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OPENSEQ.org
grasx1
Genes: A B A+B
Length: 307 346 558
Sequences: 1803 4826 402
Seq/Len: 5.87 13.95 0.72
MirrorTree (Pazo et al. 2001) 0.30
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.00 0.00
2 0.03 0.00 0.03
5 0.03 0.00 0.04
10 0.03 0.01 0.05
20 0.03 0.01 0.08
100 0.03 0.03 0.14
∞ 0.08 0.13 0.62
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
18_L 269_I 1.43 0.62 0.00
111_Y 247_V 1.29 0.50 0.00
112_I 247_V 1.19 0.41 0.00
251_A 191_M 1.14 0.38 0.00
7_L 227_C 1.12 0.36 0.00
68_A 90_P 1.08 0.33 0.00
5_V 312_L 0.98 0.26 0.00
26_A 208_I 0.96 0.25 0.00
169_T 326_L 0.96 0.24 0.00
28_L 262_I 0.95 0.24 0.00
9_G 129_H 0.95 0.24 0.00
9_G 237_N 0.95 0.24 0.00
11_T 142_I 0.94 0.23 0.00
196_D 231_I 0.94 0.23 0.00
15_G 297_G 0.93 0.23 0.00
9_G 295_G 0.93 0.23 0.00
62_M 309_G 0.93 0.23 0.00
174_V 90_P 0.93 0.23 0.00
113_P 262_I 0.92 0.22 0.00
209_L 247_V 0.92 0.22 0.00
252_V 326_L 0.92 0.22 0.00
191_T 220_V 0.91 0.21 0.00
105_Q 55_L 0.89 0.20 0.00
102_A 161_I 0.89 0.20 0.00
9_G 298_L 0.88 0.20 0.00
184_T 166_D 0.88 0.20 0.00
165_P 160_R 0.88 0.20 0.00
240_G 66_V 0.87 0.20 0.00
12_G 129_H 0.87 0.20 0.00
12_G 237_N 0.87 0.20 0.00
9_G 297_G 0.87 0.19 0.00
159_T 125_T 0.86 0.19 0.00
97_F 159_S 0.85 0.18 0.00
172_N 249_I 0.84 0.18 0.00
197_Q 301_V 0.84 0.18 0.00
252_V 53_L 0.83 0.18 0.00
109_V 300_L 0.83 0.18 0.00
68_A 270_S 0.83 0.17 0.00
15_G 295_G 0.83 0.17 0.00
110_I 70_R 0.82 0.17 0.00
12_G 295_G 0.82 0.17 0.00
68_A 224_I 0.81 0.17 0.00
30_T 254_I 0.81 0.17 0.00
18_L 326_L 0.81 0.16 0.00
259_D 268_G 0.80 0.16 0.00
110_I 256_Q 0.80 0.16 0.00
9_G 134_P 0.80 0.16 0.00
15_G 129_H 0.80 0.16 0.00
15_G 237_N 0.80 0.16 0.00
28_L 210_F 0.80 0.16 0.00
12_G 298_L 0.79 0.16 0.00
4_K 274_M 0.79 0.15 0.00
254_Y 72_F 0.79 0.15 0.00
98_G 240_K 0.78 0.15 0.00
184_T 136_T 0.78 0.15 0.00
120_E 235_L 0.78 0.15 0.00
252_V 304_V 0.77 0.15 0.00
160_M 305_K 0.77 0.15 0.00
101_A 306_D 0.77 0.15 0.00
31_I 238_A 0.77 0.15 0.00
12_G 297_G 0.77 0.15 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
10137 0.09 grasx10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10135 0.09 Grasx9 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-06, 4) msa: HHblits (2015_06) 0.01 Done - Shared
10134 0 Grasx8 Δgene:(1, 1) A:(1E-60, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
10133 0 Grasx7 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) Killed - Shared
10131 1.18 Grasx6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 2) msa: HHblits (2015_06) 0.00 Done - Shared
10130 1.2 Grasx5 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10129 0.68 Grasx4 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10128 0.16 Grasx3 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10127 0.09 grasx2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10126 0.72 grasx1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10124 1.16 Grasx Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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