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OPENSEQ.org
GTUB_SPC97
Genes: A B A+B
Length: 473 823 1225
Sequences: 982 648 169
Seq/Len: 2.08 0.79 0.14
MirrorTree (Pazo et al. 2001) 0.10
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 0.08 0.03 0.00
2 0.09 0.03 0.00
5 0.10 0.04 0.00
10 0.10 0.04 0.00
20 0.11 0.04 0.01
100 0.12 0.05 0.03
∞ 0.16 0.08 0.13
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
125_K 700_F 1.27 0.17 0.00
162_Y 646_Y 1.13 0.13 0.00
301_P 440_T 1.07 0.12 0.00
236_S 271_L 1.07 0.12 0.00
238_V 631_V 0.98 0.10 0.00
81_N 119_L 0.98 0.10 0.00
208_S 170_I 0.98 0.10 0.00
62_F 713_M 0.95 0.09 0.00
141_S 290_G 0.94 0.09 0.00
154_L 106_S 0.93 0.09 0.00
67_I 64_L 0.92 0.09 0.00
69_M 189_L 0.92 0.09 0.00
154_L 713_M 0.91 0.09 0.00
271_S 624_R 0.90 0.08 0.00
8_L 364_P 0.89 0.08 0.00
448_D 414_D 0.88 0.08 0.00
26_A 634_A 0.88 0.08 0.00
223_D 681_T 0.88 0.08 0.00
81_N 621_V 0.88 0.08 0.00
214_G 640_I 0.88 0.08 0.00
197_D 674_N 0.87 0.08 0.00
31_I 94_I 0.87 0.08 0.00
315_Y 146_L 0.87 0.08 0.00
82_T 142_I 0.87 0.08 0.00
117_D 93_K 0.86 0.08 0.00
196_E 170_I 0.85 0.08 0.00
162_Y 137_R 0.85 0.07 0.00
162_Y 298_E 0.85 0.07 0.00
231_I 394_V 0.84 0.07 0.00
212_I 419_L 0.84 0.07 0.00
8_L 420_K 0.84 0.07 0.00
198_S 768_I 0.84 0.07 0.00
447_D 574_I 0.83 0.07 0.00
185_Y 299_F 0.83 0.07 0.00
162_Y 683_I 0.83 0.07 0.00
385_N 786_L 0.83 0.07 0.00
262_S 681_T 0.82 0.07 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
2552 0.14 GTUB_SPC97 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2548 0 GTUB_SPC97 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
2545 0.01 GTUB_SPC97 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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