May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
Grasx
Genes: A B A+B
Length: 307 346 553
Sequences: 1803 19045 641
Seq/Len: 5.87 55.04 1.16
MirrorTree (Pazo et al. 2001) 0.22
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 0.01 0.03
5 0.03 0.02 0.04
10 0.03 0.04 0.08
20 0.03 0.07 0.11
100 0.03 0.15 0.38
∞ 0.08 0.22 0.98
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
45_M 102_Q 0.87 0.27 0.00
249_E 311_Q 0.87 0.27 0.00
208_P 135_V 0.86 0.26 0.00
11_T 267_R 0.86 0.26 0.00
96_N 208_I 0.85 0.26 0.00
11_T 273_D 0.85 0.25 0.00
12_G 129_H 0.84 0.24 0.00
12_G 237_N 0.84 0.24 0.00
12_G 297_G 0.84 0.24 0.00
44_E 277_I 0.78 0.20 0.00
185_K 249_I 0.78 0.20 0.00
46_T 144_Q 0.76 0.19 0.00
160_M 59_I 0.76 0.19 0.00
171_K 145_E 0.75 0.18 0.00
46_T 258_V 0.74 0.18 0.00
240_G 166_D 0.74 0.18 0.00
58_V 102_Q 0.74 0.18 0.00
103_I 251_T 0.74 0.18 0.00
105_Q 250_S 0.73 0.17 0.00
12_G 295_G 0.73 0.17 0.00
191_T 192_V 0.73 0.17 0.00
63_N 326_L 0.72 0.17 0.00
196_D 194_D 0.71 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
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
Page generated in 0.1934 seconds.