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pred_1KKL_l_u_XpdbXfas_1KKL_r_u_ApdbAfastable_PRtxt
Genes: A B A+B
Length: 87 157 238
Sequences: 3244 784 376
Seq/Len: 37.29 4.99 1.58
MirrorTree (Pazo et al. 2001) 0.39
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 0.07 0.18
2 0.01 0.07 0.43
5 0.01 0.07 1.19
10 0.01 0.07 1.30
20 0.01 0.07 1.54
100 0.06 0.07 1.90
∞ 0.14 0.07 2.69
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
42_N 37_G 1.48 0.86 0.17
34_L 4_S 1.45 0.84 0.16
76_L 151_L 1.21 0.67 0.08
56_K 18_I 1.20 0.66 0.08
20_V 29_T 1.18 0.64 0.07
24_T 16_V 1.15 0.61 0.07
59_E 46_V 1.14 0.60 0.06
49_V 7_V 1.14 0.60 0.06
40_T 46_V 1.06 0.52 0.05
42_N 8_L 1.05 0.51 0.05
17_P 84_G 1.03 0.48 0.04
18_A 24_V 1.02 0.48 0.04
18_A 42_A 1.01 0.47 0.04
42_N 13_G 1.00 0.46 0.04
14_H 113_P 1.00 0.45 0.04
42_N 38_H 0.99 0.44 0.04
68_D 118_P 0.98 0.44 0.04
37_N 68_L 0.98 0.43 0.04
2_Q 141_Y 0.98 0.43 0.04
80_M 147_F 0.96 0.42 0.03
68_D 16_V 0.96 0.42 0.03
31_D 21_D 0.96 0.42 0.03
42_N 130_E 0.96 0.41 0.03
82_C 18_I 0.96 0.41 0.03
58_A 130_E 0.96 0.41 0.03
13_I 154_L 0.95 0.41 0.03
5_F 47_D 0.95 0.40 0.03
41_V 45_R 0.94 0.40 0.03
13_I 153_H 0.94 0.39 0.03
17_P 148_E 0.94 0.39 0.03
17_P 136_R 0.93 0.39 0.03
10_D 62_P 0.93 0.38 0.03
60_I 53_E 0.93 0.38 0.03
47_M 48_V 0.92 0.38 0.03
2_Q 22_S 0.92 0.37 0.03
44_K 15_G 0.91 0.37 0.03
44_K 130_E 0.91 0.36 0.03
49_V 142_D 0.91 0.36 0.03
44_K 37_G 0.90 0.36 0.03
70_N 95_I 0.90 0.35 0.03
44_K 119_V 0.90 0.35 0.03
6_K 49_Y 0.90 0.35 0.03
44_K 118_P 0.89 0.35 0.03
50_V 67_L 0.89 0.35 0.03
15_A 85_A 0.88 0.34 0.03
62_I 65_S 0.87 0.32 0.02
53_G 109_D 0.86 0.32 0.02
12_G 113_P 0.85 0.31 0.02
52_L 81_F 0.85 0.31 0.02
68_D 36_R 0.84 0.30 0.02
26_S 48_V 0.84 0.30 0.02
58_A 64_L 0.84 0.30 0.02
50_V 132_A 0.84 0.30 0.02
17_P 53_E 0.83 0.29 0.02
44_K 28_E 0.83 0.29 0.02
5_F 95_I 0.83 0.29 0.02
44_K 38_H 0.83 0.29 0.02
19_T 144_T 0.83 0.29 0.02
13_I 156_E 0.83 0.29 0.02
43_L 13_G 0.82 0.29 0.02
24_T 5_H 0.82 0.28 0.02
60_I 65_S 0.82 0.28 0.02
50_V 151_L 0.82 0.28 0.02
58_A 36_R 0.81 0.28 0.02
43_L 38_H 0.81 0.27 0.02
6_K 132_A 0.80 0.27 0.02
44_K 125_L 0.80 0.26 0.02
28_Y 6_G 0.80 0.26 0.02
13_I 135_F 0.80 0.26 0.02
23_Q 69_E 0.80 0.26 0.02
34_L 135_F 0.79 0.26 0.02
34_L 114_K 0.79 0.26 0.02
68_D 92_I 0.79 0.26 0.02
26_S 97_H 0.78 0.25 0.02
7_V 144_T 0.78 0.25 0.02
16_R 94_L 0.78 0.25 0.02
9_A 152_N 0.78 0.25 0.02
50_V 127_I 0.78 0.25 0.02
18_A 18_I 0.78 0.25 0.02
7_V 109_D 0.78 0.25 0.02
23_Q 32_E 0.77 0.24 0.02
44_K 58_G 0.77 0.24 0.02
33_N 138_K 0.77 0.24 0.02
73_L 132_A 0.77 0.24 0.02
32_V 75_I 0.77 0.24 0.02
63_S 95_I 0.77 0.24 0.02
56_K 130_E 0.77 0.24 0.02
13_I 145_K 0.77 0.24 0.02
47_M 64_L 0.77 0.24 0.02
44_K 122_G 0.77 0.24 0.02
53_G 96_V 0.76 0.24 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)
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