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OPENSEQ.org
A-C
Genes: A B A+B
Length: 397 493 759
Sequences: 9225 7539 3546
Seq/Len: 23.24 15.29 4.67
MirrorTree (Pazo et al. 2001) 0.65
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 0.03 0.00 1.71
2 0.03 0.00 3.50
5 0.04 0.01 3.83
10 0.05 0.03 3.91
20 0.06 0.05 3.98
100 0.11 0.11 4.45
∞ 0.19 0.18 5.15
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 2.32 1.00 0.99
131_K 386_V 1.91 1.00 0.98
136_Q 173_I 1.69 0.99 0.96
135_T 164_Q 1.56 0.99 0.94
136_Q 166_F 1.44 0.97 0.90
137_Y 382_A 1.36 0.96 0.87
129_Y 388_T 1.29 0.94 0.83
129_Y 170_L 1.20 0.91 0.77
135_T 378_D 1.09 0.85 0.67
139_S 172_A 1.06 0.82 0.63
131_K 168_V 1.01 0.79 0.58
136_Q 157_R 0.97 0.74 0.53
135_T 160_D 0.96 0.73 0.52
137_Y 379_A 0.91 0.68 0.46
142_E 383_G 0.89 0.65 0.43
137_Y 164_Q 0.85 0.60 0.39
137_Y 161_Q 0.83 0.57 0.36
136_Q 385_S 0.72 0.42 0.23
76_I 219_N 0.68 0.37 0.20
141_Q 170_L 0.68 0.36 0.19
132_L 388_T 0.67 0.35 0.19
132_L 393_D 0.65 0.33 0.17
135_T 167_N 0.64 0.31 0.16
132_L 170_L 0.63 0.30 0.15
349_V 409_A 0.62 0.28 0.14
102_Q 310_F 0.57 0.23 0.11
142_E 170_L 0.54 0.21 0.09
243_K 209_G 0.53 0.20 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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