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OPENSEQ.org
1TYG_BA
Genes: A B A+B
Length: 65 242 302
Sequences: 1635 1080 1036
Seq/Len: 25.15 4.46 3.43
MirrorTree (Pazo et al. 2001) 0.53
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 2.68
2 0.00 0.00 3.06
5 0.00 0.00 3.31
10 0.00 0.00 3.34
20 0.00 0.00 3.37
100 0.00 0.00 3.44
∞ 0.01 0.00 3.78
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
35_E 81_R 2.16 1.00 0.99
62_F 90_G 1.64 0.98 0.94
40_I 85_L 1.34 0.93 0.82
33_I 88_A 1.24 0.88 0.75
62_F 92_C 1.12 0.80 0.64
58_E 43_R 1.04 0.73 0.55
63_V 41_A 1.00 0.69 0.50
34_V 80_V 0.98 0.67 0.48
35_E 84_R 0.97 0.65 0.47
35_E 90_G 0.95 0.63 0.45
60_V 42_V 0.95 0.63 0.45
60_V 138_A 0.88 0.54 0.35
64_G 92_C 0.85 0.50 0.32
33_I 89_S 0.82 0.47 0.29
46_Y 89_S 0.82 0.46 0.29
40_I 81_R 0.81 0.46 0.28
42_G 88_A 0.81 0.45 0.28
58_E 78_E 0.80 0.44 0.27
18_I 36_D 0.80 0.44 0.27
23_A 177_V 0.79 0.43 0.26
35_E 92_C 0.79 0.42 0.26
38_K 77_E 0.78 0.41 0.25
17_T 77_E 0.78 0.41 0.24
46_Y 45_M 0.77 0.40 0.24
39_E 84_R 0.77 0.40 0.24
62_F 42_V 0.77 0.40 0.23
51_L 220_A 0.76 0.39 0.23
31_I 89_S 0.74 0.36 0.21
31_I 99_V 0.74 0.36 0.21
62_F 56_L 0.74 0.36 0.21
63_V 158_S 0.73 0.36 0.20
4_L 168_L 0.73 0.35 0.20
26_Q 154_S 0.73 0.35 0.20
63_V 206_T 0.72 0.34 0.19
42_G 67_L 0.72 0.34 0.19
6_G 218_A 0.72 0.34 0.19
10_K 80_V 0.72 0.34 0.19
4_L 153_A 0.72 0.34 0.19
53_D 216_K 0.70 0.32 0.17
22_L 170_F 0.70 0.32 0.17
64_G 19_K 0.70 0.32 0.17
38_K 173_E 0.69 0.31 0.17
26_Q 63_K 0.69 0.31 0.17
20_D 10_Q 0.68 0.29 0.15
19_Q 122_E 0.68 0.29 0.15
4_L 63_K 0.68 0.29 0.15
62_F 81_R 0.67 0.28 0.15
32_V 84_R 0.67 0.28 0.15
14_D 215_V 0.66 0.28 0.14
53_D 225_V 0.66 0.28 0.14
46_Y 149_I 0.66 0.28 0.14
41_I 88_A 0.66 0.27 0.14
64_G 81_R 0.66 0.27 0.14
21_L 86_A 0.65 0.27 0.14
10_K 24_D 0.65 0.27 0.14
22_L 179_V 0.65 0.26 0.14
60_V 73_A 0.65 0.26 0.14
4_L 91_L 0.65 0.26 0.13
51_L 22_S 0.64 0.25 0.13
31_I 169_S 0.63 0.25 0.12
7_K 48_F 0.63 0.25 0.12
56_V 30_V 0.63 0.25 0.12
63_V 131_T 0.63 0.25 0.12
7_K 218_A 0.63 0.24 0.12
41_I 212_D 0.63 0.24 0.12
2_L 114_L 0.63 0.24 0.12
28_E 75_T 0.62 0.24 0.12
63_V 148_A 0.62 0.24 0.12
31_I 92_C 0.62 0.23 0.11
6_G 43_R 0.61 0.23 0.11
41_I 139_R 0.61 0.23 0.11
12_K 28_E 0.61 0.23 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)
ID Seq/Len Name Options I_Prob Status
10450 0 1TYG_BA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
0269 3.43 1TYG_BA Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.99 Done
0268 0.08 1TYG_BA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed
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