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OPENSEQ.org
cI_1_60_cI_2_40_tt
Genes: A B A+B
Length: 438 181 594
Sequences: 2227 2565 1739
Seq/Len: 5.08 14.17 2.93
MirrorTree (Pazo et al. 2001) 0.84
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 2.42
2 0.01 0.00 2.56
5 0.01 0.01 2.73
10 0.02 0.01 2.75
20 0.02 0.02 2.75
100 0.04 0.04 2.76
∞ 0.12 0.10 2.81
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 1.44 0.94 0.59
212_W 25_A 1.24 0.85 0.41
195_L 59_E 1.20 0.82 0.37
284_L 91_A 1.10 0.75 0.29
101_F 129_H 1.10 0.74 0.28
196_R 62_G 1.04 0.69 0.24
339_D 94_E 1.04 0.68 0.24
350_H 123_E 0.95 0.58 0.17
174_H 18_Y 0.91 0.53 0.15
181_I 66_F 0.85 0.46 0.12
174_H 89_K 0.84 0.44 0.11
105_Y 129_H 0.83 0.43 0.11
343_N 85_T 0.82 0.42 0.10
367_M 65_S 0.78 0.37 0.09
136_G 69_Y 0.75 0.34 0.08
177_A 28_M 0.74 0.33 0.08
160_K 153_L 0.70 0.29 0.06
169_F 126_G 0.69 0.28 0.06
69_G 81_Q 0.69 0.28 0.06
238_F 114_D 0.68 0.27 0.06
122_G 140_P 0.68 0.27 0.06
253_Q 129_H 0.68 0.27 0.06
348_Y 123_E 0.68 0.27 0.06
196_R 39_G 0.67 0.26 0.05
175_R 122_V 0.67 0.25 0.05
227_V 146_T 0.66 0.25 0.05
173_V 9_D 0.66 0.25 0.05
179_A 66_F 0.65 0.24 0.05
251_L 126_G 0.64 0.23 0.05
73_G 127_S 0.64 0.23 0.05
259_K 91_A 0.64 0.23 0.05
327_G 129_H 0.64 0.23 0.05
117_G 122_V 0.64 0.23 0.05
179_A 70_Y 0.64 0.23 0.05
186_T 92_G 0.63 0.22 0.04
101_F 127_S 0.63 0.22 0.04
329_I 90_L 0.63 0.22 0.04
53_V 98_D 0.62 0.21 0.04
412_G 71_Q 0.62 0.21 0.04
69_G 131_A 0.62 0.21 0.04
202_K 125_L 0.62 0.21 0.04
129_V 24_R 0.61 0.21 0.04
292_P 123_E 0.61 0.21 0.04
331_I 90_L 0.61 0.21 0.04
343_N 84_A 0.60 0.20 0.04
165_T 6_D 0.60 0.20 0.04
195_L 31_L 0.60 0.20 0.04
174_H 25_A 0.60 0.20 0.04
146_E 98_D 0.60 0.19 0.04
158_L 154_L 0.59 0.19 0.04
238_F 127_S 0.59 0.19 0.04
198_N 70_Y 0.59 0.19 0.04
233_R 78_Y 0.59 0.19 0.04
335_V 46_I 0.59 0.19 0.04
162_L 117_F 0.59 0.19 0.04
104_R 143_E 0.58 0.18 0.03
51_D 152_A 0.58 0.18 0.03
295_S 85_T 0.58 0.18 0.03
196_R 59_E 0.58 0.18 0.03
260_R 71_Q 0.58 0.18 0.03
429_R 93_A 0.58 0.18 0.03
363_V 90_L 0.58 0.18 0.03
174_H 29_P 0.57 0.18 0.03
100_S 85_T 0.57 0.18 0.03
344_L 86_L 0.57 0.18 0.03
115_I 9_D 0.57 0.18 0.03
421_Y 86_L 0.57 0.17 0.03
211_L 29_P 0.57 0.17 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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