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OPENSEQ.org
ParAChpT
Genes: A B A+B
Length: 267 225 465
Sequences: 14735 276 185
Seq/Len: 55.19 1.23 0.4
MirrorTree (Pazo et al. 2001) 0.15
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 0.02 0.00 0.00
2 0.03 0.00 0.00
5 0.03 0.00 0.00
10 0.05 0.00 0.00
20 0.06 0.00 0.03
100 0.10 0.00 0.13
∞ 0.18 0.00 0.38
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
208_A 208_I 1.43 0.44 0.00
33_A 161_A 1.33 0.38 0.00
129_L 208_I 1.30 0.35 0.00
152_V 50_E 1.21 0.30 0.00
235_V 219_I 1.09 0.23 0.00
130_I 106_A 1.09 0.23 0.00
181_R 192_V 1.07 0.22 0.00
24_A 50_E 1.06 0.22 0.00
188_V 69_A 1.06 0.21 0.00
86_L 31_L 1.06 0.21 0.00
242_C 62_M 1.06 0.21 0.00
131_D 33_H 1.03 0.20 0.00
38_V 205_G 1.03 0.20 0.00
30_A 203_A 1.01 0.19 0.00
187_V 127_R 1.00 0.18 0.00
219_I 173_E 0.99 0.18 0.00
44_D 33_H 0.97 0.18 0.00
74_V 148_V 0.96 0.17 0.00
204_K 23_F 0.96 0.17 0.00
17_G 33_H 0.94 0.16 0.00
53_L 49_L 0.94 0.16 0.00
37_R 109_R 0.94 0.16 0.00
10_A 86_S 0.94 0.16 0.00
200_E 160_I 0.93 0.16 0.00
8_V 158_S 0.93 0.16 0.00
131_D 80_R 0.91 0.15 0.00
241_K 122_N 0.91 0.15 0.00
129_L 94_S 0.91 0.15 0.00
24_A 22_D 0.91 0.15 0.00
131_D 34_D 0.91 0.15 0.00
188_V 51_D 0.90 0.15 0.00
27_L 45_G 0.90 0.15 0.00
255_V 51_D 0.90 0.15 0.00
222_N 165_G 0.90 0.15 0.00
85_G 148_V 0.90 0.15 0.00
257_S 192_V 0.89 0.14 0.00
112_L 206_G 0.89 0.14 0.00
87_D 214_E 0.88 0.14 0.00
42_D 33_H 0.88 0.14 0.00
19_G 33_H 0.88 0.14 0.00
16_G 33_H 0.88 0.14 0.00
112_L 161_A 0.87 0.14 0.00
168_M 111_T 0.87 0.14 0.00
117_E 27_L 0.87 0.14 0.00
188_V 123_K 0.87 0.14 0.00
31_L 23_F 0.85 0.13 0.00
116_L 51_D 0.85 0.13 0.00
188_V 39_A 0.85 0.13 0.00
44_D 80_R 0.85 0.13 0.00
11_I 201_V 0.85 0.13 0.00
240_L 215_D 0.85 0.13 0.00
44_D 34_D 0.84 0.13 0.00
211_G 219_I 0.84 0.13 0.00
124_P 217_A 0.84 0.13 0.00
252_A 85_A 0.83 0.12 0.00
147_A 36_I 0.83 0.12 0.00
188_V 133_A 0.83 0.12 0.00
17_G 80_R 0.82 0.12 0.00
27_L 28_A 0.82 0.12 0.00
49_C 83_F 0.81 0.12 0.00
17_G 34_D 0.81 0.12 0.00
117_E 29_A 0.81 0.12 0.00
252_A 45_G 0.81 0.12 0.00
255_V 187_L 0.81 0.12 0.00
9_L 23_F 0.81 0.12 0.00
24_A 112_L 0.81 0.12 0.00
33_A 62_M 0.80 0.12 0.00
103_G 69_A 0.80 0.12 0.00
10_A 38_P 0.80 0.12 0.00
151_F 46_L 0.80 0.12 0.00
253_R 30_R 0.80 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
12166 0.4 ParAChpT Δgene:(1, ∞) A:(1E-20, 4) B:(1E-10, 4) msa: HHblits (2015_06) 0.00 Done - Shared
12163 25.33 ParAChpT Δgene:(1, ∞) A:(1E-10, 4) B:(1E-06, 4) msa: HHblits (2015_06) 0.00 Done - Shared
12148 25.89 ParAChpT Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
12147 27.69 ParAChpT Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
12137 0.4 ParAChpT Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
12132 0.03 ParAChpT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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