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OPENSEQ.org
1FS0-2
Genes: A B A+B
Length: 134 230 359
Sequences: 2592 3213 1836
Seq/Len: 19.34 13.97 5.11
MirrorTree (Pazo et al. 2001) 0.76
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 0.09 0.09 0.09
2 0.09 0.09 4.80
5 0.09 0.09 4.97
10 0.09 0.09 4.99
20 0.09 0.09 5.04
100 0.09 0.09 5.12
∞ 0.09 0.10 5.36
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
38_A 189_L 1.38 0.97 0.69
80_D 150_L 1.21 0.93 0.53
28_E 197_L 1.19 0.92 0.51
41_L 38_L 1.14 0.90 0.46
67_I 203_R 1.13 0.89 0.45
39_P 47_H 1.12 0.89 0.44
80_D 204_R 1.04 0.83 0.35
47_G 13_K 1.02 0.81 0.34
69_E 30_T 0.96 0.76 0.29
6_D 30_T 0.93 0.73 0.26
28_E 191_E 0.92 0.71 0.25
41_L 34_V 0.91 0.70 0.24
76_T 128_L 0.91 0.70 0.24
78_L 34_V 0.88 0.66 0.22
10_A 128_L 0.88 0.66 0.21
69_E 188_Y 0.87 0.65 0.21
39_P 186_W 0.85 0.63 0.20
21_K 224_A 0.85 0.62 0.19
77_V 202_L 0.84 0.61 0.19
10_A 12_S 0.84 0.61 0.18
50_R 72_G 0.83 0.60 0.18
36_G 37_H 0.81 0.57 0.17
32_G 205_Y 0.80 0.55 0.16
67_I 35_I 0.79 0.55 0.15
72_P 186_W 0.79 0.54 0.15
84_R 8_M 0.78 0.53 0.15
30_E 72_G 0.78 0.53 0.15
129_V 154_S 0.78 0.53 0.15
69_E 226_M 0.78 0.53 0.15
77_V 210_V 0.78 0.52 0.15
22_I 161_M 0.78 0.52 0.14
3_Y 28_A 0.76 0.49 0.13
41_L 188_Y 0.76 0.49 0.13
56_G 63_V 0.75 0.48 0.13
82_A 34_V 0.75 0.48 0.13
20_E 87_T 0.74 0.47 0.12
127_L 82_L 0.74 0.46 0.12
71_Q 37_H 0.73 0.46 0.12
70_V 152_I 0.73 0.46 0.12
117_S 210_V 0.73 0.46 0.12
124_I 193_D 0.73 0.46 0.12
93_A 171_L 0.73 0.45 0.12
124_I 31_M 0.73 0.45 0.12
31_L 227_V 0.73 0.45 0.12
23_Q 224_A 0.73 0.45 0.12
7_V 197_L 0.72 0.44 0.11
8_V 215_V 0.71 0.43 0.11
68_L 21_M 0.71 0.43 0.11
82_A 126_P 0.71 0.43 0.11
69_E 8_M 0.70 0.42 0.10
52_V 139_L 0.70 0.42 0.10
8_V 217_N 0.70 0.41 0.10
43_A 197_L 0.70 0.41 0.10
65_G 27_Y 0.69 0.40 0.10
87_D 145_G 0.69 0.40 0.10
63_L 230_K 0.69 0.40 0.10
127_L 75_I 0.69 0.40 0.10
128_R 77_L 0.68 0.39 0.10
26_G 191_E 0.68 0.38 0.09
31_L 219_A 0.68 0.38 0.09
13_Q 29_E 0.68 0.38 0.09
77_V 142_Y 0.67 0.38 0.09
26_G 64_S 0.67 0.37 0.09
81_T 12_S 0.66 0.36 0.09
11_E 100_I 0.66 0.36 0.09
124_I 79_K 0.66 0.35 0.08
47_G 74_N 0.66 0.35 0.08
37_H 219_A 0.66 0.35 0.08
105_S 97_L 0.66 0.35 0.08
97_K 79_K 0.65 0.34 0.08
25_T 41_G 0.65 0.34 0.08
127_L 129_S 0.65 0.34 0.08
79_A 34_V 0.64 0.34 0.08
8_V 188_Y 0.64 0.34 0.08
96_A 150_L 0.64 0.34 0.08
7_V 135_V 0.64 0.33 0.08
92_R 162_S 0.64 0.33 0.07
113_Y 77_L 0.63 0.32 0.07
32_G 70_C 0.63 0.32 0.07
114_A 12_S 0.63 0.32 0.07
101_E 114_N 0.63 0.32 0.07
78_L 129_S 0.62 0.31 0.07
131_E 137_V 0.62 0.31 0.07
25_T 70_C 0.62 0.31 0.07
79_A 147_L 0.62 0.31 0.07
9_S 1_K 0.62 0.31 0.07
82_A 214_V 0.62 0.30 0.07
50_R 35_I 0.62 0.30 0.07
38_A 173_L 0.62 0.30 0.07
51_I 7_E 0.62 0.30 0.07
84_R 202_L 0.62 0.30 0.07
22_I 116_V 0.61 0.30 0.07
70_V 151_Y 0.61 0.30 0.07
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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