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OPENSEQ.org
ACRA_TOLC
Genes: A B A+B
Length: 397 493 797
Sequences: 17232 14400 3782
Seq/Len: 43.41 29.21 4.75
MirrorTree (Pazo et al. 2001) 0.66
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 0.07 0.05 4.25
2 0.08 0.06 7.74
5 0.10 0.08 8.43
10 0.11 0.10 8.58
20 0.13 0.12 8.73
100 0.17 0.16 9.43
∞ 0.22 0.21 10.35
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 2.21 1.00 0.99
135_T 164_Q 1.68 0.99 0.96
131_K 386_V 1.66 0.99 0.95
136_Q 173_I 1.42 0.97 0.89
137_Y 382_A 1.27 0.94 0.82
131_K 168_V 1.25 0.94 0.80
139_S 172_A 1.23 0.93 0.79
129_Y 388_T 1.16 0.90 0.73
136_Q 166_F 1.08 0.85 0.66
141_Q 170_L 0.98 0.76 0.54
129_Y 170_L 0.97 0.75 0.53
137_Y 379_A 0.91 0.68 0.45
137_Y 164_Q 0.83 0.57 0.35
265_V 276_T 0.77 0.48 0.28
161_K 10_G 0.73 0.43 0.24
135_T 378_D 0.71 0.40 0.22
132_L 170_L 0.71 0.40 0.22
228_Q 15_G 0.69 0.37 0.20
303_P 8_L 0.66 0.34 0.17
70_P 208_T 0.63 0.31 0.15
137_Y 383_G 0.62 0.29 0.14
142_E 383_G 0.59 0.26 0.12
127_N 150_A 0.59 0.26 0.12
313_V 277_G 0.59 0.25 0.12
56_L 25_L 0.58 0.25 0.11
137_Y 161_Q 0.57 0.23 0.10
260_L 397_A 0.56 0.23 0.10
77_L 24_N 0.56 0.23 0.10
132_L 386_V 0.55 0.22 0.10
291_M 177_Q 0.55 0.22 0.09
306_I 270_L 0.55 0.21 0.09
76_I 368_Q 0.54 0.21 0.09
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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