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OPENSEQ.org
BsuPcrA vs NusA
Genes: A B A+B
Length: 739 371 994
Sequences: 3698 1751 1151
Seq/Len: 5 4.72 1.16
MirrorTree (Pazo et al. 2001) 0.35
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 0.09 0.00 0.00
2 0.09 0.00 0.00
5 0.09 0.00 0.00
10 0.09 0.00 0.01
20 0.09 0.00 0.02
100 0.10 0.00 0.15
∞ 0.16 0.00 1.04
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
377_N 221_E 1.68 0.89 0.28
221_H 34_A 1.34 0.69 0.11
562_L 244_V 1.17 0.54 0.07
182_K 286_A 1.05 0.42 0.04
259_W 304_T 1.02 0.39 0.04
303_N 273_V 0.98 0.36 0.03
144_I 185_V 0.97 0.34 0.03
360_T 20_K 0.95 0.33 0.03
487_I 21_E 0.93 0.31 0.03
558_D 127_Y 0.91 0.30 0.03
294_R 286_A 0.90 0.29 0.02
356_I 249_S 0.90 0.29 0.02
211_E 142_V 0.90 0.29 0.02
152_K 215_I 0.90 0.29 0.02
89_I 15_E 0.90 0.28 0.02
538_L 52_E 0.89 0.28 0.02
560_I 77_I 0.89 0.28 0.02
89_I 130_F 0.86 0.26 0.02
337_A 297_V 0.86 0.26 0.02
94_S 244_V 0.86 0.26 0.02
82_P 137_I 0.85 0.26 0.02
460_A 152_V 0.85 0.25 0.02
494_R 130_F 0.85 0.25 0.02
108_G 90_G 0.84 0.25 0.02
583_E 77_I 0.84 0.24 0.02
515_F 126_I 0.83 0.24 0.02
49_M 77_I 0.83 0.24 0.02
29_L 120_E 0.83 0.24 0.02
356_I 95_I 0.83 0.24 0.02
234_M 126_I 0.82 0.23 0.02
62_I 275_W 0.80 0.22 0.02
487_I 291_K 0.80 0.22 0.02
41_L 36_K 0.80 0.22 0.02
581_L 258_V 0.80 0.21 0.02
402_V 133_R 0.80 0.21 0.02
322_S 130_F 0.79 0.21 0.01
229_N 337_I 0.79 0.21 0.01
401_L 176_D 0.79 0.21 0.01
222_V 292_V 0.79 0.21 0.01
356_I 184_K 0.79 0.21 0.01
483_L 109_T 0.79 0.21 0.01
281_L 5_L 0.79 0.21 0.01
568_A 74_E 0.78 0.20 0.01
35_S 66_D 0.78 0.20 0.01
176_V 261_I 0.78 0.20 0.01
100_L 50_N 0.78 0.20 0.01
461_L 126_I 0.77 0.20 0.01
312_W 235_I 0.76 0.19 0.01
229_N 272_I 0.76 0.19 0.01
492_E 287_L 0.76 0.19 0.01
345_S 25_E 0.76 0.19 0.01
15_V 226_A 0.75 0.19 0.01
58_N 178_I 0.75 0.19 0.01
208_E 19_S 0.75 0.19 0.01
315_N 79_E 0.75 0.19 0.01
216_K 16_K 0.75 0.19 0.01
492_E 258_V 0.75 0.18 0.01
265_T 282_F 0.75 0.18 0.01
556_G 130_F 0.74 0.18 0.01
518_V 8_A 0.74 0.18 0.01
367_I 130_F 0.74 0.18 0.01
377_N 178_I 0.74 0.18 0.01
263_D 282_F 0.74 0.18 0.01
134_L 130_F 0.74 0.18 0.01
609_I 18_I 0.74 0.18 0.01
558_D 194_I 0.73 0.17 0.01
183_K 261_I 0.73 0.17 0.01
522_F 206_R 0.73 0.17 0.01
608_G 303_A 0.73 0.17 0.01
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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