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OPENSEQ.org
Pol II_3
Genes: A B A+B
Length: 171 569 649
Sequences: 1120 6553 424
Seq/Len: 6.55 11.52 0.65
MirrorTree (Pazo et al. 2001) 0.04
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 0.03 0.00
2 0.03 0.04 0.01
5 0.03 0.04 0.02
10 0.03 0.05 0.02
20 0.03 0.07 0.04
100 0.04 0.12 0.23
∞ 0.08 0.19 0.57
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
80_K 251_S 1.38 0.55 0.00
46_L 422_S 1.26 0.45 0.00
110_V 555_S 1.18 0.38 0.00
72_V 422_S 1.17 0.38 0.00
46_L 388_V 1.09 0.32 0.00
146_K 327_V 0.98 0.24 0.00
79_F 287_I 0.96 0.23 0.00
162_S 367_S 0.94 0.22 0.00
51_Y 518_I 0.90 0.20 0.00
148_E 146_T 0.89 0.20 0.00
86_V 497_V 0.86 0.18 0.00
121_F 123_I 0.86 0.18 0.00
121_F 138_Q 0.86 0.18 0.00
140_K 453_D 0.85 0.18 0.00
164_K 543_R 0.85 0.17 0.00
91_V 152_M 0.85 0.17 0.00
79_F 331_D 0.84 0.17 0.00
79_F 208_K 0.84 0.17 0.00
78_V 368_K 0.84 0.17 0.00
139_I 284_F 0.83 0.17 0.00
139_I 216_L 0.83 0.16 0.00
121_F 408_D 0.83 0.16 0.00
171_I 215_I 0.81 0.15 0.00
11_I 499_L 0.79 0.15 0.00
13_L 300_Q 0.79 0.14 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
13423 0.65 Pol II_3 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13422 0.03 Pol II_2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
13414 0.03 Reta Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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