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OPENSEQ.org
lolo3_2
Genes: A B A+B
Length: 125 110 215
Sequences: 3161 111 72
Seq/Len: 25.29 1.01 0.33
MirrorTree (Pazo et al. 2001) 0.14
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 0.05 0.01 0.00
2 0.06 0.01 0.00
5 0.07 0.01 0.00
10 0.07 0.01 0.01
20 0.08 0.01 0.03
100 0.11 0.01 0.11
∞ 0.16 0.01 0.31
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
101_M 50_N 1.24 0.28 0.00
96_R 17_V 1.23 0.27 0.00
95_N 45_I 1.23 0.27 0.00
24_R 13_K 1.14 0.23 0.00
64_Y 66_V 1.09 0.20 0.00
99_Q 17_V 1.05 0.18 0.00
43_G 86_P 1.01 0.17 0.00
55_E 102_R 0.99 0.16 0.00
104_K 89_V 0.98 0.16 0.00
117_Y 94_S 0.96 0.15 0.00
105_K 95_K 0.95 0.15 0.00
17_V 29_K 0.95 0.15 0.00
99_Q 94_S 0.91 0.13 0.00
118_G 53_S 0.91 0.13 0.00
69_D 29_K 0.86 0.12 0.00
22_Y 103_K 0.84 0.11 0.00
100_K 78_Q 0.84 0.11 0.00
94_A 32_I 0.84 0.11 0.00
95_N 94_S 0.83 0.11 0.00
68_F 78_Q 0.81 0.11 0.00
108_E 66_V 0.81 0.10 0.00
64_Y 78_Q 0.79 0.10 0.00
45_I 42_L 0.79 0.10 0.00
108_E 68_D 0.78 0.10 0.00
40_G 44_R 0.78 0.10 0.00
45_I 31_V 0.78 0.10 0.00
82_V 105_Y 0.77 0.10 0.00
36_Y 66_V 0.76 0.09 0.00
39_F 79_E 0.76 0.09 0.00
115_E 95_K 0.76 0.09 0.00
75_D 59_V 0.75 0.09 0.00
96_R 78_Q 0.75 0.09 0.00
115_E 77_I 0.75 0.09 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
3987 0.36 14Avs14B_mk Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3902 0.65 14Avs14B_staszek Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3897 0.58 14Avs14B_staszek Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3896 0.33 lolo3_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3895 0.33 lolo3_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3894 0 lolo3 Δgene:(1, 5) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
3893 0.41 14Avs14B Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done
3879 0.58 14Avs14B Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3878 0.07 14Avs14B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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