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OPENSEQ.org
cI_1_4_cI_2_4_tt
Genes: A B A+B
Length: 438 181 588
Sequences: 2611 2539 1720
Seq/Len: 5.96 14.03 2.93
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 2.39
2 0.01 0.00 2.53
5 0.01 0.01 2.71
10 0.02 0.01 2.73
20 0.03 0.02 2.73
100 0.05 0.04 2.74
∞ 0.14 0.10 2.78
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 0.60
212_W 25_A 1.21 0.83 0.39
195_L 59_E 1.20 0.83 0.38
101_F 129_H 1.09 0.73 0.28
339_D 94_E 1.08 0.73 0.28
284_L 91_A 1.08 0.72 0.28
196_R 62_G 1.02 0.67 0.23
350_H 123_E 0.94 0.57 0.17
174_H 18_Y 0.90 0.51 0.15
174_H 89_K 0.84 0.45 0.12
343_N 85_T 0.83 0.43 0.11
105_Y 129_H 0.83 0.43 0.11
181_I 66_F 0.83 0.43 0.11
122_G 140_P 0.81 0.41 0.10
136_G 69_Y 0.77 0.36 0.09
367_M 65_S 0.74 0.33 0.08
160_K 153_L 0.73 0.32 0.07
177_A 28_M 0.73 0.32 0.07
169_F 126_G 0.69 0.28 0.06
69_G 81_Q 0.69 0.28 0.06
348_Y 123_E 0.69 0.28 0.06
327_G 129_H 0.69 0.27 0.06
175_R 122_V 0.67 0.26 0.06
73_G 127_S 0.66 0.25 0.05
53_V 98_D 0.65 0.24 0.05
196_R 39_G 0.65 0.24 0.05
253_Q 129_H 0.65 0.24 0.05
129_V 24_R 0.65 0.24 0.05
331_I 90_L 0.65 0.24 0.05
292_P 123_E 0.64 0.23 0.05
251_L 126_G 0.64 0.23 0.05
179_A 70_Y 0.64 0.23 0.05
179_A 66_F 0.64 0.23 0.05
195_L 31_L 0.63 0.22 0.05
101_F 127_S 0.63 0.22 0.04
117_G 122_V 0.63 0.22 0.04
227_V 146_T 0.63 0.22 0.04
202_K 125_L 0.63 0.22 0.04
186_T 92_G 0.63 0.22 0.04
343_N 84_A 0.63 0.22 0.04
329_I 90_L 0.62 0.21 0.04
69_G 131_A 0.62 0.21 0.04
412_G 71_Q 0.62 0.21 0.04
146_E 98_D 0.61 0.21 0.04
300_L 127_S 0.61 0.20 0.04
104_R 143_E 0.61 0.20 0.04
166_D 105_G 0.60 0.20 0.04
174_H 29_P 0.60 0.20 0.04
165_T 6_D 0.59 0.19 0.04
196_R 59_E 0.59 0.19 0.04
233_R 78_Y 0.59 0.19 0.04
339_D 93_A 0.59 0.19 0.04
380_E 9_D 0.59 0.19 0.04
198_N 70_Y 0.58 0.18 0.04
238_F 127_S 0.58 0.18 0.04
344_L 86_L 0.58 0.18 0.04
218_I 32_R 0.58 0.18 0.04
259_K 91_A 0.58 0.18 0.04
259_K 23_R 0.58 0.18 0.03
363_V 90_L 0.58 0.18 0.03
295_S 85_T 0.58 0.18 0.03
177_A 32_R 0.57 0.17 0.03
334_R 131_A 0.57 0.17 0.03
44_V 120_Q 0.57 0.17 0.03
96_S 126_G 0.57 0.17 0.03
202_K 59_E 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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