299_V 0.84 0.32 0.00
350_A 372_G 0.83 0.32 0.00
325_L 26_I 0.82 0.31 0.00
108_V 272_V 0.82 0.30 0.00
59_I 292_F 0.81 0.30 0.00
33_F 366_T 0.81 0.30 0.00
3_I 324_S 0.81 0.30 0.00
222_I 352_T 0.81 0.29 0.00
88_L 334_I 0.81 0.29 0.00
46_I 334_I 0.81 0.29 0.00
315_E 70_L 0.80 0.29 0.00
11_G 104_S 0.79 0.28 0.00
17_A 225_Y 0.79 0.28 0.00
90_E 86_I 0.79 0.28 0.00
283_V 118_F 0.79 0.28 0.00
188_T 352_T 0.79 0.28 0.00
199_A 81_G 0.79 0.28 0.00
345_L 286_I 0.79 0.28 0.00
38_T 126_M 0.78 0.27 0.00
168_V 183_F 0.78 0.27 0.00
247_K 340_Q 0.77 0.26 0.00
273_A 376_V 0.76 0.25 0.00
247_K 375_I 0.76 0.25 0.00
250_L 257_I 0.76 0.25 0.00
281_P 335_V 0.76 0.25 0.00
358_L 164_L 0.75 0.25 0.00
76_R 118_F 0.75 0.25 0.00
192_F 358_F 0.75 0.25 0.00
141_V 373_F 0.75 0.25 0.00
156_K 305_L 0.75 0.25 0.00
133_F 62_L 0.75 0.24 0.00
337_E 50_V 0.74 0.24 0.00
78_L 293_I 0.74 0.23 0.00
327_R 65_F 0.74 0.23 0.00
316_L 312_L 0.74 0.23 0.00
360_E 79_I 0.73 0.23 0.00
120_V 189_W 0.73 0.23 0.00
310_V 316_I 0.73 0.23 0.00
52_I 87_I 0.73 0.23 0.00
41_G 302_F 0.73 0.23 0.00
321_L 256_A 0.73 0.23 0.00
353_R 108_I 0.73 0.23 0.00
287_S 344_M 0.73 0.23 0.00
3_I 21_G 0.73 0.23 0.00
53_P 60_T 0.73 0.23 0.00
289_Y 102_A 0.73 0.23 0.00
189_V 78_F 0.72 0.23 0.00
188_T 351_V 0.72 0.22 0.00
233_N 200_I 0.72 0.22 0.00
205_V 202_L 0.72 0.22 0.00
317_S 25_I 0.72 0.22 0.00
169_V 78_F 0.72 0.22 0.00
281_P 284_S 0.72 0.22 0.00
222_I 255_M 0.71 0.22 0.00
49_R 355_P 0.71 0.22 0.00
233_N 161_G 0.71 0.22 0.00
205_V 69_Q 0.71 0.22 0.00
328_I 245_N 0.71 0.21 0.00
291_T 166_Q 0.71 0.21 0.00
79_K 307_Y 0.71 0.21 0.00
86_S 61_V 0.71 0.21 0.00
290_V 104_S 0.71 0.21 0.00
114_M 222_I 0.71 0.21 0.00
248_P 298_V 0.71 0.21 0.00
6_S 374_G 0.70 0.21 0.00
196_R 173_I 0.70 0.21 0.00
273_A 309_L 0.70 0.21 0.00
332_E 76_Y 0.70 0.21 0.00
104_C 367_L 0.70 0.21 0.00
222_I 308_R 0.70 0.20 0.00
102_Y 327_C 0.70 0.20 0.00
277_A 302_F 0.70 0.20 0.00
31_V 364_S 0.69 0.20 0.00
5_I 107_R 0.69 0.20 0.00
120_V 245_N 0.69 0.20 0.00
352_A 60_T 0.69 0.20 0.00
70_N 257_I 0.69 0.20 0.00
15_Y 355_P 0.69 0.20 0.00
292_A 351_V 0.69 0.20 0.00
257_L 354_I 0.69 0.20 0.00
189_V 72_K 0.69 0.20 0.00
142_A 182_V 0.69 0.20 0.00
280_I 334_I 0.69 0.20 0.00
113_K 26_I 0.69 0.20 0.00
265_A 65_F 0.69 0.20 0.00
78_L 86_I 0.69 0.20 0.00
3_I 119_M 0.68 0.20 0.00
234_E 172_G 0.68 0.20 0.00
190_L 131_I 0.68 0.20 0.00
105_G 308_R 0.68 0.19 0.00
287_S 373_F 0.68 0.19 0.00
14_I 185_S 0.68 0.19 0.00
52_I 170_T 0.68 0.19 0.00
341_R 292_F 0.68 0.19 0.00
219_V 253_A 0.68 0.19 0.00
52_I 106_F 0.68 0.19 0.00
103_V 116_S 0.68 0.19 0.00
120_V 122_G 0.68 0.19 0.00
126_L 169_G 0.67 0.19 0.00
46_I 265_N 0.67 0.19 0.00
356_S 300_I 0.67 0.19 0.00
42_L 48_Q 0.67 0.19 0.00
109_Y 338_T 0.67 0.19 0.00
86_S 200_I 0.67 0.19 0.00
290_V 272_V 0.67 0.19 0.00
102_Y 47_Q 0.67 0.19 0.00
218_Q 284_S 0.67 0.19 0.00
3_I 121_V 0.67 0.18 0.00
263_I 306_I 0.67 0.18 0.00
160_T 329_G 0.67 0.18 0.00
201_I 253_A 0.67 0.18 0.00
336_K 204_S 0.67 0.18 0.00
250_L 305_L 0.67 0.18 0.00
201_I 122_G 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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