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OPENSEQ.org
1TYG_B_A
Genes: A B A+B
Length: 87 253 322
Sequences: 388 1444 266
Seq/Len: 4.46 5.71 0.83
MirrorTree (Pazo et al. 2001) 0.75
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 0.08 0.71
2 0.01 0.08 0.74
5 0.01 0.08 0.76
10 0.01 0.08 0.77
20 0.01 0.08 0.78
100 0.01 0.08 0.80
∞ 0.01 0.08 0.86
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
81_V 43_R 1.55 0.75 0.01
56_E 81_R 1.51 0.72 0.01
85_G 92_C 1.36 0.61 0.01
27_G 218_A 1.34 0.59 0.01
79_E 43_R 1.33 0.58 0.01
46_Y 117_S 1.32 0.57 0.01
52_I 89_S 1.29 0.54 0.01
72_L 220_A 1.25 0.51 0.01
76_D 158_S 1.24 0.50 0.01
61_I 85_L 1.18 0.45 0.01
83_F 92_C 1.17 0.44 0.00
56_E 92_C 1.14 0.41 0.00
67_Y 147_H 1.13 0.40 0.00
54_I 88_A 1.12 0.40 0.00
64_K 63_K 1.12 0.40 0.00
57_R 6_G 1.08 0.37 0.00
43_L 78_E 1.06 0.35 0.00
58_N 158_S 1.05 0.34 0.00
81_V 144_L 1.04 0.33 0.00
83_F 97_V 1.03 0.32 0.00
51_K 181_V 1.02 0.32 0.00
84_V 2_L 1.01 0.30 0.00
53_V 138_A 0.98 0.29 0.00
21_H 227_A 0.98 0.29 0.00
83_F 171_I 0.97 0.28 0.00
67_Y 149_I 0.97 0.28 0.00
81_V 117_S 0.97 0.28 0.00
78_I 76_A 0.97 0.28 0.00
49_E 22_S 0.96 0.28 0.00
65_E 110_P 0.95 0.27 0.00
84_V 206_T 0.95 0.26 0.00
52_I 135_V 0.94 0.26 0.00
83_F 90_G 0.94 0.26 0.00
43_L 21_P 0.93 0.25 0.00
21_H 204_L 0.93 0.25 0.00
56_E 84_R 0.93 0.25 0.00
39_I 232_Y 0.93 0.25 0.00
80_I 153_A 0.92 0.24 0.00
63_G 180_I 0.92 0.24 0.00
23_L 122_E 0.91 0.24 0.00
67_Y 135_V 0.91 0.24 0.00
67_Y 81_R 0.91 0.24 0.00
72_L 114_L 0.90 0.23 0.00
61_I 81_R 0.89 0.23 0.00
81_V 138_A 0.89 0.23 0.00
32_W 208_V 0.89 0.23 0.00
53_V 93_D 0.87 0.21 0.00
58_N 24_D 0.86 0.21 0.00
42_L 143_E 0.86 0.21 0.00
47_Q 206_T 0.85 0.20 0.00
58_N 8_S 0.85 0.20 0.00
81_V 247_S 0.84 0.20 0.00
63_G 88_A 0.84 0.20 0.00
38_T 197_L 0.83 0.19 0.00
78_I 230_L 0.83 0.19 0.00
67_Y 89_S 0.83 0.19 0.00
51_K 142_E 0.83 0.19 0.00
41_D 123_E 0.83 0.19 0.00
31_K 224_A 0.83 0.19 0.00
42_L 40_F 0.83 0.19 0.00
81_V 58_Q 0.82 0.19 0.00
65_E 95_I 0.82 0.18 0.00
83_F 247_S 0.81 0.18 0.00
42_L 185_I 0.81 0.18 0.00
53_V 139_R 0.81 0.18 0.00
67_Y 148_A 0.81 0.18 0.00
81_V 99_V 0.81 0.18 0.00
76_D 101_G 0.80 0.17 0.00
81_V 100_I 0.80 0.17 0.00
62_I 231_S 0.79 0.17 0.00
37_G 154_S 0.79 0.17 0.00
61_I 82_I 0.79 0.17 0.00
32_W 8_S 0.79 0.17 0.00
81_V 74_S 0.79 0.17 0.00
83_F 42_V 0.78 0.17 0.00
48_L 247_S 0.78 0.17 0.00
49_E 158_S 0.78 0.17 0.00
64_K 35_S 0.78 0.16 0.00
43_L 205_N 0.77 0.16 0.00
78_I 35_S 0.77 0.16 0.00
81_V 253_P 0.77 0.16 0.00
29_D 75_T 0.77 0.16 0.00
67_Y 37_I 0.77 0.16 0.00
25_L 153_A 0.76 0.16 0.00
62_I 222_K 0.76 0.15 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)
ID Seq/Len Name Options I_Prob Status
7268 0.83 1TYG_B_A Δgene:(1, 20) A:(1E-04, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
7252 0 1TYG_B_A Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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