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OPENSEQ.org
cI_1_60_cI_2_40_tt
Genes: A B A+B
Length: 438 181 600
Sequences: 2227 1903 1365
Seq/Len: 5.08 10.51 2.27
MirrorTree (Pazo et al. 2001) 0.83
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 0.01 0.00 1.82
2 0.01 0.00 1.97
5 0.01 0.01 2.13
10 0.02 0.01 2.15
20 0.02 0.01 2.15
100 0.04 0.02 2.16
∞ 0.12 0.04 2.21
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
138_Y 126_G 1.52 0.94 0.60
212_W 25_A 1.46 0.92 0.55
195_L 59_E 1.35 0.87 0.45
101_F 129_H 1.29 0.83 0.39
284_L 91_A 1.11 0.68 0.24
174_H 18_Y 1.05 0.62 0.20
350_H 123_E 1.04 0.61 0.20
105_Y 129_H 1.04 0.60 0.19
343_N 85_T 0.94 0.50 0.14
227_V 146_T 0.90 0.45 0.12
174_H 89_K 0.89 0.44 0.11
196_R 62_G 0.89 0.43 0.11
238_F 127_S 0.84 0.38 0.09
117_G 122_V 0.83 0.37 0.09
331_I 90_L 0.81 0.34 0.08
343_N 84_A 0.79 0.33 0.07
101_F 127_S 0.78 0.32 0.07
160_K 153_L 0.77 0.31 0.07
175_R 122_V 0.77 0.30 0.07
169_F 126_G 0.77 0.30 0.07
186_T 92_G 0.75 0.29 0.06
367_M 65_S 0.75 0.29 0.06
348_Y 123_E 0.75 0.28 0.06
73_G 127_S 0.74 0.28 0.06
177_A 28_M 0.74 0.28 0.06
253_Q 129_H 0.73 0.27 0.06
175_R 28_M 0.72 0.26 0.05
379_G 153_L 0.71 0.25 0.05
292_P 123_E 0.71 0.25 0.05
300_L 63_V 0.70 0.24 0.05
373_K 23_R 0.70 0.24 0.05
327_G 129_H 0.69 0.23 0.05
381_E 65_S 0.68 0.22 0.04
344_L 86_L 0.67 0.22 0.04
258_V 46_I 0.67 0.22 0.04
258_V 47_E 0.67 0.22 0.04
52_E 100_L 0.67 0.21 0.04
277_Y 110_E 0.66 0.21 0.04
339_D 94_E 0.66 0.21 0.04
174_H 122_V 0.66 0.21 0.04
119_I 102_E 0.65 0.20 0.04
127_A 96_L 0.65 0.20 0.04
216_T 131_A 0.65 0.20 0.04
255_S 122_V 0.65 0.20 0.04
195_L 31_L 0.65 0.20 0.04
173_V 116_L 0.65 0.20 0.04
171_L 153_L 0.65 0.20 0.04
96_S 85_T 0.64 0.20 0.04
174_H 123_E 0.64 0.20 0.04
51_D 152_A 0.64 0.20 0.04
166_D 105_G 0.64 0.20 0.04
270_T 105_G 0.64 0.19 0.04
208_Q 104_L 0.64 0.19 0.04
223_T 28_M 0.64 0.19 0.04
68_A 149_R 0.63 0.19 0.03
198_N 70_Y 0.63 0.19 0.03
173_V 9_D 0.63 0.19 0.03
165_T 6_D 0.63 0.19 0.03
238_F 24_R 0.63 0.19 0.03
300_L 127_S 0.63 0.18 0.03
298_P 85_T 0.62 0.18 0.03
321_S 81_Q 0.62 0.18 0.03
175_R 32_R 0.61 0.18 0.03
125_I 136_V 0.61 0.17 0.03
80_P 127_S 0.61 0.17 0.03
321_S 123_E 0.61 0.17 0.03
136_G 69_Y 0.61 0.17 0.03
231_M 105_G 0.61 0.17 0.03
382_K 106_I 0.60 0.17 0.03
196_R 59_E 0.60 0.17 0.03
320_G 111_V 0.60 0.17 0.03
124_A 125_L 0.60 0.17 0.03
378_Q 13_E 0.60 0.17 0.03
429_R 93_A 0.60 0.17 0.03
71_P 136_V 0.60 0.17 0.03
335_V 46_I 0.60 0.17 0.03
141_A 87_S 0.60 0.17 0.03
335_V 41_I 0.59 0.16 0.03
89_L 118_S 0.59 0.16 0.03
53_V 98_D 0.59 0.16 0.03
274_E 96_L 0.59 0.16 0.03
291_I 87_S 0.59 0.16 0.03
150_K 13_E 0.59 0.16 0.03
202_K 59_E 0.59 0.16 0.03
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
4733 2.91 cI_1_20_cI_2_4_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.56 Done - Shared
4732 2.93 cI_1_4_cI_2_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.60 Done - Shared
4731 2.27 cI_1_80_cI_2_40_tt Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.58 Done - Shared
4730 2.93 cI_1_60_cI_2_40_tt Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.59 Done - Shared
4729 2.27 cI_1_60_cI_2_40_tt Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.60 Done - Shared
4728 0.02 cI_1_60_cI_2_60_tt Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) Killed - Shared
4727 2.28 cI_1_40_cI_2_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.57 Done - Shared
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