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OPENSEQ.org
YidC YfgMM
Genes: A B A+B
Length: 548 442 967
Sequences: 1547 10879 857
Seq/Len: 2.82 24.61 0.89
MirrorTree (Pazo et al. 2001) 0.21
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 0.10 0.00
2 0.08 0.11 0.00
5 0.08 0.15 0.01
10 0.08 0.16 0.03
20 0.08 0.19 0.04
100 0.08 0.21 0.15
∞ 0.08 0.27 0.87
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
328_V 367_Y 1.21 0.49 0.00
297_P 365_A 1.06 0.37 0.00
7_L 141_D 1.05 0.36 0.00
368_I 149_R 0.98 0.30 0.00
68_L 372_T 0.97 0.29 0.00
349_S 363_L 0.96 0.28 0.00
391_Q 348_G 0.94 0.27 0.00
228_E 408_V 0.93 0.27 0.00
428_I 273_I 0.93 0.26 0.00
166_V 23_I 0.92 0.25 0.00
363_F 37_L 0.90 0.24 0.00
529_Q 309_L 0.90 0.24 0.00
166_V 59_V 0.90 0.24 0.00
360_I 3_I 0.89 0.24 0.00
131_Y 373_I 0.89 0.24 0.00
149_V 372_T 0.89 0.24 0.00
21_Q 211_E 0.89 0.23 0.00
22_A 23_I 0.87 0.23 0.00
501_I 276_L 0.87 0.22 0.00
529_Q 58_I 0.87 0.22 0.00
511_S 222_R 0.87 0.22 0.00
501_I 27_N 0.87 0.22 0.00
453_L 2_L 0.86 0.22 0.00
495_M 256_I 0.85 0.21 0.00
370_Y 193_V 0.85 0.21 0.00
297_P 25_I 0.85 0.21 0.00
466_I 178_R 0.84 0.20 0.00
61_I 350_E 0.83 0.20 0.00
315_D 101_E 0.83 0.20 0.00
347_I 365_A 0.83 0.20 0.00
370_Y 119_C 0.83 0.20 0.00
265_I 362_L 0.83 0.20 0.00
282_G 137_S 0.81 0.19 0.00
328_V 47_K 0.81 0.19 0.00
143_G 371_L 0.81 0.19 0.00
421_G 4_L 0.81 0.19 0.00
284_A 4_L 0.80 0.18 0.00
365_V 32_A 0.80 0.18 0.00
35_Q 54_V 0.80 0.18 0.00
132_N 208_A 0.80 0.18 0.00
177_N 371_L 0.79 0.18 0.00
428_I 405_V 0.79 0.18 0.00
498_M 386_N 0.79 0.17 0.00
265_I 32_A 0.79 0.17 0.00
31_P 357_G 0.78 0.17 0.00
79_V 405_V 0.78 0.17 0.00
17_F 252_Q 0.78 0.17 0.00
174_V 278_Q 0.78 0.17 0.00
501_I 122_V 0.78 0.17 0.00
318_A 352_M 0.77 0.17 0.00
365_V 342_A 0.77 0.17 0.00
51_G 3_I 0.77 0.17 0.00
427_L 144_L 0.77 0.17 0.00
511_S 140_R 0.77 0.17 0.00
533_R 336_L 0.77 0.17 0.00
13_L 360_F 0.76 0.16 0.00
511_S 46_F 0.76 0.16 0.00
413_K 323_K 0.76 0.16 0.00
31_P 145_K 0.76 0.16 0.00
14_F 267_Y 0.76 0.16 0.00
428_I 392_A 0.75 0.16 0.00
382_K 252_Q 0.75 0.16 0.00
38_Q 145_K 0.75 0.16 0.00
391_Q 408_V 0.74 0.15 0.00
435_A 342_A 0.74 0.15 0.00
382_K 363_L 0.74 0.15 0.00
393_M 268_L 0.74 0.15 0.00
328_V 271_D 0.74 0.15 0.00
237_T 193_V 0.74 0.15 0.00
511_S 193_V 0.74 0.15 0.00
181_Q 343_K 0.73 0.15 0.00
254_A 371_L 0.73 0.15 0.00
523_V 403_V 0.73 0.15 0.00
511_S 372_T 0.73 0.15 0.00
265_I 400_V 0.73 0.15 0.00
50_Q 23_I 0.73 0.15 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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