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OPENSEQ.org
4501
Genes: A B A+B
Length: 118 92 195
Sequences: 1619 644 305
Seq/Len: 13.72 7 1.56
MirrorTree (Pazo et al. 2001) 0.67
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 1.45
2 0.01 0.01 1.46
5 0.02 0.01 1.46
10 0.03 0.02 1.46
20 0.03 0.02 1.46
100 0.05 0.02 1.47
∞ 0.09 0.04 1.51
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
23_I 74_G 2.06 0.99 0.94
61_D 52_K 1.60 0.91 0.78
36_Y 60_F 1.56 0.90 0.75
29_K 78_G 1.38 0.80 0.59
38_D 75_A 1.28 0.73 0.49
23_I 72_D 1.17 0.62 0.38
29_K 53_F 1.13 0.59 0.34
54_A 74_G 1.11 0.56 0.31
68_A 42_T 1.10 0.56 0.31
20_E 73_K 1.09 0.54 0.30
20_E 72_D 1.09 0.54 0.29
50_E 29_W 1.08 0.54 0.29
93_I 10_R 1.07 0.53 0.28
62_C 66_H 1.03 0.49 0.25
32_N 29_W 1.03 0.48 0.24
22_D 38_A 1.03 0.48 0.24
112_R 18_V 1.02 0.47 0.23
83_V 30_D 1.01 0.46 0.23
54_A 73_K 1.01 0.46 0.22
39_F 18_V 1.00 0.46 0.22
19_F 31_D 0.99 0.44 0.21
28_G 66_H 0.95 0.40 0.18
26_F 18_V 0.95 0.40 0.18
11_K 48_G 0.94 0.39 0.17
27_R 78_G 0.93 0.38 0.17
30_F 29_W 0.93 0.38 0.16
86_H 13_K 0.91 0.36 0.15
76_Q 62_T 0.91 0.36 0.15
67_I 54_Q 0.90 0.35 0.15
57_E 50_R 0.90 0.35 0.14
71_R 44_K 0.89 0.34 0.14
54_A 75_A 0.89 0.34 0.14
41_A 69_N 0.88 0.33 0.13
67_I 59_K 0.88 0.33 0.13
57_E 52_K 0.88 0.33 0.13
85_H 70_V 0.85 0.30 0.12
12_G 66_H 0.83 0.29 0.11
87_I 37_K 0.83 0.29 0.11
36_Y 56_G 0.82 0.28 0.10
102_K 36_I 0.82 0.28 0.10
43_S 81_E 0.82 0.28 0.10
28_G 63_H 0.81 0.27 0.10
56_D 76_V 0.81 0.27 0.10
71_R 10_R 0.80 0.26 0.09
15_A 76_V 0.80 0.26 0.09
23_I 75_A 0.80 0.26 0.09
17_V 19_M 0.80 0.26 0.09
21_A 52_K 0.79 0.26 0.09
66_G 40_G 0.79 0.26 0.09
64_E 44_K 0.79 0.25 0.09
54_A 61_S 0.79 0.25 0.09
7_I 79_L 0.78 0.24 0.08
89_S 7_L 0.78 0.24 0.08
40_V 74_G 0.77 0.24 0.08
21_A 9_S 0.77 0.24 0.08
85_H 76_V 0.77 0.24 0.08
16_A 18_V 0.76 0.23 0.08
30_F 57_T 0.76 0.23 0.07
73_E 79_L 0.75 0.22 0.07
62_C 63_H 0.74 0.22 0.07
61_D 61_S 0.74 0.22 0.07
30_F 82_W 0.74 0.22 0.07
79_L 38_A 0.74 0.21 0.07
48_Y 24_K 0.73 0.21 0.07
66_G 69_N 0.73 0.21 0.07
69_P 66_H 0.73 0.21 0.07
18_T 69_N 0.73 0.21 0.07
59_M 47_N 0.73 0.21 0.07
91_L 30_D 0.72 0.20 0.06
69_P 63_H 0.72 0.20 0.06
78_R 27_I 0.72 0.20 0.06
84_P 85_N 0.72 0.20 0.06
45_E 34_A 0.72 0.20 0.06
41_A 15_F 0.72 0.20 0.06
62_C 65_P 0.71 0.20 0.06
104_Q 82_W 0.71 0.20 0.06
67_I 72_D 0.71 0.20 0.06
65_D 54_Q 0.71 0.20 0.06
91_L 41_G 0.71 0.20 0.06
107_V 36_I 0.71 0.20 0.06
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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