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OPENSEQ.org
14Avs14B_staszek
Genes: A B A+B
Length: 125 110 224
Sequences: 8021 102 129
Seq/Len: 64.17 0.93 0.58
MirrorTree (Pazo et al. 2001) 0.07
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 0.01 0.00
2 0.11 0.01 0.01
5 0.13 0.01 0.02
10 0.13 0.01 0.02
20 0.14 0.01 0.06
100 0.19 0.01 0.22
∞ 0.23 0.01 0.55
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
66_D 59_V 1.20 0.38 0.00
107_E 45_I 1.09 0.29 0.00
96_R 13_K 0.97 0.22 0.00
66_D 18_A 0.90 0.18 0.00
36_Y 66_V 0.88 0.17 0.00
16_E 59_V 0.87 0.17 0.00
34_E 59_V 0.85 0.16 0.00
38_I 45_I 0.83 0.15 0.00
83_C 59_V 0.81 0.15 0.00
53_T 60_I 0.80 0.14 0.00
66_D 104_K 0.80 0.14 0.00
35_M 10_F 0.78 0.13 0.00
79_G 89_V 0.77 0.13 0.00
28_Y 24_E 0.76 0.13 0.00
68_F 59_V 0.75 0.12 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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