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OPENSEQ.org
4qko_B_A
Genes: A B A+B
Length: 134 95 217
Sequences: 134 205 103
Seq/Len: 1 2.16 0.47
MirrorTree (Pazo et al. 2001) 0.52
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 0.27 0.44
2 0.03 0.31 0.45
5 0.03 0.34 0.45
10 0.03 0.34 0.45
20 0.03 0.34 0.45
100 0.03 0.34 0.45
∞ 0.06 0.36 0.45
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
88_E 52_D 2.04 0.86 0.24
74_S 56_Y 1.71 0.69 0.11
96_I 39_L 1.69 0.68 0.10
88_E 42_K 1.59 0.61 0.08
17_V 83_G 1.58 0.60 0.07
127_I 64_S 1.47 0.52 0.05
73_G 21_Y 1.45 0.51 0.05
85_Y 38_V 1.33 0.41 0.03
92_A 64_S 1.29 0.38 0.03
59_A 78_S 1.23 0.34 0.02
77_V 38_V 1.22 0.33 0.02
77_V 31_E 1.21 0.33 0.02
97_K 38_V 1.21 0.33 0.02
97_K 37_A 1.20 0.32 0.02
119_V 53_L 1.19 0.32 0.02
118_L 2_K 1.18 0.31 0.02
131_K 6_S 1.18 0.31 0.02
108_D 55_Y 1.15 0.29 0.02
74_S 68_V 1.13 0.28 0.02
78_M 42_K 1.11 0.27 0.02
71_N 63_D 1.10 0.26 0.01
55_Q 72_V 1.10 0.26 0.01
98_I 45_T 1.06 0.24 0.01
94_G 36_Q 1.06 0.24 0.01
10_A 62_E 1.06 0.24 0.01
98_I 54_L 1.02 0.22 0.01
42_R 73_K 1.01 0.21 0.01
97_K 35_I 1.01 0.21 0.01
44_K 3_S 1.01 0.21 0.01
115_M 64_S 0.99 0.20 0.01
85_Y 42_K 0.99 0.20 0.01
87_R 52_D 0.98 0.20 0.01
3_P 72_V 0.98 0.20 0.01
3_P 81_L 0.97 0.20 0.01
63_D 46_E 0.97 0.19 0.01
91_Q 51_S 0.95 0.18 0.01
50_R 62_E 0.93 0.17 0.01
23_G 74_E 0.91 0.17 0.01
99_E 67_G 0.91 0.17 0.01
39_D 8_Y 0.90 0.16 0.01
105_R 16_F 0.90 0.16 0.01
69_Q 16_F 0.88 0.15 0.01
111_G 53_L 0.88 0.15 0.01
113_Y 57_P 0.88 0.15 0.01
98_I 16_F 0.88 0.15 0.01
61_A 6_S 0.87 0.15 0.01
91_Q 67_G 0.86 0.15 0.01
98_I 20_I 0.86 0.15 0.01
79_R 49_S 0.86 0.15 0.01
99_E 64_S 0.86 0.15 0.01
68_K 53_L 0.86 0.14 0.01
104_V 81_L 0.86 0.14 0.01
100_I 51_S 0.85 0.14 0.01
108_D 16_F 0.85 0.14 0.01
26_S 7_E 0.83 0.14 0.01
118_L 55_Y 0.82 0.13 0.01
11_T 37_A 0.81 0.13 0.01
42_R 47_H 0.81 0.13 0.01
17_V 79_K 0.81 0.13 0.01
90_E 17_V 0.81 0.13 0.01
1_R 78_S 0.80 0.12 0.01
17_V 77_A 0.80 0.12 0.01
120_A 11_K 0.80 0.12 0.00
43_G 60_N 0.79 0.12 0.00
59_A 39_L 0.79 0.12 0.00
45_T 78_S 0.79 0.12 0.00
37_I 30_T 0.79 0.12 0.00
112_V 67_G 0.79 0.12 0.00
112_V 8_Y 0.78 0.12 0.00
61_A 53_L 0.78 0.12 0.00
101_H 10_E 0.78 0.12 0.00
59_A 43_K 0.78 0.12 0.00
11_T 44_L 0.78 0.12 0.00
3_P 80_G 0.78 0.12 0.00
116_G 35_I 0.78 0.12 0.00
63_D 81_L 0.78 0.12 0.00
118_L 6_S 0.78 0.12 0.00
48_N 78_S 0.78 0.12 0.00
81_G 54_L 0.77 0.12 0.00
13_K 69_V 0.77 0.12 0.00
65_E 72_V 0.77 0.12 0.00
106_I 55_Y 0.77 0.12 0.00
61_A 70_K 0.77 0.12 0.00
63_D 12_E 0.77 0.12 0.00
127_I 57_P 0.77 0.12 0.00
97_K 31_E 0.77 0.12 0.00
120_A 82_P 0.77 0.11 0.00
41_L 12_E 0.77 0.11 0.00
3_P 74_E 0.76 0.11 0.00
74_S 55_Y 0.76 0.11 0.00
16_P 78_S 0.76 0.11 0.00
55_Q 66_A 0.76 0.11 0.00
123_P 82_P 0.75 0.11 0.00
86_V 53_L 0.75 0.11 0.00
78_M 52_D 0.75 0.11 0.00
98_I 24_N 0.75 0.11 0.00
65_E 20_I 0.74 0.11 0.00
82_G 26_K 0.74 0.11 0.00
128_E 16_F 0.74 0.11 0.00
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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