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OPENSEQ.org
TT
Genes: A B A+B
Length: 88 96 173
Sequences: 174 223 116
Seq/Len: 1.98 2.32 0.67
MirrorTree (Pazo et al. 2001) 0.76
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 0.00 0.00 0.63
2 0.00 0.00 0.63
5 0.00 0.00 0.63
10 0.01 0.00 0.63
20 0.01 0.01 0.63
100 0.01 0.01 0.64
∞ 0.03 0.03 0.66
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
55_L 61_Y 2.39 0.97 0.91
59_E 61_Y 2.17 0.95 0.84
32_E 48_P 1.81 0.84 0.62
57_E 9_R 1.77 0.82 0.59
68_D 18_W 1.61 0.73 0.44
70_D 9_R 1.57 0.70 0.41
67_F 18_W 1.51 0.66 0.36
77_S 30_A 1.47 0.63 0.32
67_F 38_Q 1.46 0.62 0.31
57_E 15_D 1.45 0.61 0.30
4_K 94_H 1.43 0.60 0.29
34_I 64_C 1.42 0.59 0.28
52_R 26_G 1.41 0.58 0.27
69_F 26_G 1.41 0.58 0.27
69_F 38_Q 1.39 0.57 0.26
78_R 56_N 1.38 0.55 0.25
62_G 85_L 1.36 0.54 0.23
9_V 71_V 1.34 0.53 0.23
45_E 83_R 1.34 0.53 0.22
52_R 48_P 1.28 0.47 0.18
34_I 79_V 1.24 0.44 0.16
30_A 7_S 1.20 0.41 0.14
55_L 58_R 1.19 0.40 0.13
66_D 71_V 1.19 0.40 0.13
67_F 30_A 1.16 0.38 0.12
18_I 53_P 1.16 0.38 0.12
77_S 31_A 1.14 0.36 0.11
32_E 73_Y 1.12 0.35 0.10
34_I 44_I 1.12 0.34 0.10
4_K 9_R 1.11 0.34 0.10
55_L 82_I 1.11 0.34 0.10
72_F 18_W 1.10 0.33 0.10
10_L 14_L 1.09 0.33 0.09
28_G 63_R 1.09 0.32 0.09
54_A 18_W 1.08 0.32 0.09
32_E 57_L 1.08 0.32 0.09
21_Q 70_V 1.08 0.32 0.09
9_V 23_Q 1.07 0.31 0.08
9_V 19_T 1.07 0.31 0.08
63_F 76_G 1.07 0.31 0.08
73_I 14_L 1.06 0.30 0.08
73_I 35_R 1.05 0.29 0.08
73_I 88_S 1.05 0.29 0.08
61_S 83_R 1.05 0.29 0.08
66_D 8_R 1.05 0.29 0.08
79_A 87_Q 1.04 0.29 0.07
76_R 26_G 1.03 0.28 0.07
59_E 74_R 1.03 0.28 0.07
50_A 20_Y 1.02 0.28 0.07
59_E 58_R 1.02 0.28 0.07
73_I 94_H 1.01 0.27 0.07
22_V 50_M 1.01 0.27 0.07
18_I 75_V 1.01 0.27 0.06
10_L 70_V 0.99 0.26 0.06
77_S 27_V 0.98 0.25 0.06
73_I 34_A 0.98 0.25 0.06
54_A 83_R 0.98 0.25 0.06
13_H 90_N 0.97 0.24 0.05
66_D 73_Y 0.96 0.23 0.05
77_S 22_E 0.96 0.23 0.05
79_A 31_A 0.95 0.23 0.05
49_A 84_V 0.95 0.23 0.05
4_K 44_I 0.95 0.23 0.05
75_E 11_K 0.94 0.22 0.05
75_E 55_E 0.93 0.22 0.05
48_L 73_Y 0.93 0.22 0.04
73_I 26_G 0.93 0.22 0.04
40_L 85_L 0.93 0.22 0.04
20_S 62_R 0.93 0.22 0.04
40_L 83_R 0.93 0.22 0.04
17_F 85_L 0.92 0.21 0.04
5_N 14_L 0.92 0.21 0.04
9_V 88_S 0.91 0.21 0.04
57_E 16_D 0.91 0.21 0.04
30_A 80_E 0.90 0.20 0.04
3_S 81_I 0.90 0.20 0.04
22_V 5_R 0.90 0.20 0.04
55_L 47_H 0.89 0.20 0.04
64_I 82_I 0.89 0.20 0.04
49_A 75_V 0.89 0.20 0.04
20_S 84_V 0.89 0.20 0.04
47_K 23_Q 0.88 0.19 0.04
48_L 34_A 0.88 0.19 0.04
18_I 84_V 0.88 0.19 0.04
68_D 30_A 0.86 0.18 0.03
73_I 22_E 0.85 0.18 0.03
40_L 1_M 0.85 0.18 0.03
4_K 92_R 0.85 0.17 0.03
21_Q 66_S 0.84 0.17 0.03
70_D 37_L 0.84 0.17 0.03
28_G 91_A 0.84 0.17 0.03
29_S 68_S 0.84 0.17 0.03
19_D 22_E 0.84 0.17 0.03
41_L 55_E 0.83 0.17 0.03
69_F 7_S 0.83 0.17 0.03
46_A 47_H 0.83 0.17 0.03
3_S 16_D 0.83 0.17 0.03
53_A 3_P 0.83 0.17 0.03
54_A 30_A 0.83 0.17 0.03
77_S 18_W 0.82 0.17 0.03
47_K 54_D 0.81 0.16 0.03
64_I 8_R 0.81 0.16 0.03
30_A 63_R 0.81 0.16 0.03
37_G 64_C 0.81 0.16 0.03
8_V 26_G 0.81 0.16 0.03
32_E 51_G 0.81 0.16 0.03
5_N 68_S 0.81 0.16 0.03
44_N 91_A 0.81 0.16 0.03
22_V 46_E 0.80 0.15 0.02
12_D 47_H 0.80 0.15 0.02
16_A 59_A 0.80 0.15 0.02
22_V 88_S 0.80 0.15 0.02
3_S 35_R 0.80 0.15 0.02
8_V 43_M 0.80 0.15 0.02
22_V 9_R 0.80 0.15 0.02
76_R 9_R 0.80 0.15 0.02
75_E 79_V 0.79 0.15 0.02
72_F 30_A 0.79 0.15 0.02
53_A 5_R 0.79 0.15 0.02
32_E 89_M 0.78 0.15 0.02
15_Q 21_S 0.78 0.15 0.02
48_L 49_G 0.78 0.14 0.02
74_E 76_G 0.78 0.14 0.02
8_V 40_T 0.78 0.14 0.02
24_D 78_R 0.78 0.14 0.02
53_A 32_D 0.78 0.14 0.02
51_L 74_R 0.78 0.14 0.02
40_L 72_F 0.77 0.14 0.02
14_F 84_V 0.77 0.14 0.02
4_K 37_L 0.77 0.14 0.02
36_A 90_N 0.77 0.14 0.02
5_N 71_V 0.77 0.14 0.02
36_A 25_W 0.77 0.14 0.02
24_D 5_R 0.77 0.14 0.02
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
1175 0.67 TT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.91 Done - Shared
0718 3.72 3KXE Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0663 3.67 Caulobacter ParD-ParE Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
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