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OPENSEQ.org
PltL (Q9X3R0) PltF L401-G498
Genes: A B A+B
Length: 88 98 182
Sequences: 370 26003 265
Seq/Len: 4.2 265.34 1.46
MirrorTree (Pazo et al. 2001) 0.51
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.09 0.55
2 0.01 0.11 0.83
5 0.05 0.13 1.22
10 0.05 0.17 1.37
20 0.05 0.19 1.42
100 0.06 0.24 1.58
∞ 0.12 0.30 1.78
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
65_I 8_I 1.46 0.83 0.09
58_V 64_L 1.40 0.80 0.08
49_M 39_L 1.28 0.71 0.06
72_D 81_R 1.26 0.69 0.05
70_F 1_L 1.25 0.68 0.05
54_D 84_N 1.19 0.63 0.04
52_I 62_Q 1.17 0.61 0.04
14_I 23_V 1.15 0.58 0.04
7_K 69_I 1.14 0.58 0.04
48_L 84_N 1.14 0.58 0.04
8_E 79_L 1.10 0.54 0.03
28_L 89_R 1.09 0.53 0.03
76_I 82_N 1.09 0.52 0.03
78_R 81_R 1.02 0.46 0.03
14_I 45_A 1.02 0.46 0.03
55_E 13_V 1.00 0.43 0.02
10_I 36_N 0.96 0.39 0.02
43_M 3_V 0.95 0.39 0.02
49_M 48_R 0.95 0.39 0.02
69_Y 80_P 0.94 0.37 0.02
35_L 13_V 0.93 0.36 0.02
33_P 27_A 0.92 0.36 0.02
73_L 42_V 0.92 0.35 0.02
60_I 36_N 0.90 0.33 0.02
40_L 56_L 0.90 0.33 0.02
53_R 70_I 0.88 0.32 0.01
2_D 8_I 0.88 0.32 0.01
18_L 42_V 0.86 0.30 0.01
46_V 13_V 0.86 0.30 0.01
8_E 64_L 0.85 0.29 0.01
8_E 16_A 0.85 0.29 0.01
69_Y 17_L 0.85 0.29 0.01
32_T 28_V 0.85 0.29 0.01
73_L 62_Q 0.84 0.29 0.01
48_L 58_R 0.84 0.29 0.01
53_R 17_L 0.84 0.28 0.01
28_L 18_L 0.84 0.28 0.01
65_I 10_R 0.84 0.28 0.01
53_R 92_L 0.84 0.28 0.01
79_T 39_L 0.83 0.28 0.01
60_I 62_Q 0.83 0.28 0.01
42_S 86_K 0.83 0.28 0.01
60_I 87_V 0.83 0.27 0.01
36_E 78_A 0.82 0.27 0.01
33_P 53_L 0.82 0.27 0.01
85_A 89_R 0.82 0.27 0.01
76_I 4_R 0.82 0.27 0.01
22_S 88_D 0.81 0.26 0.01
12_R 22_Q 0.81 0.26 0.01
49_M 64_L 0.81 0.26 0.01
60_I 61_A 0.81 0.26 0.01
72_D 73_V 0.81 0.26 0.01
50_V 26_A 0.81 0.26 0.01
13_Y 18_L 0.81 0.26 0.01
13_Y 34_G 0.81 0.26 0.01
10_I 38_Q 0.80 0.26 0.01
6_V 16_A 0.80 0.25 0.01
5_E 19_A 0.80 0.25 0.01
49_M 79_L 0.80 0.25 0.01
47_K 43_L 0.80 0.25 0.01
45_I 64_L 0.80 0.25 0.01
38_G 88_D 0.79 0.25 0.01
64_H 93_A 0.79 0.25 0.01
26_D 87_V 0.79 0.24 0.01
68_K 34_G 0.78 0.24 0.01
13_Y 2_K 0.78 0.23 0.01
59_S 52_S 0.78 0.23 0.01
77_S 54_I 0.78 0.23 0.01
20_G 87_V 0.78 0.23 0.01
49_M 33_E 0.78 0.23 0.01
76_I 40_W 0.77 0.23 0.01
82_Q 4_R 0.77 0.23 0.01
55_E 25_E 0.77 0.23 0.01
86_E 77_D 0.76 0.22 0.01
75_A 28_V 0.76 0.22 0.01
69_Y 87_V 0.76 0.22 0.01
58_V 74_L 0.76 0.22 0.01
23_A 55_D 0.76 0.22 0.01
59_S 21_P 0.76 0.22 0.01
52_I 45_A 0.76 0.22 0.01
34_L 45_A 0.76 0.22 0.01
80_V 21_P 0.75 0.21 0.01
81_E 3_V 0.75 0.21 0.01
82_Q 57_K 0.75 0.21 0.01
11_R 59_H 0.75 0.21 0.01
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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