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OPENSEQ.org
cI_H_40_cIII_isp_2_Pdenitr
Genes: A B A+B
Length: 345 190 515
Sequences: 4228 1785 484
Seq/Len: 12.26 9.39 0.94
MirrorTree (Pazo et al. 2001) 0.55
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.01 0.01 0.01
100 0.01 0.02 0.07
∞ 0.02 0.05 0.90
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
281_V 34_A 1.03 0.35 0.00
15_M 187_I 1.03 0.35 0.00
165_I 125_W 1.01 0.34 0.00
289_Y 168_G 0.98 0.31 0.00
208_S 23_T 0.98 0.31 0.00
27_M 15_R 0.97 0.30 0.00
12_A 33_A 0.97 0.30 0.00
328_L 32_G 0.96 0.29 0.00
81_K 70_K 0.94 0.28 0.00
124_S 145_G 0.94 0.28 0.00
326_A 15_R 0.93 0.27 0.00
28_G 28_T 0.93 0.27 0.00
12_A 32_G 0.93 0.27 0.00
12_A 65_T 0.90 0.25 0.00
170_I 117_R 0.89 0.24 0.00
80_D 179_A 0.88 0.23 0.00
74_V 22_A 0.87 0.23 0.00
197_P 123_G 0.86 0.22 0.00
172_T 48_V 0.86 0.22 0.00
24_A 188_K 0.85 0.22 0.00
203_V 88_A 0.84 0.21 0.00
223_A 89_G 0.84 0.21 0.00
137_A 131_V 0.84 0.21 0.00
206_F 163_G 0.84 0.21 0.00
254_M 19_L 0.83 0.21 0.00
199_L 174_L 0.83 0.21 0.00
113_I 151_F 0.83 0.21 0.00
313_V 176_I 0.83 0.21 0.00
204_L 157_S 0.83 0.21 0.00
121_F 78_I 0.83 0.21 0.00
137_A 68_T 0.83 0.20 0.00
51_N 22_A 0.82 0.20 0.00
126_L 140_I 0.80 0.19 0.00
96_L 56_V 0.80 0.19 0.00
242_L 159_Y 0.80 0.19 0.00
96_L 39_V 0.80 0.19 0.00
284_M 88_A 0.80 0.19 0.00
159_V 125_W 0.80 0.19 0.00
86_L 98_I 0.79 0.18 0.00
119_F 29_V 0.78 0.18 0.00
328_L 159_Y 0.78 0.18 0.00
203_V 27_G 0.78 0.18 0.00
233_T 26_A 0.78 0.18 0.00
172_T 18_F 0.78 0.18 0.00
200_P 163_G 0.78 0.18 0.00
280_M 32_G 0.77 0.17 0.00
117_I 53_S 0.77 0.17 0.00
102_I 18_F 0.77 0.17 0.00
175_M 174_L 0.77 0.17 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
3041 0.92 cI_H_40_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3040 0.94 cI_H_40_cIII_isp_2_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3038 0.95 cI_H_40_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2723 1.03 cI_H_cIII_ISP_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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