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OPENSEQ.org
1TYG_B_A (A, 20-87)
Genes: A B A+B
Length: 68 253 319
Sequences: 4009 1444 1404
Seq/Len: 58.96 5.71 4.4
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 0.02 0.08 3.49
2 0.02 0.08 3.96
5 0.02 0.08 4.27
10 0.02 0.08 4.33
20 0.02 0.08 4.37
100 0.03 0.08 4.52
∞ 0.12 0.08 4.92
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
37_E 81_R 2.01 1.00 0.98
42_I 85_L 1.52 0.98 0.92
35_I 88_A 1.19 0.90 0.73
2_H 227_A 0.97 0.73 0.51
65_V 41_A 0.93 0.68 0.45
60_E 43_R 0.88 0.62 0.40
64_F 90_G 0.87 0.60 0.38
64_F 92_C 0.86 0.59 0.36
9_K 48_F 0.83 0.56 0.34
48_Y 89_S 0.83 0.55 0.33
44_G 88_A 0.81 0.53 0.31
23_L 191_A 0.80 0.51 0.30
62_V 138_A 0.79 0.49 0.28
64_F 42_V 0.79 0.49 0.28
35_I 89_S 0.79 0.49 0.28
41_E 84_R 0.78 0.48 0.28
40_K 77_E 0.77 0.46 0.26
64_F 81_R 0.76 0.45 0.25
37_E 84_R 0.76 0.45 0.25
21_Q 122_E 0.75 0.44 0.24
53_L 220_A 0.74 0.43 0.23
42_I 81_R 0.74 0.43 0.23
33_I 99_V 0.74 0.42 0.23
11_V 122_E 0.73 0.42 0.23
65_V 158_S 0.72 0.40 0.21
65_V 206_T 0.71 0.38 0.20
33_I 89_S 0.71 0.38 0.20
64_F 86_A 0.70 0.38 0.20
9_K 218_A 0.69 0.36 0.19
60_E 78_E 0.69 0.36 0.19
62_V 85_L 0.69 0.36 0.19
24_L 179_V 0.69 0.36 0.19
66_G 92_C 0.69 0.36 0.18
16_D 154_S 0.69 0.36 0.18
62_V 253_P 0.69 0.35 0.18
44_G 67_L 0.68 0.35 0.18
62_V 43_R 0.68 0.34 0.17
4_L 211_A 0.68 0.34 0.17
19_T 77_E 0.67 0.34 0.17
35_I 82_I 0.67 0.33 0.17
27_Y 117_S 0.67 0.33 0.17
64_F 56_L 0.67 0.33 0.17
41_E 8_S 0.66 0.33 0.16
20_I 80_V 0.66 0.33 0.16
8_G 218_A 0.66 0.33 0.16
37_E 92_C 0.65 0.31 0.15
66_G 73_A 0.65 0.31 0.15
46_E 29_A 0.65 0.31 0.15
65_V 131_T 0.65 0.31 0.15
20_I 36_D 0.65 0.31 0.15
19_T 8_S 0.64 0.30 0.15
47_R 143_E 0.64 0.30 0.15
35_I 91_L 0.64 0.30 0.15
60_E 81_R 0.64 0.30 0.14
66_G 40_F 0.63 0.29 0.14
62_V 73_A 0.62 0.28 0.13
37_E 90_G 0.61 0.27 0.13
63_H 85_L 0.61 0.27 0.12
66_G 169_S 0.60 0.26 0.12
65_V 78_E 0.60 0.26 0.12
48_Y 45_M 0.60 0.25 0.12
8_G 43_R 0.59 0.25 0.11
44_G 237_I 0.59 0.25 0.11
65_V 175_A 0.59 0.25 0.11
13_W 139_R 0.59 0.25 0.11
37_E 85_L 0.59 0.25 0.11
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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