May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
CarO-Oxa23
Genes: A B A+B
Length: 246 273 470
Sequences: 374 11388 172
Seq/Len: 1.52 41.71 0.37
MirrorTree (Pazo et al. 2001) 0.25
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 0.01 0.05 0.00
2 0.01 0.05 0.01
5 0.01 0.06 0.01
10 0.01 0.07 0.01
20 0.01 0.08 0.01
100 0.04 0.13 0.12
∞ 0.13 0.23 0.33
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
122_A 231_T 1.36 0.38 0.00
174_G 218_G 1.23 0.29 0.00
63_V 258_I 1.19 0.27 0.00
242_V 246_L 1.09 0.22 0.00
46_V 243_A 1.08 0.21 0.00
155_V 201_N 1.06 0.21 0.00
174_G 151_G 1.05 0.20 0.00
198_T 90_L 1.03 0.19 0.00
71_G 51_G 1.02 0.19 0.00
121_G 218_G 1.02 0.18 0.00
174_G 126_S 1.02 0.18 0.00
107_A 199_V 1.00 0.18 0.00
100_A 129_P 1.00 0.18 0.00
174_G 79_S 0.97 0.17 0.00
195_G 57_T 0.97 0.17 0.00
196_N 67_A 0.96 0.16 0.00
174_G 216_K 0.96 0.16 0.00
182_N 80_T 0.95 0.16 0.00
183_W 209_N 0.94 0.15 0.00
174_G 82_K 0.94 0.15 0.00
46_V 87_L 0.94 0.15 0.00
246_W 139_G 0.94 0.15 0.00
120_A 90_L 0.93 0.15 0.00
103_R 63_L 0.92 0.15 0.00
144_N 245_A 0.92 0.15 0.00
118_V 174_P 0.92 0.15 0.00
242_V 150_I 0.91 0.14 0.00
129_Y 52_V 0.90 0.14 0.00
197_P 245_A 0.89 0.14 0.00
155_V 123_M 0.89 0.14 0.00
242_V 122_A 0.88 0.13 0.00
102_I 134_L 0.88 0.13 0.00
179_I 66_N 0.87 0.13 0.00
120_A 62_N 0.87 0.13 0.00
124_Y 193_E 0.86 0.13 0.00
188_E 77_P 0.86 0.13 0.00
205_G 239_G 0.86 0.13 0.00
123_A 213_I 0.86 0.13 0.00
65_L 199_V 0.86 0.13 0.00
245_F 172_V 0.85 0.12 0.00
67_L 261_E 0.85 0.12 0.00
44_A 184_L 0.85 0.12 0.00
185_V 244_F 0.84 0.12 0.00
243_N 231_T 0.84 0.12 0.00
94_N 184_L 0.84 0.12 0.00
240_V 119_L 0.84 0.12 0.00
194_T 192_S 0.84 0.12 0.00
158_N 192_S 0.84 0.12 0.00
89_L 46_E 0.84 0.12 0.00
74_I 184_L 0.84 0.12 0.00
118_V 178_V 0.84 0.12 0.00
91_M 192_S 0.84 0.12 0.00
65_L 243_A 0.83 0.12 0.00
95_N 231_T 0.83 0.12 0.00
52_G 69_S 0.82 0.12 0.00
138_T 269_Q 0.82 0.12 0.00
173_F 35_G 0.82 0.12 0.00
58_Q 40_I 0.82 0.12 0.00
244_F 57_T 0.82 0.11 0.00
98_L 89_G 0.82 0.11 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
2771 0.04 CarO-Oxa23 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
2770 0.37 CarO-Oxa23 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
1299 0.18 CarO-Oxa23 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0696 0.23 CarO-Oxa23redo4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed - Shared
0692 0.14 CarO-Oxa23redo4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0690 0.01 CarO-Oxa23redo3 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0688 0 CarO-Oxa23 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
Page generated in 0.1202 seconds.