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OPENSEQ.org
xs-1
Genes: A B A+B
Length: 307 239 512
Sequences: 201 92904 146
Seq/Len: 0.65 388.72 0.29
MirrorTree (Pazo et al. 2001) 0.34
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 0.00 0.04 0.00
2 0.00 0.07 0.04
5 0.00 0.11 0.05
10 0.00 0.14 0.08
20 0.00 0.19 0.11
100 0.00 0.29 0.23
∞ 0.03 0.32 0.27
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
5_V 183_I 1.53 0.43 0.00
123_E 136_I 1.43 0.36 0.00
45_M 183_I 1.29 0.28 0.00
11_T 38_K 1.21 0.24 0.00
10_G 225_G 1.18 0.23 0.00
127_A 74_Q 1.15 0.21 0.00
56_E 155_I 1.15 0.21 0.00
7_L 166_L 1.14 0.21 0.00
212_F 144_A 1.14 0.21 0.00
130_T 62_Y 1.12 0.20 0.00
89_L 98_V 1.11 0.20 0.00
244_F 143_N 1.05 0.17 0.00
244_F 203_G 1.05 0.17 0.00
61_A 106_R 1.05 0.17 0.00
244_F 170_D 1.04 0.17 0.00
244_F 172_G 1.03 0.17 0.00
25_D 166_L 1.03 0.17 0.00
128_Y 46_L 1.02 0.16 0.00
206_V 141_L 1.02 0.16 0.00
60_A 24_N 1.02 0.16 0.00
8_A 168_I 1.02 0.16 0.00
244_F 174_G 1.01 0.16 0.00
5_V 223_T 0.99 0.15 0.00
103_I 44_M 0.98 0.15 0.00
112_I 137_I 0.98 0.15 0.00
9_G 35_H 0.98 0.15 0.00
22_I 140_I 0.97 0.14 0.00
268_I 141_L 0.97 0.14 0.00
46_T 183_I 0.95 0.14 0.00
71_F 41_V 0.95 0.14 0.00
188_F 206_L 0.94 0.14 0.00
87_R 232_L 0.94 0.13 0.00
92_I 166_L 0.94 0.13 0.00
22_I 170_D 0.93 0.13 0.00
249_E 72_D 0.93 0.13 0.00
54_H 214_L 0.92 0.13 0.00
127_A 177_K 0.92 0.13 0.00
190_K 168_I 0.92 0.13 0.00
260_Y 43_A 0.92 0.13 0.00
189_V 100_D 0.91 0.12 0.00
218_A 225_G 0.91 0.12 0.00
63_N 161_D 0.91 0.12 0.00
37_N 202_M 0.90 0.12 0.00
22_I 174_G 0.90 0.12 0.00
16_K 228_T 0.90 0.12 0.00
27_E 116_F 0.90 0.12 0.00
59_V 180_M 0.89 0.12 0.00
139_F 49_D 0.89 0.12 0.00
9_G 143_N 0.88 0.12 0.00
9_G 203_G 0.88 0.12 0.00
61_A 137_I 0.88 0.12 0.00
139_F 70_M 0.88 0.12 0.00
232_V 155_I 0.88 0.12 0.00
63_N 92_V 0.88 0.12 0.00
181_M 49_D 0.87 0.11 0.00
54_H 92_V 0.87 0.11 0.00
4_K 226_K 0.87 0.11 0.00
189_V 90_D 0.87 0.11 0.00
255_I 111_V 0.86 0.11 0.00
172_N 140_I 0.86 0.11 0.00
52_I 31_T 0.85 0.11 0.00
125_L 168_I 0.85 0.11 0.00
67_I 82_S 0.85 0.11 0.00
56_E 141_L 0.85 0.11 0.00
122_I 8_Q 0.84 0.11 0.00
26_A 133_C 0.84 0.11 0.00
104_N 125_Y 0.84 0.11 0.00
170_L 140_I 0.84 0.11 0.00
10_G 107_H 0.84 0.10 0.00
260_Y 158_E 0.84 0.10 0.00
15_G 143_N 0.84 0.10 0.00
15_G 203_G 0.84 0.10 0.00
186_G 228_T 0.84 0.10 0.00
263_R 41_V 0.84 0.10 0.00
117_Y 23_L 0.83 0.10 0.00
4_K 205_Y 0.83 0.10 0.00
133_E 105_T 0.83 0.10 0.00
126_G 128_T 0.83 0.10 0.00
233_K 141_L 0.82 0.10 0.00
104_N 90_D 0.82 0.10 0.00
26_A 231_R 0.82 0.10 0.00
209_L 157_T 0.81 0.10 0.00
5_V 185_E 0.81 0.10 0.00
77_N 41_V 0.81 0.10 0.00
10_G 202_M 0.81 0.10 0.00
37_N 183_I 0.81 0.10 0.00
63_N 153_I 0.81 0.10 0.00
93_A 108_I 0.81 0.10 0.00
222_I 175_I 0.80 0.10 0.00
210_A 87_M 0.80 0.10 0.00
144_V 178_K 0.80 0.10 0.00
25_D 130_I 0.80 0.10 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
13438 0.29 xs-1 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13437 1.9 xs Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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