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OPENSEQ.org
TA_five
Genes: A B A+B
Length: 82 111 189
Sequences: 1785 2857 618
Seq/Len: 21.77 25.74 3.27
MirrorTree (Pazo et al. 2001) 0.75
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 0.01 0.01 3.20
2 0.01 0.01 3.20
5 0.02 0.01 3.28
10 0.02 0.02 3.31
20 0.03 0.03 3.38
100 0.04 0.06 3.55
∞ 0.09 0.10 4.46
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
59_V 60_F 1.51 0.96 0.77
56_A 38_M 1.41 0.94 0.70
73_W 79_K 1.39 0.94 0.68
62_I 60_F 1.26 0.89 0.57
59_V 58_Y 1.25 0.88 0.56
53_F 104_A 1.18 0.84 0.49
9_W 25_Q 1.10 0.77 0.41
14_A 54_Q 1.07 0.75 0.38
58_L 105_K 1.07 0.74 0.37
79_K 84_R 1.05 0.73 0.36
72_D 64_L 1.00 0.67 0.30
73_W 48_C 0.99 0.66 0.30
39_D 65_S 0.98 0.66 0.29
42_L 102_I 0.98 0.65 0.28
62_I 59_P 0.97 0.63 0.27
26_N 12_L 0.97 0.63 0.27
62_I 76_D 0.95 0.61 0.26
9_W 27_G 0.94 0.61 0.26
66_N 58_Y 0.94 0.60 0.25
21_L 55_S 0.93 0.59 0.24
16_R 76_D 0.92 0.57 0.23
59_V 59_P 0.91 0.56 0.22
6_V 57_G 0.90 0.56 0.22
21_L 35_S 0.87 0.52 0.20
19_A 48_C 0.87 0.51 0.19
10_G 77_Q 0.87 0.51 0.19
59_V 75_A 0.85 0.49 0.18
54_T 45_M 0.84 0.48 0.17
10_G 86_R 0.84 0.47 0.17
25_L 72_V 0.83 0.47 0.17
46_P 62_V 0.83 0.46 0.16
21_L 97_E 0.82 0.46 0.16
14_A 47_L 0.82 0.46 0.16
10_G 24_E 0.82 0.45 0.16
12_S 25_Q 0.81 0.44 0.15
67_L 53_T 0.81 0.43 0.15
49_K 85_A 0.80 0.43 0.15
4_S 99_L 0.80 0.43 0.15
32_E 73_A 0.80 0.42 0.15
23_Q 100_Q 0.79 0.42 0.14
55_L 32_V 0.79 0.42 0.14
53_F 101_L 0.78 0.40 0.14
55_L 39_Y 0.78 0.40 0.13
57_E 62_V 0.77 0.39 0.13
30_D 51_C 0.76 0.38 0.13
36_D 93_T 0.76 0.38 0.13
21_L 96_P 0.76 0.38 0.12
24_A 27_G 0.76 0.38 0.12
2_I 49_V 0.76 0.37 0.12
66_N 76_D 0.75 0.36 0.12
17_I 102_I 0.74 0.35 0.11
9_W 45_M 0.73 0.34 0.11
68_H 61_E 0.73 0.34 0.11
58_L 44_G 0.73 0.34 0.11
3_H 91_K 0.73 0.34 0.11
10_G 50_P 0.72 0.34 0.10
24_A 93_T 0.72 0.34 0.10
62_I 74_L 0.72 0.33 0.10
63_T 78_V 0.70 0.31 0.09
55_L 61_E 0.70 0.30 0.09
12_S 76_D 0.69 0.30 0.09
80_E 82_A 0.69 0.29 0.09
35_I 7_P 0.69 0.29 0.09
26_N 71_G 0.69 0.29 0.09
61_D 102_I 0.69 0.29 0.09
62_I 58_Y 0.69 0.29 0.09
35_I 97_E 0.68 0.29 0.09
48_R 15_V 0.68 0.29 0.09
10_G 22_G 0.68 0.29 0.09
63_T 99_L 0.68 0.29 0.08
3_H 100_Q 0.68 0.29 0.08
44_I 102_I 0.68 0.28 0.08
23_Q 98_E 0.68 0.28 0.08
23_Q 110_I 0.67 0.28 0.08
8_R 98_E 0.67 0.28 0.08
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
4753 3.27 TA_five Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.77 Done - Shared
0721 2.49 1UB4_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.69 Done - Shared
0719 1.61 1UB4 Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.79 Done - Shared
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