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OPENSEQ.org
ACRA_TOLC
Genes: A B A+B
Length: 397 493 785
Sequences: 3744 11324 2051
Seq/Len: 9.43 22.97 2.61
MirrorTree (Pazo et al. 2001) 0.74
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.05 0.31
2 0.02 0.05 2.00
5 0.03 0.07 2.30
10 0.05 0.09 2.34
20 0.06 0.11 2.37
100 0.08 0.15 2.60
∞ 0.16 0.20 3.12
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
135_T 382_A 2.78 1.00 1.00
136_Q 166_F 1.81 0.99 0.96
131_K 386_V 1.80 0.99 0.96
136_Q 173_I 1.77 0.98 0.95
136_Q 157_R 1.25 0.83 0.72
129_Y 388_T 1.23 0.82 0.70
135_T 378_D 1.23 0.82 0.70
137_Y 379_A 1.16 0.77 0.64
135_T 160_D 1.14 0.75 0.62
135_T 164_Q 1.07 0.68 0.54
142_E 165_R 1.06 0.67 0.52
137_Y 161_Q 0.98 0.58 0.43
135_T 167_N 0.94 0.53 0.38
129_Y 170_L 0.90 0.49 0.34
306_I 39_L 0.90 0.48 0.33
215_D 389_R 0.82 0.39 0.24
131_K 168_V 0.81 0.38 0.23
364_L 39_L 0.80 0.37 0.23
137_Y 382_A 0.79 0.36 0.22
178_S 384_Y 0.78 0.35 0.21
332_V 129_L 0.75 0.32 0.18
206_V 333_G 0.75 0.32 0.18
349_V 397_A 0.72 0.29 0.16
142_E 170_L 0.70 0.27 0.14
79_R 343_R 0.69 0.26 0.14
42_V 374_Q 0.69 0.26 0.14
236_K 122_T 0.69 0.25 0.13
138_I 108_L 0.68 0.24 0.13
188_N 269_T 0.67 0.24 0.13
144_D 32_A 0.67 0.24 0.12
14_L 81_G 0.67 0.24 0.12
327_G 271_D 0.67 0.23 0.12
223_F 124_Q 0.66 0.23 0.12
125_T 170_L 0.66 0.23 0.12
178_S 185_T 0.66 0.23 0.12
165_E 270_L 0.66 0.23 0.12
354_K 88_S 0.65 0.22 0.11
163_A 156_Y 0.65 0.22 0.11
34_G 311_S 0.65 0.22 0.11
154_N 234_L 0.65 0.22 0.11
349_V 234_L 0.64 0.22 0.11
357_D 274_A 0.64 0.21 0.11
295_A 398_T 0.64 0.21 0.10
191_E 264_D 0.64 0.21 0.10
324_L 67_G 0.64 0.21 0.10
173_Y 394_V 0.63 0.21 0.10
357_D 310_F 0.63 0.21 0.10
17_S 64_L 0.63 0.21 0.10
383_N 341_A 0.62 0.20 0.10
357_D 131_T 0.62 0.20 0.10
139_S 339_E 0.62 0.20 0.10
12_V 314_I 0.62 0.20 0.10
178_S 94_T 0.62 0.20 0.09
297_L 134_A 0.62 0.20 0.09
289_P 346_V 0.62 0.20 0.09
184_I 190_E 0.62 0.20 0.09
284_D 425_A 0.61 0.19 0.09
76_I 212_Y 0.61 0.19 0.09
376_Q 364_N 0.61 0.19 0.09
328_A 150_A 0.61 0.19 0.09
337_I 49_A 0.61 0.19 0.09
360_V 137_N 0.61 0.19 0.09
76_I 326_Q 0.61 0.19 0.09
62_A 406_Q 0.60 0.19 0.09
271_T 345_V 0.60 0.18 0.09
170_N 61_L 0.60 0.18 0.08
292_F 103_W 0.60 0.18 0.08
360_V 173_I 0.60 0.18 0.08
145_Q 241_R 0.59 0.18 0.08
280_F 135_Y 0.59 0.18 0.08
103_A 257_E 0.59 0.18 0.08
375_A 163_T 0.59 0.18 0.08
295_A 354_N 0.59 0.18 0.08
193_A 406_Q 0.59 0.18 0.08
351_E 364_N 0.59 0.17 0.08
172_A 130_N 0.59 0.17 0.08
201_T 387_G 0.59 0.17 0.08
198_G 59_P 0.59 0.17 0.08
169_I 304_N 0.59 0.17 0.08
234_T 160_D 0.59 0.17 0.08
71_Q 148_T 0.59 0.17 0.08
232_N 160_D 0.58 0.17 0.08
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
5917 6.61 acra-tolc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
4292 2.61 ACRA_TOLC Δgene:(1, 5) A:(1E-80, 4) B:(1E-40, 4) msa: Jackhmmer (2015_06) 1.00 Done
4290 0.35 ACRA_TOLC Δgene:(1, 1) A:(1E-80, 4) B:(1E-40, 4) msa: Jackhmmer (2015_06) 0.01 Done
4288 0.03 ACRA_TOLC Δgene:(1, 1) A:(1E-80, 4) B:(1E-60, 4) msa: Jackhmmer (2015_06) Killed
4286 0.02 ACRA_TOLC Δgene:(1, 1) A:(1E-80, 4) B:(1E-80, 4) msa: Jackhmmer (2015_06) Killed
4283 4.75 ACRA_TOLC Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.99 Done
4276 9.31 ACRA_TOLC Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done
0669 4.67 A-C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.99 Done
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