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OPENSEQ.org
GatAC_truncated
Genes: A B A+B
Length: 121 100 216
Sequences: 2277 2469 1881
Seq/Len: 18.82 24.69 8.71
MirrorTree (Pazo et al. 2001) 0.70
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 7.22
2 0.00 0.00 7.42
5 0.00 0.00 7.47
10 0.00 0.00 7.44
20 0.00 0.00 7.49
100 0.01 0.00 7.57
∞ 0.02 0.00 8.51
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
78_K 47_T 3.67 1.00 1.00
84_T 53_T 3.67 1.00 1.00
4_K 41_Q 3.34 1.00 1.00
46_M 19_Q 2.89 1.00 1.00
57_K 24_E 2.61 1.00 1.00
45_K 14_N 2.42 1.00 1.00
49_S 18_L 1.91 1.00 0.98
54_K 27_E 1.85 1.00 0.98
41_E 17_R 1.78 1.00 0.98
87_K 53_T 1.72 1.00 0.97
81_K 48_E 1.67 1.00 0.96
82_V 45_A 1.53 1.00 0.94
5_F 44_S 1.52 1.00 0.94
4_K 44_S 1.51 1.00 0.94
88_N 51_E 1.49 1.00 0.93
8_P 41_Q 1.42 0.99 0.91
82_V 42_N 1.40 0.99 0.90
65_F 8_E 1.40 0.99 0.90
7_I 38_F 1.33 0.99 0.87
120_L 38_F 1.32 0.99 0.87
61_F 28_M 1.31 0.99 0.86
45_K 19_Q 1.28 0.98 0.85
78_K 43_D 1.28 0.98 0.85
64_T 16_A 1.23 0.98 0.82
5_F 45_A 1.23 0.98 0.82
85_L 50_V 1.23 0.98 0.81
60_I 18_L 1.11 0.95 0.72
54_K 24_E 1.07 0.94 0.69
84_T 51_E 1.04 0.93 0.65
80_Q 52_P 1.02 0.91 0.62
81_K 49_G 1.01 0.91 0.61
12_V 39_A 0.96 0.88 0.56
85_L 47_T 0.96 0.88 0.55
49_S 4_V 0.94 0.87 0.54
104_T 90_K 0.94 0.86 0.54
88_N 50_V 0.94 0.86 0.53
84_T 56_V 0.93 0.85 0.52
77_K 52_P 0.92 0.85 0.51
33_H 82_K 0.90 0.83 0.48
61_F 20_I 0.90 0.83 0.48
84_T 58_D 0.87 0.80 0.44
57_K 21_S 0.86 0.79 0.43
43_L 12_I 0.85 0.78 0.42
20_S 53_T 0.80 0.72 0.36
84_T 52_P 0.80 0.72 0.35
82_V 47_T 0.80 0.71 0.35
58_R 35_I 0.78 0.69 0.33
74_A 43_D 0.78 0.69 0.33
15_S 36_L 0.77 0.67 0.32
80_Q 88_Q 0.76 0.66 0.31
80_Q 54_Y 0.76 0.66 0.30
61_F 18_L 0.76 0.65 0.30
36_E 7_E 0.75 0.65 0.30
8_P 38_F 0.74 0.64 0.29
66_A 34_S 0.74 0.63 0.28
62_L 36_L 0.74 0.62 0.28
29_R 77_A 0.73 0.62 0.27
9_S 75_E 0.73 0.61 0.27
58_R 31_T 0.72 0.60 0.26
104_T 7_E 0.72 0.60 0.26
49_S 53_T 0.71 0.58 0.25
42_E 19_Q 0.70 0.57 0.24
74_A 35_I 0.68 0.54 0.22
24_R 18_L 0.68 0.54 0.22
65_F 36_L 0.68 0.53 0.22
9_S 45_A 0.68 0.53 0.21
76_Y 20_I 0.67 0.51 0.20
40_L 91_V 0.66 0.50 0.20
92_K 49_G 0.66 0.50 0.20
24_R 15_L 0.66 0.50 0.20
33_H 92_P 0.66 0.49 0.19
47_S 91_V 0.65 0.48 0.19
78_K 42_N 0.65 0.47 0.18
114_E 23_E 0.65 0.47 0.18
61_F 9_V 0.64 0.47 0.18
71_Y 15_L 0.64 0.47 0.18
30_Y 34_S 0.64 0.47 0.18
64_T 12_I 0.64 0.46 0.18
62_L 55_H 0.64 0.46 0.18
76_Y 32_L 0.64 0.46 0.18
105_A 91_V 0.63 0.45 0.17
47_S 20_I 0.63 0.45 0.17
81_K 47_T 0.63 0.45 0.17
12_V 72_I 0.63 0.44 0.17
44_Y 91_V 0.62 0.44 0.17
35_K 67_K 0.62 0.43 0.16
3_T 95_M 0.62 0.43 0.16
84_T 50_V 0.62 0.43 0.16
88_N 49_G 0.62 0.43 0.16
54_K 26_E 0.62 0.43 0.16
115_E 94_I 0.61 0.42 0.16
76_Y 89_F 0.61 0.42 0.15
67_L 15_L 0.61 0.42 0.15
16_S 39_A 0.60 0.41 0.15
68_S 15_L 0.60 0.40 0.15
78_K 46_D 0.60 0.39 0.14
56_V 15_L 0.59 0.39 0.14
39_S 93_T 0.59 0.39 0.14
37_A 71_G 0.59 0.39 0.14
84_T 90_K 0.59 0.38 0.14
5_F 33_E 0.59 0.38 0.14
13_I 63_L 0.58 0.36 0.13
25_F 88_Q 0.58 0.36 0.13
14_A 92_P 0.57 0.36 0.13
54_K 10_E 0.57 0.36 0.13
96_N 65_E 0.57 0.36 0.12
97_Y 90_K 0.57 0.35 0.12
13_I 75_E 0.56 0.34 0.12
117_D 27_E 0.56 0.34 0.12
61_F 13_A 0.56 0.34 0.12
101_V 73_P 0.56 0.34 0.12
28_I 47_T 0.56 0.34 0.12
20_S 33_E 0.56 0.34 0.12
92_K 84_T 0.56 0.34 0.12
36_E 75_E 0.56 0.33 0.11
11_Y 15_L 0.56 0.33 0.11
97_Y 33_E 0.56 0.33 0.11
49_S 20_I 0.56 0.33 0.11
15_S 88_Q 0.55 0.33 0.11
74_A 15_L 0.55 0.33 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)
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