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OPENSEQ.org
Nadia
Genes: A B A+B
Length: 471 379 818
Sequences: 5407 9518 2019
Seq/Len: 11.48 25.11 2.47
MirrorTree (Pazo et al. 2001) 0.60
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 0.07 0.07 2.05
2 0.08 0.08 2.28
5 0.14 0.10 2.31
10 0.14 0.10 2.34
20 0.14 0.11 2.38
100 0.16 0.12 2.59
∞ 0.25 0.20 3.26
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
191_Y 233_T 0.97 0.55 0.00
284_T 92_I 0.91 0.48 0.00
71_S 233_T 0.85 0.41 0.00
457_V 199_L 0.84 0.40 0.00
291_A 215_V 0.81 0.37 0.00
129_A 37_L 0.81 0.37 0.00
382_L 84_A 0.81 0.36 0.00
443_L 45_G 0.80 0.36 0.00
47_A 243_E 0.80 0.36 0.00
186_D 18_V 0.79 0.34 0.00
337_A 11_G 0.78 0.34 0.00
67_L 136_R 0.78 0.33 0.00
179_V 166_A 0.77 0.33 0.00
321_F 279_A 0.77 0.32 0.00
301_G 97_A 0.77 0.32 0.00
193_S 24_V 0.75 0.30 0.00
323_D 209_V 0.75 0.30 0.00
90_V 152_T 0.75 0.30 0.00
305_E 348_A 0.75 0.30 0.00
297_V 201_V 0.73 0.29 0.00
51_R 349_R 0.73 0.29 0.00
308_A 106_Y 0.73 0.29 0.00
252_V 37_L 0.73 0.28 0.00
427_D 352_A 0.72 0.27 0.00
314_F 21_L 0.72 0.27 0.00
271_D 243_E 0.71 0.27 0.00
107_V 313_E 0.71 0.26 0.00
287_A 303_E 0.71 0.26 0.00
188_L 99_V 0.70 0.26 0.00
354_A 370_V 0.70 0.26 0.00
108_A 131_P 0.69 0.25 0.00
322_E 24_V 0.69 0.24 0.00
80_L 350_M 0.69 0.24 0.00
90_V 93_D 0.69 0.24 0.00
323_D 277_A 0.68 0.24 0.00
71_S 80_R 0.68 0.24 0.00
109_V 61_V 0.68 0.24 0.00
378_F 366_V 0.68 0.24 0.00
292_A 311_V 0.68 0.24 0.00
67_L 356_T 0.68 0.23 0.00
388_A 124_V 0.68 0.23 0.00
123_A 139_S 0.67 0.23 0.00
377_E 268_A 0.67 0.23 0.00
166_S 128_N 0.67 0.23 0.00
347_L 46_L 0.67 0.23 0.00
254_V 277_A 0.67 0.23 0.00
326_T 368_A 0.67 0.23 0.00
449_D 142_A 0.67 0.23 0.00
317_T 236_G 0.66 0.23 0.00
322_E 366_V 0.66 0.22 0.00
141_V 125_H 0.66 0.22 0.00
303_P 7_V 0.66 0.22 0.00
449_D 202_S 0.66 0.22 0.00
360_L 334_V 0.65 0.22 0.00
420_T 9_L 0.65 0.21 0.00
110_A 21_L 0.65 0.21 0.00
430_R 170_D 0.65 0.21 0.00
73_V 114_A 0.64 0.21 0.00
459_E 99_V 0.64 0.21 0.00
312_G 348_A 0.64 0.21 0.00
179_V 81_L 0.64 0.20 0.00
61_V 353_A 0.64 0.20 0.00
295_A 314_A 0.64 0.20 0.00
391_T 294_Y 0.64 0.20 0.00
303_P 352_A 0.63 0.20 0.00
47_A 293_V 0.63 0.20 0.00
266_V 102_G 0.63 0.20 0.00
68_V 348_A 0.63 0.20 0.00
413_V 134_A 0.63 0.20 0.00
362_L 283_C 0.63 0.20 0.00
372_R 359_V 0.63 0.20 0.00
92_H 164_L 0.62 0.19 0.00
191_Y 18_V 0.62 0.19 0.00
266_V 341_P 0.62 0.19 0.00
389_V 93_D 0.62 0.19 0.00
277_V 137_L 0.62 0.19 0.00
323_D 18_V 0.62 0.19 0.00
322_E 233_T 0.62 0.19 0.00
51_R 75_L 0.62 0.19 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)
ID Seq/Len Name Options I_Prob Status
11968 Nadia Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Running - Shared
11916 2.47 Nadia Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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