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OPENSEQ.org
DivL_PAS_BCD-CckA_PAS_B-end
Genes: A B A+B
Length: 369 497 850
Sequences: 4022 10602 254
Seq/Len: 10.9 21.33 0.3
MirrorTree (Pazo et al. 2001) 0.53
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 0.02 0.07
2 0.02 0.03 0.11
5 0.02 0.05 0.15
10 0.03 0.06 0.21
20 0.04 0.08 0.29
100 0.08 0.13 0.72
∞ 0.18 0.22 1.47
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
30_G 137_I 1.24 0.26 0.00
226_P 481_I 1.20 0.24 0.00
111_T 340_A 1.20 0.24 0.00
117_R 323_V 1.15 0.21 0.00
156_E 283_V 1.13 0.21 0.00
271_G 426_L 1.12 0.20 0.00
111_T 314_L 1.11 0.20 0.00
366_V 286_D 1.09 0.19 0.00
252_L 454_M 1.06 0.18 0.00
36_N 346_L 1.04 0.17 0.00
109_D 314_L 1.02 0.17 0.00
110_V 342_F 1.02 0.16 0.00
239_I 125_G 1.00 0.16 0.00
221_K 481_I 0.99 0.15 0.00
111_T 342_F 0.98 0.15 0.00
112_E 405_E 0.97 0.15 0.00
317_W 317_A 0.96 0.14 0.00
249_Y 180_R 0.94 0.14 0.00
244_R 408_D 0.93 0.13 0.00
229_L 180_R 0.93 0.13 0.00
55_G 379_I 0.92 0.13 0.00
16_V 191_L 0.92 0.13 0.00
27_G 200_V 0.90 0.12 0.00
252_L 212_L 0.90 0.12 0.00
109_D 380_L 0.90 0.12 0.00
109_D 176_L 0.88 0.12 0.00
111_T 195_I 0.87 0.12 0.00
23_C 109_Q 0.87 0.12 0.00
287_W 481_I 0.87 0.12 0.00
97_P 457_S 0.85 0.11 0.00
240_T 141_L 0.85 0.11 0.00
240_T 343_R 0.84 0.11 0.00
158_W 113_A 0.84 0.11 0.00
52_A 332_V 0.84 0.11 0.00
142_S 490_V 0.83 0.11 0.00
109_D 396_L 0.83 0.11 0.00
36_N 31_N 0.83 0.10 0.00
127_H 286_D 0.83 0.10 0.00
162_P 324_K 0.82 0.10 0.00
109_D 123_A 0.81 0.10 0.00
89_R 408_D 0.81 0.10 0.00
34_W 444_A 0.81 0.10 0.00
354_L 321_G 0.81 0.10 0.00
246_K 139_L 0.81 0.10 0.00
119_A 101_S 0.81 0.10 0.00
209_D 293_D 0.80 0.10 0.00
222_V 426_L 0.80 0.10 0.00
157_L 171_L 0.80 0.10 0.00
267_V 281_I 0.80 0.10 0.00
138_V 454_M 0.80 0.10 0.00
152_T 137_I 0.79 0.10 0.00
49_Q 472_T 0.79 0.10 0.00
78_A 279_A 0.78 0.09 0.00
240_T 439_T 0.78 0.09 0.00
36_N 126_V 0.78 0.09 0.00
348_L 144_L 0.78 0.09 0.00
12_F 490_V 0.78 0.09 0.00
113_I 475_T 0.78 0.09 0.00
109_D 171_L 0.78 0.09 0.00
146_R 130_F 0.77 0.09 0.00
274_G 74_L 0.77 0.09 0.00
239_I 493_Q 0.77 0.09 0.00
368_D 432_M 0.77 0.09 0.00
267_V 126_V 0.76 0.09 0.00
248_Q 110_L 0.76 0.09 0.00
110_V 322_I 0.76 0.09 0.00
263_L 340_A 0.76 0.09 0.00
276_L 165_G 0.76 0.09 0.00
151_N 383_E 0.76 0.09 0.00
226_P 293_D 0.75 0.09 0.00
366_V 298_I 0.75 0.09 0.00
127_H 283_V 0.75 0.09 0.00
362_A 65_G 0.75 0.09 0.00
366_V 491_K 0.75 0.09 0.00
185_P 237_L 0.75 0.09 0.00
110_V 381_F 0.75 0.09 0.00
271_G 290_I 0.75 0.09 0.00
48_A 412_A 0.75 0.09 0.00
367_T 337_N 0.75 0.09 0.00
274_G 390_S 0.74 0.09 0.00
247_A 408_D 0.74 0.09 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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