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OPENSEQ.org
hA9_1-93_hTLR4_1-631
Genes: A B A+B
Length: 92 631 678
Sequences: 6477 1697 183
Seq/Len: 70.4 2.69 0.27
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 0.06 0.07 0.01
2 0.06 0.07 0.01
5 0.07 0.07 0.01
10 0.07 0.08 0.02
20 0.08 0.08 0.02
100 0.11 0.09 0.10
∞ 0.17 0.11 0.25
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
76_F 77_F 1.74 0.55 0.00
19_F 114_I 1.42 0.34 0.00
76_F 416_S 1.23 0.24 0.00
74_L 110_T 1.20 0.22 0.00
32_L 150_K 1.16 0.21 0.00
79_F 114_I 1.15 0.20 0.00
19_F 546_L 1.11 0.19 0.00
18_T 180_L 1.10 0.18 0.00
30_D 434_L 1.10 0.18 0.00
15_I 126_S 1.08 0.18 0.00
41_V 233_L 1.08 0.17 0.00
71_D 136_T 1.08 0.17 0.00
67_D 511_L 1.07 0.17 0.00
36_E 476_L 1.06 0.17 0.00
20_H 531_N 1.04 0.16 0.00
74_L 195_L 1.03 0.16 0.00
45_L 77_F 1.02 0.15 0.00
36_E 106_T 1.01 0.15 0.00
19_F 231_L 1.00 0.15 0.00
28_H 149_L 0.99 0.14 0.00
83_M 454_I 0.98 0.14 0.00
12_I 74_F 0.98 0.14 0.00
74_L 548_V 0.98 0.14 0.00
78_E 530_N 0.97 0.14 0.00
62_I 290_L 0.97 0.14 0.00
36_E 128_L 0.97 0.14 0.00
29_P 415_S 0.96 0.14 0.00
15_I 82_V 0.96 0.14 0.00
37_F 59_L 0.96 0.13 0.00
36_E 96_G 0.96 0.13 0.00
77_E 146_I 0.96 0.13 0.00
76_F 454_I 0.95 0.13 0.00
35_G 182_L 0.94 0.13 0.00
29_P 559_S 0.94 0.13 0.00
75_S 385_L 0.93 0.12 0.00
45_L 101_L 0.93 0.12 0.00
28_H 114_I 0.92 0.12 0.00
74_L 114_I 0.92 0.12 0.00
19_F 525_L 0.92 0.12 0.00
80_I 138_L 0.91 0.12 0.00
77_E 516_F 0.90 0.12 0.00
41_V 414_M 0.89 0.12 0.00
37_F 176_N 0.89 0.11 0.00
40_L 157_V 0.88 0.11 0.00
38_K 133_A 0.88 0.11 0.00
58_V 472_S 0.87 0.11 0.00
28_H 210_L 0.87 0.11 0.00
32_L 190_I 0.87 0.11 0.00
25_K 515_A 0.86 0.11 0.00
80_I 351_K 0.86 0.11 0.00
41_V 576_L 0.86 0.11 0.00
70_A 455_S 0.84 0.10 0.00
79_F 112_N 0.84 0.10 0.00
77_E 48_I 0.84 0.10 0.00
83_M 474_E 0.84 0.10 0.00
83_M 74_F 0.84 0.10 0.00
15_I 324_K 0.83 0.10 0.00
39_E 87_R 0.83 0.10 0.00
71_D 180_L 0.83 0.10 0.00
32_L 67_R 0.82 0.10 0.00
36_E 131_L 0.82 0.10 0.00
16_I 337_L 0.82 0.10 0.00
74_L 339_N 0.82 0.10 0.00
74_L 563_E 0.82 0.10 0.00
19_F 549_L 0.81 0.10 0.00
63_M 151_T 0.81 0.10 0.00
79_F 208_L 0.81 0.10 0.00
19_F 85_L 0.81 0.09 0.00
39_E 109_L 0.80 0.09 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
10394 0.27 hA9_1-93_hTLR4_1-631 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10392 0.37 hA9_1-93_hTLR4_1-631 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10380 0.01 hA9_1-93_hTLR4_1-631 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
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