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OPENSEQ.org
TA_eight
Genes: A B A+B
Length: 88 440 505
Sequences: 23291 1914 310
Seq/Len: 264.67 4.35 0.61
MirrorTree (Pazo et al. 2001) 0.71
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 0.06 0.01 0.59
2 0.07 0.02 0.61
5 0.09 0.03 0.66
10 0.10 0.03 0.70
20 0.12 0.04 0.80
100 0.18 0.07 1.24
∞ 0.22 0.12 2.26
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
26_W 13_V 1.58 0.69 0.00
63_S 227_N 1.25 0.42 0.00
58_F 249_R 1.23 0.40 0.00
41_T 16_L 1.21 0.39 0.00
61_L 104_I 1.19 0.38 0.00
28_Q 100_A 1.18 0.37 0.00
66_L 394_D 1.16 0.35 0.00
16_A 40_P 1.15 0.35 0.00
60_I 369_I 1.14 0.34 0.00
32_A 328_T 1.13 0.33 0.00
66_L 238_R 1.12 0.32 0.00
27_T 375_L 1.11 0.32 0.00
45_F 279_M 1.09 0.30 0.00
16_A 256_C 1.08 0.30 0.00
44_N 92_E 1.07 0.29 0.00
13_L 211_K 1.07 0.29 0.00
14_A 45_L 1.06 0.28 0.00
70_L 326_R 1.06 0.28 0.00
41_T 236_F 1.06 0.28 0.00
57_F 328_T 1.06 0.28 0.00
55_T 399_I 1.05 0.27 0.00
30_E 397_R 1.04 0.27 0.00
32_A 6_T 1.04 0.27 0.00
13_L 264_S 1.01 0.26 0.00
20_V 26_F 1.01 0.25 0.00
39_Q 75_I 1.00 0.25 0.00
64_L 41_L 0.98 0.23 0.00
16_A 75_I 0.97 0.23 0.00
66_L 150_S 0.97 0.23 0.00
60_I 32_W 0.97 0.23 0.00
25_G 306_G 0.97 0.23 0.00
25_G 398_M 0.96 0.23 0.00
48_N 279_M 0.96 0.23 0.00
37_I 418_V 0.95 0.22 0.00
23_Q 221_E 0.95 0.22 0.00
15_N 216_N 0.94 0.21 0.00
65_E 279_M 0.94 0.21 0.00
68_M 160_L 0.93 0.21 0.00
52_T 258_T 0.93 0.20 0.00
13_L 46_P 0.92 0.20 0.00
75_N 216_N 0.92 0.20 0.00
37_I 46_P 0.91 0.20 0.00
69_T 374_F 0.91 0.20 0.00
17_M 205_Y 0.91 0.20 0.00
28_Q 94_G 0.91 0.20 0.00
64_L 154_A 0.91 0.19 0.00
35_I 59_N 0.91 0.19 0.00
11_T 180_I 0.90 0.19 0.00
13_L 416_E 0.90 0.19 0.00
34_K 180_I 0.90 0.19 0.00
22_Q 261_L 0.90 0.19 0.00
64_L 58_F 0.89 0.19 0.00
26_W 166_D 0.89 0.18 0.00
31_L 40_P 0.89 0.18 0.00
25_G 225_A 0.89 0.18 0.00
17_M 395_F 0.89 0.18 0.00
64_L 103_L 0.88 0.18 0.00
26_W 41_L 0.88 0.18 0.00
17_M 416_E 0.87 0.18 0.00
54_L 243_E 0.87 0.18 0.00
76_A 376_A 0.87 0.17 0.00
31_L 26_F 0.87 0.17 0.00
59_K 220_A 0.87 0.17 0.00
59_K 121_T 0.87 0.17 0.00
43_S 231_L 0.86 0.17 0.00
57_F 4_L 0.86 0.17 0.00
65_E 131_A 0.86 0.17 0.00
47_N 207_L 0.85 0.17 0.00
80_S 277_R 0.85 0.17 0.00
27_T 160_L 0.85 0.17 0.00
32_A 127_E 0.84 0.16 0.00
54_L 45_L 0.84 0.16 0.00
54_L 242_A 0.83 0.16 0.00
32_A 160_L 0.83 0.16 0.00
57_F 79_Y 0.83 0.16 0.00
21_R 153_G 0.82 0.15 0.00
21_R 157_K 0.82 0.15 0.00
21_R 181_K 0.82 0.15 0.00
21_R 311_H 0.82 0.15 0.00
21_R 332_D 0.82 0.15 0.00
24_N 41_L 0.82 0.15 0.00
17_M 85_Q 0.82 0.15 0.00
59_K 180_I 0.82 0.15 0.00
14_A 204_Y 0.82 0.15 0.00
41_T 182_L 0.82 0.15 0.00
14_A 357_N 0.82 0.15 0.00
68_M 312_A 0.82 0.15 0.00
22_Q 36_R 0.82 0.15 0.00
40_A 312_A 0.82 0.15 0.00
42_I 271_G 0.81 0.15 0.00
28_Q 105_P 0.81 0.15 0.00
17_M 288_A 0.81 0.15 0.00
42_I 26_F 0.81 0.15 0.00
29_S 328_T 0.81 0.15 0.00
19_L 349_D 0.81 0.15 0.00
29_S 404_D 0.81 0.15 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
4756 0.61 TA_eight Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
0733 0.46 3DNV_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed
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