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OPENSEQ.org
14Avs14B_mk
Genes: A B A+B
Length: 125 110 214
Sequences: 1898 111 78
Seq/Len: 15.18 1.01 0.36
MirrorTree (Pazo et al. 2001) 0.23
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 0.05 0.01 0.00
5 0.05 0.01 0.00
10 0.06 0.01 0.01
20 0.07 0.01 0.06
100 0.09 0.01 0.13
∞ 0.17 0.01 0.33
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
116_K 29_K 1.43 0.42 0.00
29_K 57_R 1.25 0.30 0.00
74_C 57_R 1.22 0.29 0.00
42_Y 45_I 1.20 0.27 0.00
65_E 78_Q 1.12 0.23 0.00
64_Y 31_V 1.07 0.21 0.00
35_M 38_R 1.05 0.20 0.00
68_F 47_D 1.05 0.20 0.00
17_V 29_K 1.04 0.19 0.00
117_Y 94_S 0.99 0.17 0.00
50_V 66_V 0.98 0.17 0.00
25_N 31_V 0.96 0.16 0.00
117_Y 76_T 0.92 0.14 0.00
26_L 94_S 0.89 0.14 0.00
33_E 70_Y 0.89 0.13 0.00
46_R 9_I 0.88 0.13 0.00
81_N 59_V 0.88 0.13 0.00
29_K 9_I 0.87 0.13 0.00
87_L 59_V 0.87 0.13 0.00
104_K 32_I 0.86 0.12 0.00
20_I 93_S 0.86 0.12 0.00
112_L 18_A 0.86 0.12 0.00
25_N 2_A 0.85 0.12 0.00
104_K 53_S 0.84 0.12 0.00
50_V 10_F 0.83 0.12 0.00
25_N 26_C 0.82 0.11 0.00
104_K 9_I 0.81 0.11 0.00
56_T 47_D 0.80 0.11 0.00
45_I 26_C 0.80 0.11 0.00
96_R 70_Y 0.79 0.10 0.00
87_L 63_G 0.79 0.10 0.00
21_L 82_R 0.78 0.10 0.00
41_K 38_R 0.78 0.10 0.00
83_C 91_L 0.77 0.10 0.00
25_N 88_I 0.77 0.10 0.00
113_L 45_I 0.77 0.10 0.00
44_P 9_I 0.77 0.10 0.00
29_K 45_I 0.77 0.10 0.00
95_N 45_I 0.76 0.10 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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