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OPENSEQ.org
S10_S14_test
Genes: A B A+B
Length: 103 101 203
Sequences: 705 1451 398
Seq/Len: 6.84 14.37 1.96
MirrorTree (Pazo et al. 2001) 0.65
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.00 0.06
20 0.00 0.00 1.95
100 0.00 0.00 2.22
∞ 0.00 0.00 2.96
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
48_R 99_A 2.85 1.00 1.00
50_T 74_L 1.57 0.93 0.87
47_E 76_K 1.55 0.93 0.86
60_D 89_M 1.43 0.88 0.79
101_S 42_W 1.38 0.85 0.75
89_R 54_D 1.33 0.82 0.71
13_F 29_A 1.26 0.78 0.65
80_T 79_L 1.22 0.74 0.60
64_Q 93_I 1.19 0.71 0.57
56_H 55_S 1.18 0.70 0.56
22_T 80_S 1.16 0.68 0.54
17_L 49_Q 1.13 0.66 0.51
18_I 74_L 1.09 0.61 0.45
69_T 70_P 1.05 0.57 0.41
84_V 76_K 1.04 0.56 0.40
18_I 87_A 1.03 0.55 0.39
74_V 97_K 1.02 0.55 0.38
18_I 49_Q 1.02 0.55 0.38
58_N 83_K 1.01 0.53 0.37
67_I 71_H 1.01 0.53 0.37
67_I 96_L 1.01 0.53 0.37
52_L 10_E 1.00 0.52 0.36
63_D 10_E 1.00 0.52 0.36
67_I 87_A 0.99 0.51 0.35
17_L 9_R 0.99 0.50 0.34
40_I 55_S 0.98 0.49 0.33
78_E 21_F 0.98 0.49 0.33
58_N 72_G 0.98 0.49 0.33
58_N 6_M 0.97 0.49 0.33
65_Y 89_M 0.96 0.47 0.31
53_I 87_A 0.95 0.47 0.30
91_D 84_V 0.95 0.46 0.30
18_I 89_M 0.93 0.44 0.28
22_T 55_S 0.92 0.43 0.27
79_P 76_K 0.92 0.43 0.27
58_N 55_S 0.92 0.42 0.27
48_R 55_S 0.92 0.42 0.27
60_D 87_A 0.91 0.42 0.26
60_D 54_D 0.91 0.42 0.26
17_L 12_K 0.91 0.42 0.26
37_R 50_T 0.91 0.41 0.26
58_N 58_S 0.90 0.41 0.25
61_A 89_M 0.90 0.40 0.25
17_L 77_F 0.89 0.40 0.24
93_A 45_V 0.89 0.39 0.24
58_N 74_L 0.88 0.39 0.23
82_K 10_E 0.88 0.39 0.23
49_F 15_A 0.88 0.39 0.23
81_E 89_M 0.88 0.38 0.23
63_D 89_M 0.87 0.38 0.22
77_V 92_E 0.87 0.37 0.22
61_A 92_E 0.86 0.37 0.22
61_A 6_M 0.86 0.37 0.22
44_T 19_K 0.86 0.37 0.22
5_R 37_S 0.86 0.37 0.22
20_Q 72_G 0.85 0.36 0.21
63_D 58_S 0.85 0.35 0.20
65_Y 87_A 0.84 0.35 0.20
17_L 19_K 0.84 0.35 0.20
53_I 54_D 0.83 0.34 0.19
18_I 12_K 0.83 0.34 0.19
30_K 91_G 0.83 0.33 0.19
61_A 87_A 0.83 0.33 0.19
13_F 8_A 0.82 0.33 0.18
98_V 74_L 0.82 0.33 0.18
17_L 78_G 0.82 0.32 0.18
13_F 46_L 0.81 0.32 0.17
37_R 97_K 0.80 0.31 0.17
13_F 84_V 0.80 0.31 0.17
86_A 23_K 0.80 0.30 0.16
46_K 10_E 0.80 0.30 0.16
85_D 49_Q 0.79 0.30 0.16
45_R 23_K 0.79 0.30 0.16
21_A 93_I 0.79 0.30 0.16
60_D 6_M 0.79 0.29 0.16
77_V 8_A 0.78 0.29 0.15
101_S 72_G 0.78 0.28 0.15
58_N 10_E 0.78 0.28 0.15
12_A 22_A 0.77 0.28 0.14
73_L 16_L 0.77 0.28 0.14
57_V 78_G 0.77 0.27 0.14
52_L 4_Q 0.76 0.27 0.14
50_T 28_K 0.76 0.27 0.14
74_V 98_K 0.76 0.27 0.13
12_A 73_F 0.76 0.27 0.13
81_E 5_S 0.75 0.26 0.13
70_H 55_S 0.75 0.26 0.13
46_K 66_Q 0.75 0.26 0.13
54_S 77_F 0.75 0.26 0.13
8_I 93_I 0.75 0.26 0.13
3_N 72_G 0.75 0.26 0.13
69_T 76_K 0.75 0.26 0.13
102_L 15_A 0.75 0.26 0.13
68_R 4_Q 0.75 0.26 0.13
93_A 71_H 0.74 0.26 0.13
63_D 88_A 0.74 0.26 0.13
80_T 44_A 0.74 0.26 0.13
102_L 71_H 0.74 0.25 0.12
47_E 96_L 0.74 0.25 0.12
35_Q 72_G 0.74 0.25 0.12
65_Y 88_A 0.73 0.25 0.12
53_I 42_W 0.73 0.24 0.12
61_A 60_Q 0.73 0.24 0.12
36_V 48_L 0.73 0.24 0.12
60_D 90_R 0.72 0.24 0.12
44_T 62_N 0.72 0.24 0.11
49_F 62_N 0.72 0.24 0.11
53_I 96_L 0.72 0.23 0.11
84_V 51_L 0.72 0.23 0.11
86_A 28_K 0.72 0.23 0.11
20_Q 97_K 0.71 0.23 0.11
20_Q 77_F 0.71 0.23 0.11
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
7673 2.1 3i1o_J_N Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
2502 1.96 S10_S14_test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done
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