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OPENSEQ.org
1XQS_l_u_Apdb 1XQS_r_u_Apdb
Genes: A B A+B
Length: 193 259 403
Sequences: 14616 2110 114
Seq/Len: 75.73 8.15 0.28
MirrorTree (Pazo et al. 2001) 0.33
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 0.05 0.04 0.05
2 0.06 0.05 0.08
5 0.06 0.05 0.12
10 0.06 0.05 0.17
20 0.08 0.05 0.25
100 0.14 0.06 0.73
∞ 0.22 0.12 1.44
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
16_F 124_A 1.42 0.35 0.00
48_L 204_A 1.35 0.31 0.00
165_F 125_I 1.35 0.31 0.00
8_I 31_D 1.30 0.28 0.00
5_N 102_L 1.26 0.26 0.00
108_I 188_A 1.22 0.24 0.00
116_L 78_A 1.18 0.22 0.00
152_T 167_N 1.17 0.21 0.00
98_L 86_S 1.11 0.19 0.00
161_L 125_I 1.10 0.19 0.00
137_L 60_H 1.09 0.18 0.00
128_V 56_Q 1.05 0.17 0.00
180_V 125_I 1.05 0.17 0.00
145_L 36_E 1.03 0.16 0.00
137_L 184_Q 1.02 0.16 0.00
170_L 209_V 1.01 0.15 0.00
145_L 74_L 1.00 0.15 0.00
183_G 205_L 1.00 0.15 0.00
70_A 186_L 0.99 0.15 0.00
86_S 85_C 0.98 0.14 0.00
142_I 185_Q 0.98 0.14 0.00
180_V 165_L 0.98 0.14 0.00
78_C 186_L 0.97 0.14 0.00
142_I 72_A 0.96 0.14 0.00
101_G 129_V 0.94 0.13 0.00
128_V 81_L 0.94 0.13 0.00
142_I 125_I 0.94 0.13 0.00
12_G 208_L 0.94 0.13 0.00
183_G 82_I 0.93 0.13 0.00
10_D 186_L 0.93 0.13 0.00
75_R 209_V 0.92 0.12 0.00
77_A 59_G 0.92 0.12 0.00
169_D 227_E 0.92 0.12 0.00
32_A 169_L 0.91 0.12 0.00
70_A 201_V 0.91 0.12 0.00
162_Q 85_C 0.91 0.12 0.00
51_H 121_A 0.91 0.12 0.00
162_Q 114_C 0.91 0.12 0.00
152_T 205_L 0.91 0.12 0.00
101_G 122_L 0.90 0.12 0.00
128_V 149_R 0.90 0.12 0.00
88_S 108_L 0.89 0.12 0.00
20_I 117_V 0.89 0.12 0.00
82_K 208_L 0.89 0.12 0.00
13_G 125_I 0.89 0.12 0.00
131_A 187_V 0.89 0.12 0.00
64_I 85_C 0.88 0.12 0.00
183_G 63_V 0.88 0.11 0.00
55_E 205_L 0.87 0.11 0.00
182_Y 228_E 0.87 0.11 0.00
161_L 60_H 0.87 0.11 0.00
9_F 211_D 0.87 0.11 0.00
131_A 162_A 0.87 0.11 0.00
14_G 208_L 0.86 0.11 0.00
8_I 61_L 0.86 0.11 0.00
169_D 189_L 0.86 0.11 0.00
12_G 190_V 0.85 0.11 0.00
151_S 45_L 0.85 0.11 0.00
8_I 234_C 0.85 0.11 0.00
149_G 208_L 0.85 0.10 0.00
170_L 81_L 0.85 0.10 0.00
18_V 174_E 0.84 0.10 0.00
151_S 183_V 0.84 0.10 0.00
90_Q 82_I 0.84 0.10 0.00
165_F 169_L 0.83 0.10 0.00
24_D 133_E 0.83 0.10 0.00
140_A 187_V 0.82 0.10 0.00
177_D 49_D 0.82 0.10 0.00
70_A 132_Q 0.82 0.10 0.00
149_G 82_I 0.81 0.10 0.00
16_F 158_K 0.81 0.10 0.00
182_Y 127_C 0.81 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
6951 0.28 1XQS_l_u_Apdb 1XQS_r_u_Apdb Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6943 0.02 1XQS_l_u_Apdb 1XQS_r_u_Apdb Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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