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OPENSEQ.org
hA9_1-93_hTLR4_1-500
Genes: A B A+B
Length: 92 531 589
Sequences: 7243 259 57
Seq/Len: 78.73 0.49 0.1
MirrorTree (Pazo et al. 2001) 0.55
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.12 0.09 0.00
2 0.13 0.09 0.00
5 0.13 0.09 0.00
10 0.13 0.09 0.00
20 0.14 0.09 0.03
100 0.17 0.10 0.04
∞ 0.20 0.10 0.09
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
79_F 424_L 1.55 0.22 0.00
19_F 152_L 1.47 0.19 0.00
8_L 430_Q 1.42 0.18 0.00
76_F 428_D 1.40 0.17 0.00
29_P 482_S 1.31 0.15 0.00
62_I 373_P 1.30 0.15 0.00
19_F 424_L 1.27 0.14 0.00
23_S 424_L 1.20 0.12 0.00
79_F 177_L 1.16 0.11 0.00
16_I 496_R 1.16 0.11 0.00
66_L 409_N 1.16 0.11 0.00
21_Q 105_S 1.14 0.11 0.00
11_N 430_Q 1.14 0.11 0.00
19_F 83_L 1.08 0.10 0.00
15_I 473_L 1.07 0.10 0.00
23_S 449_L 1.07 0.10 0.00
37_F 85_L 1.07 0.10 0.00
23_S 177_L 1.06 0.10 0.00
72_K 356_L 1.06 0.10 0.00
75_S 376_E 1.06 0.10 0.00
32_L 418_F 1.04 0.09 0.00
8_L 57_K 1.04 0.09 0.00
8_L 471_S 1.04 0.09 0.00
19_F 80_L 1.04 0.09 0.00
67_D 353_L 1.02 0.09 0.00
76_F 182_L 1.02 0.09 0.00
23_S 83_L 1.02 0.09 0.00
79_F 476_L 1.01 0.09 0.00
67_D 404_L 1.00 0.09 0.00
19_F 104_L 1.00 0.09 0.00
74_L 434_L 1.00 0.09 0.00
22_Y 454_I 0.99 0.08 0.00
10_R 387_F 0.98 0.08 0.00
30_D 498_L 0.98 0.08 0.00
23_S 80_L 0.96 0.08 0.00
83_M 249_G 0.96 0.08 0.00
14_T 136_T 0.96 0.08 0.00
30_D 404_L 0.96 0.08 0.00
55_N 354_K 0.96 0.08 0.00
15_I 381_S 0.96 0.08 0.00
66_L 155_L 0.96 0.08 0.00
71_D 263_F 0.95 0.08 0.00
59_I 488_L 0.94 0.08 0.00
33_N 470_L 0.94 0.08 0.00
59_I 95_D 0.94 0.08 0.00
79_F 107_L 0.94 0.08 0.00
84_A 317_S 0.94 0.08 0.00
23_S 104_L 0.94 0.08 0.00
78_E 449_L 0.94 0.08 0.00
69_N 215_M 0.93 0.08 0.00
19_F 85_L 0.93 0.07 0.00
77_E 381_S 0.93 0.07 0.00
53_N 253_L 0.92 0.07 0.00
22_Y 409_N 0.92 0.07 0.00
67_D 80_L 0.92 0.07 0.00
36_E 363_G 0.92 0.07 0.00
59_I 141_L 0.91 0.07 0.00
8_L 202_P 0.91 0.07 0.00
15_I 174_L 0.91 0.07 0.00
17_N 61_L 0.91 0.07 0.00
76_F 454_I 0.91 0.07 0.00
28_H 233_L 0.90 0.07 0.00
63_M 399_T 0.90 0.07 0.00
36_E 476_L 0.90 0.07 0.00
86_L 50_D 0.90 0.07 0.00
16_I 125_L 0.90 0.07 0.00
72_K 385_L 0.90 0.07 0.00
71_D 363_G 0.90 0.07 0.00
62_I 418_F 0.89 0.07 0.00
29_P 59_L 0.89 0.07 0.00
40_L 143_N 0.89 0.07 0.00
79_F 131_L 0.89 0.07 0.00
19_F 155_L 0.89 0.07 0.00
56_E 379_D 0.89 0.07 0.00
30_D 429_F 0.89 0.07 0.00
74_L 364_G 0.89 0.07 0.00
76_F 430_Q 0.89 0.07 0.00
23_S 152_L 0.88 0.07 0.00
67_D 452_L 0.88 0.07 0.00
10_R 332_W 0.88 0.07 0.00
14_T 409_N 0.87 0.07 0.00
29_P 410_G 0.86 0.07 0.00
24_V 93_I 0.86 0.07 0.00
37_F 69_L 0.86 0.07 0.00
32_L 174_L 0.86 0.07 0.00
36_E 452_L 0.86 0.07 0.00
74_L 141_L 0.86 0.07 0.00
35_G 139_A 0.86 0.07 0.00
62_I 454_I 0.86 0.07 0.00
71_D 281_C 0.85 0.07 0.00
37_F 195_L 0.85 0.07 0.00
24_V 418_F 0.85 0.07 0.00
75_S 77_F 0.84 0.06 0.00
32_L 382_R 0.84 0.06 0.00
36_E 101_L 0.84 0.06 0.00
44_D 229_H 0.84 0.06 0.00
62_I 452_L 0.84 0.06 0.00
35_G 155_L 0.84 0.06 0.00
19_F 93_I 0.84 0.06 0.00
79_F 180_L 0.83 0.06 0.00
55_N 232_T 0.83 0.06 0.00
66_L 114_I 0.83 0.06 0.00
28_H 409_N 0.83 0.06 0.00
77_E 418_F 0.83 0.06 0.00
44_D 69_L 0.83 0.06 0.00
62_I 149_L 0.83 0.06 0.00
15_I 482_S 0.83 0.06 0.00
74_L 55_S 0.82 0.06 0.00
79_F 128_L 0.82 0.06 0.00
32_L 319_T 0.82 0.06 0.00
19_F 128_L 0.82 0.06 0.00
23_S 155_L 0.82 0.06 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)
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