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OPENSEQ.org
1vt2_L_E
Genes: A B A+B
Length: 144 201 344
Sequences: 2621 3150 1827
Seq/Len: 18.2 15.67 5.31
MirrorTree (Pazo et al. 2001) 0.81
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 0.08 0.01
2 0.09 0.08 0.01
5 0.09 0.08 0.03
10 0.09 0.08 0.06
20 0.09 0.09 5.30
100 0.09 0.09 5.68
∞ 0.09 0.09 5.89
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
2_R 184_D 1.96 1.00 0.98
13_K 33_V 1.96 1.00 0.98
3_L 182_A 1.07 0.86 0.64
8_P 26_A 1.06 0.85 0.62
9_A 26_A 1.02 0.82 0.58
1_M 112_L 0.95 0.76 0.50
42_S 85_F 0.88 0.68 0.41
8_P 29_H 0.84 0.62 0.35
13_K 29_H 0.80 0.57 0.32
6_L 32_V 0.80 0.57 0.31
9_A 30_Q 0.78 0.53 0.28
40_S 77_I 0.75 0.49 0.26
5_T 25_E 0.75 0.49 0.26
40_S 129_P 0.73 0.46 0.23
129_K 122_E 0.73 0.46 0.23
58_Y 72_S 0.72 0.46 0.23
55_M 61_R 0.71 0.43 0.21
74_T 86_A 0.71 0.43 0.21
23_I 79_R 0.70 0.42 0.20
117_T 116_D 0.69 0.41 0.20
92_L 97_N 0.68 0.39 0.18
24_G 19_F 0.67 0.38 0.18
57_L 60_W 0.67 0.38 0.18
7_S 193_V 0.66 0.37 0.17
109_K 147_L 0.66 0.36 0.17
31_G 125_S 0.65 0.36 0.16
143_E 198_E 0.65 0.35 0.16
82_L 191_D 0.65 0.35 0.16
47_R 85_F 0.64 0.34 0.15
13_K 96_V 0.64 0.33 0.15
90_V 140_D 0.63 0.33 0.15
42_S 49_R 0.62 0.32 0.14
141_K 134_L 0.62 0.32 0.14
2_R 176_D 0.62 0.32 0.14
8_P 95_K 0.61 0.31 0.13
70_K 46_Q 0.61 0.30 0.13
92_L 27_L 0.61 0.30 0.13
29_K 77_I 0.60 0.29 0.13
9_A 29_H 0.60 0.29 0.13
12_S 34_A 0.60 0.29 0.12
2_R 117_R 0.59 0.28 0.12
3_L 108_I 0.58 0.26 0.11
33_R 118_L 0.57 0.26 0.11
76_E 86_A 0.57 0.26 0.11
4_N 112_L 0.57 0.25 0.10
70_K 36_A 0.57 0.25 0.10
5_T 28_V 0.57 0.25 0.10
126_R 160_A 0.57 0.25 0.10
20_G 121_V 0.56 0.24 0.10
24_G 92_H 0.56 0.24 0.10
136_E 38_G 0.55 0.24 0.10
14_K 164_L 0.55 0.24 0.10
110_V 113_V 0.55 0.24 0.10
3_L 183_F 0.55 0.23 0.10
5_T 112_L 0.55 0.23 0.09
136_E 169_V 0.54 0.23 0.09
2_R 187_V 0.54 0.23 0.09
2_R 179_S 0.54 0.23 0.09
101_I 25_E 0.54 0.23 0.09
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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