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OPENSEQ.org
cI_K_6_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 101 440 481
Sequences: 4661 3285 2421
Seq/Len: 46.15 7.47 5.03
MirrorTree (Pazo et al. 2001) 0.66
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 0.00 0.00 0.22
2 0.00 0.00 1.45
5 0.01 0.00 3.19
10 0.01 0.00 3.36
20 0.01 0.00 3.45
100 0.03 0.00 3.57
∞ 0.07 0.01 4.48
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
69_V 364_K 1.35 0.97 0.62
88_R 192_N 1.09 0.87 0.38
32_I 364_K 1.08 0.85 0.36
69_V 176_I 1.07 0.85 0.36
74_A 135_I 0.95 0.74 0.25
23_F 44_W 0.92 0.70 0.22
80_I 206_A 0.90 0.68 0.21
18_G 246_P 0.88 0.66 0.20
61_V 172_V 0.88 0.66 0.19
39_M 176_I 0.87 0.65 0.19
70_A 228_E 0.87 0.65 0.19
38_L 180_L 0.87 0.64 0.18
47_F 402_A 0.86 0.63 0.18
34_M 298_F 0.83 0.60 0.16
34_M 285_P 0.83 0.59 0.16
18_G 28_L 0.82 0.58 0.16
65_F 44_W 0.82 0.58 0.15
18_G 113_F 0.82 0.57 0.15
70_A 349_L 0.81 0.56 0.15
50_F 72_H 0.80 0.55 0.14
25_N 81_E 0.79 0.53 0.13
32_I 25_I 0.77 0.50 0.12
82_V 135_I 0.76 0.49 0.12
36_I 278_D 0.76 0.49 0.12
99_M 39_K 0.76 0.49 0.12
30_I 88_N 0.75 0.48 0.12
55_G 103_L 0.74 0.47 0.11
27_K 108_V 0.74 0.46 0.11
14_L 403_Y 0.73 0.45 0.10
50_F 172_V 0.73 0.45 0.10
32_I 166_F 0.73 0.45 0.10
65_F 293_V 0.72 0.44 0.10
44_N 92_M 0.72 0.44 0.10
26_R 61_T 0.71 0.43 0.10
94_E 197_L 0.71 0.42 0.10
74_A 196_S 0.71 0.42 0.09
69_V 249_V 0.70 0.41 0.09
11_G 371_A 0.70 0.41 0.09
39_M 406_I 0.70 0.41 0.09
29_V 355_R 0.70 0.41 0.09
93_V 344_A 0.70 0.40 0.09
60_Q 412_G 0.69 0.40 0.09
93_V 44_W 0.69 0.40 0.09
26_R 20_H 0.69 0.40 0.09
15_F 22_R 0.69 0.39 0.09
25_N 267_V 0.69 0.39 0.09
80_I 362_L 0.68 0.38 0.08
21_G 110_I 0.68 0.38 0.08
83_V 376_V 0.68 0.38 0.08
36_I 178_T 0.68 0.38 0.08
67_L 175_A 0.68 0.38 0.08
15_F 59_I 0.67 0.37 0.08
25_N 254_F 0.67 0.37 0.08
68_T 56_V 0.67 0.37 0.08
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
2932 5.03 cI_K_6_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.62 Done - Shared
2930 4.29 cI_K_10_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.72 Done - Shared
2928 1.12 cI_K_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
2927 1.12 cI_K_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.52 Done - Shared
2926 1.11 cI_K_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
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