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OPENSEQ.org
hA9_1-93_hTLR4_1-631
Genes: A B A+B
Length: 92 631 679
Sequences: 8071 1745 251
Seq/Len: 87.73 2.77 0.37
MirrorTree (Pazo et al. 2001) 0.29
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 0.07 0.07 0.01
2 0.07 0.07 0.02
5 0.08 0.08 0.03
10 0.09 0.08 0.04
20 0.09 0.08 0.05
100 0.14 0.09 0.18
∞ 0.20 0.11 0.35
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
19_F 114_I 1.71 0.62 0.00
74_L 77_F 1.66 0.59 0.00
79_F 481_N 1.38 0.39 0.00
46_Q 114_I 1.36 0.37 0.00
18_T 414_M 1.15 0.25 0.00
25_K 384_G 1.13 0.24 0.00
32_L 340_C 1.10 0.22 0.00
60_E 215_M 1.05 0.20 0.00
37_F 511_L 1.04 0.19 0.00
29_P 162_I 1.03 0.19 0.00
20_H 531_N 1.03 0.19 0.00
80_I 129_Q 1.01 0.18 0.00
19_F 470_L 0.98 0.17 0.00
41_V 233_L 0.97 0.17 0.00
66_L 85_L 0.97 0.16 0.00
29_P 536_D 0.96 0.16 0.00
30_D 162_I 0.96 0.16 0.00
15_I 214_P 0.95 0.16 0.00
76_F 216_N 0.94 0.16 0.00
46_Q 223_F 0.94 0.16 0.00
80_I 420_G 0.94 0.15 0.00
79_F 549_L 0.93 0.15 0.00
40_L 454_I 0.91 0.14 0.00
20_H 233_L 0.91 0.14 0.00
74_L 180_L 0.91 0.14 0.00
76_F 507_Q 0.91 0.14 0.00
18_T 60_D 0.90 0.14 0.00
15_I 126_S 0.90 0.14 0.00
80_I 559_S 0.89 0.14 0.00
36_E 171_F 0.88 0.13 0.00
37_F 506_C 0.88 0.13 0.00
79_F 85_L 0.88 0.13 0.00
29_P 418_F 0.87 0.13 0.00
74_L 532_F 0.87 0.13 0.00
74_L 64_N 0.86 0.13 0.00
36_E 155_L 0.86 0.13 0.00
23_S 501_L 0.86 0.13 0.00
25_K 171_F 0.85 0.12 0.00
74_L 385_L 0.85 0.12 0.00
32_L 124_G 0.85 0.12 0.00
79_F 74_F 0.85 0.12 0.00
8_L 180_L 0.84 0.12 0.00
13_E 477_K 0.83 0.12 0.00
72_K 136_T 0.83 0.12 0.00
41_V 484_Q 0.82 0.12 0.00
23_S 160_N 0.82 0.12 0.00
46_Q 101_L 0.82 0.12 0.00
11_N 315_L 0.82 0.12 0.00
69_N 146_I 0.81 0.11 0.00
79_F 227_R 0.81 0.11 0.00
25_K 135_E 0.81 0.11 0.00
75_S 382_R 0.80 0.11 0.00
25_K 412_I 0.80 0.11 0.00
15_I 82_V 0.80 0.11 0.00
72_K 483_F 0.80 0.11 0.00
30_D 353_L 0.80 0.11 0.00
78_E 501_L 0.80 0.11 0.00
32_L 470_L 0.80 0.11 0.00
18_T 103_H 0.80 0.11 0.00
40_L 403_Y 0.79 0.11 0.00
70_A 338_V 0.79 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
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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