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OPENSEQ.org
test-job
Genes: A B A+B
Length: 471 497 874
Sequences: 4747 16975 965
Seq/Len: 10.08 34.15 1.1
MirrorTree (Pazo et al. 2001) 0.61
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 0.03 0.32
2 0.01 0.04 0.54
5 0.02 0.04 0.73
10 0.03 0.06 0.84
20 0.03 0.08 1.00
100 0.06 0.13 1.74
∞ 0.18 0.21 3.25
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
464_L 154_V 1.00 0.36 0.00
138_A 422_F 1.00 0.36 0.00
219_E 404_I 0.98 0.34 0.00
369_I 340_V 0.95 0.32 0.00
64_T 175_A 0.90 0.28 0.00
64_T 379_A 0.89 0.27 0.00
272_H 282_A 0.86 0.25 0.00
366_G 326_V 0.84 0.24 0.00
425_L 238_V 0.84 0.23 0.00
388_K 354_Q 0.84 0.23 0.00
53_L 278_D 0.83 0.23 0.00
89_Q 201_Y 0.83 0.23 0.00
452_F 192_T 0.82 0.23 0.00
458_D 411_E 0.81 0.22 0.00
444_V 377_F 0.81 0.21 0.00
457_A 84_R 0.80 0.21 0.00
453_E 90_M 0.80 0.21 0.00
272_H 414_V 0.80 0.21 0.00
283_D 53_P 0.80 0.21 0.00
403_L 415_G 0.79 0.21 0.00
362_A 306_V 0.79 0.20 0.00
383_D 404_I 0.79 0.20 0.00
218_A 273_V 0.79 0.20 0.00
460_F 83_L 0.79 0.20 0.00
289_N 238_V 0.79 0.20 0.00
80_N 201_Y 0.78 0.20 0.00
453_E 329_H 0.78 0.20 0.00
138_A 321_R 0.78 0.20 0.00
63_N 75_T 0.77 0.19 0.00
178_P 238_V 0.77 0.19 0.00
362_A 282_A 0.77 0.19 0.00
132_G 414_V 0.75 0.18 0.00
321_L 318_L 0.75 0.18 0.00
371_D 93_N 0.75 0.18 0.00
84_L 235_V 0.75 0.18 0.00
299_T 185_V 0.74 0.17 0.00
467_S 327_I 0.74 0.17 0.00
356_P 95_D 0.73 0.17 0.00
249_I 306_V 0.73 0.17 0.00
92_E 348_K 0.73 0.17 0.00
51_K 419_D 0.72 0.17 0.00
369_I 195_S 0.72 0.16 0.00
138_A 147_V 0.72 0.16 0.00
263_P 156_V 0.71 0.16 0.00
433_G 111_E 0.71 0.16 0.00
357_A 56_V 0.71 0.16 0.00
358_R 340_V 0.71 0.16 0.00
182_V 342_N 0.70 0.15 0.00
248_L 283_L 0.70 0.15 0.00
288_Y 228_T 0.70 0.15 0.00
130_W 294_L 0.70 0.15 0.00
53_L 192_T 0.70 0.15 0.00
378_C 317_L 0.70 0.15 0.00
357_A 362_K 0.70 0.15 0.00
357_A 210_K 0.69 0.15 0.00
283_D 318_L 0.69 0.15 0.00
246_E 416_Y 0.69 0.15 0.00
362_A 341_I 0.69 0.15 0.00
63_N 404_I 0.69 0.15 0.00
413_A 380_P 0.68 0.14 0.00
86_K 324_K 0.68 0.14 0.00
86_K 408_D 0.68 0.14 0.00
271_N 341_I 0.68 0.14 0.00
86_K 46_I 0.68 0.14 0.00
284_I 229_L 0.68 0.14 0.00
395_K 324_K 0.67 0.14 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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