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OPENSEQ.org
smt3(60-98),Ulp1(420-600)
Genes: A B A+B
Length: 39 181 215
Sequences: 346 2099 112
Seq/Len: 8.87 11.6 0.52
MirrorTree (Pazo et al. 2001) 0.20
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 0.03 0.06 0.00
2 0.04 0.07 0.01
5 0.04 0.07 0.02
10 0.05 0.07 0.03
20 0.05 0.08 0.05
100 0.07 0.09 0.15
∞ 0.07 0.12 0.51
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
8_Y 16_I 1.44 0.53 0.00
15_A 114_L 1.42 0.51 0.00
5_R 32_D 1.29 0.41 0.00
21_D 18_V 1.28 0.41 0.00
10_G 88_P 1.23 0.37 0.00
18_T 153_P 1.18 0.33 0.00
9_D 19_R 1.13 0.30 0.00
23_D 60_L 1.09 0.28 0.00
31_E 67_G 1.06 0.26 0.00
31_E 170_L 1.05 0.25 0.00
26_D 24_L 1.04 0.24 0.00
31_E 100_I 1.03 0.24 0.00
31_E 51_A 1.00 0.22 0.00
23_D 65_Y 0.99 0.22 0.00
23_D 85_I 0.98 0.21 0.00
32_A 133_V 0.96 0.20 0.00
37_I 21_F 0.95 0.20 0.00
15_A 45_S 0.93 0.19 0.00
18_T 79_I 0.93 0.18 0.00
30_I 36_E 0.93 0.18 0.00
15_A 86_F 0.92 0.18 0.00
31_E 137_S 0.92 0.18 0.00
35_E 32_D 0.92 0.18 0.00
3_S 119_N 0.92 0.18 0.00
27_N 42_I 0.91 0.17 0.00
3_S 93_Q 0.90 0.17 0.00
8_Y 125_I 0.90 0.17 0.00
18_T 37_F 0.89 0.17 0.00
29_I 42_I 0.88 0.16 0.00
37_I 82_L 0.88 0.16 0.00
3_S 146_D 0.87 0.16 0.00
5_R 23_T 0.87 0.16 0.00
17_Q 159_Y 0.87 0.16 0.00
13_I 169_T 0.87 0.16 0.00
16_D 156_P 0.86 0.16 0.00
37_I 136_E 0.86 0.16 0.00
30_I 103_L 0.85 0.15 0.00
20_E 130_Q 0.85 0.15 0.00
30_I 41_Y 0.85 0.15 0.00
31_E 97_A 0.84 0.15 0.00
9_D 6_T 0.84 0.15 0.00
16_D 107_T 0.84 0.15 0.00
14_Q 85_I 0.83 0.14 0.00
27_N 99_G 0.83 0.14 0.00
39_G 96_W 0.83 0.14 0.00
1_M 146_D 0.83 0.14 0.00
5_R 20_D 0.82 0.14 0.00
5_R 163_I 0.82 0.14 0.00
25_E 33_T 0.81 0.14 0.00
13_I 137_S 0.81 0.14 0.00
23_D 59_N 0.81 0.14 0.00
26_D 116_N 0.81 0.14 0.00
20_E 85_I 0.80 0.13 0.00
15_A 78_Q 0.80 0.13 0.00
6_F 112_D 0.80 0.13 0.00
18_T 96_W 0.80 0.13 0.00
22_L 31_N 0.80 0.13 0.00
9_D 23_T 0.80 0.13 0.00
11_I 127_T 0.79 0.13 0.00
6_F 96_W 0.78 0.13 0.00
38_G 96_W 0.78 0.13 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
5345 0.51 resubmitsmtulp Δgene:(1, ∞) A:(1E-06, 4) B:(1E-06, 4) msa: HHblits (2015_06) 0.00 Done - Shared
5341 0.52 smt3(60-98),Ulp1(420-600) Δgene:(1, ∞) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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