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OPENSEQ.org
resubmitsmtulp
Genes: A B A+B
Length: 39 181 214
Sequences: 571 2203 110
Seq/Len: 14.64 12.17 0.51
MirrorTree (Pazo et al. 2001) 0.15
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 0.05 0.05 0.00
2 0.06 0.06 0.00
5 0.06 0.06 0.01
10 0.06 0.07 0.02
20 0.07 0.07 0.04
100 0.08 0.08 0.13
∞ 0.10 0.11 0.50
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
17_Q 159_Y 1.30 0.42 0.00
26_D 46_T 1.20 0.34 0.00
8_Y 169_T 1.19 0.33 0.00
28_D 162_G 1.14 0.30 0.00
15_A 90_N 1.14 0.30 0.00
24_M 162_G 1.13 0.30 0.00
20_E 139_H 1.12 0.29 0.00
30_I 67_G 1.12 0.29 0.00
8_Y 164_Y 1.08 0.26 0.00
10_G 88_P 1.08 0.26 0.00
37_I 168_N 1.05 0.24 0.00
37_I 85_I 1.03 0.23 0.00
13_I 56_F 1.02 0.23 0.00
24_M 149_H 0.98 0.21 0.00
22_L 112_D 0.97 0.21 0.00
34_R 159_Y 0.96 0.20 0.00
21_D 84_K 0.96 0.20 0.00
32_A 36_E 0.95 0.19 0.00
31_E 151_D 0.95 0.19 0.00
23_D 21_F 0.94 0.19 0.00
32_A 115_S 0.94 0.19 0.00
14_Q 85_I 0.93 0.19 0.00
32_A 133_V 0.93 0.19 0.00
26_D 160_D 0.93 0.18 0.00
37_I 21_F 0.93 0.18 0.00
23_D 50_V 0.93 0.18 0.00
28_D 96_W 0.91 0.17 0.00
26_D 155_Q 0.91 0.17 0.00
24_M 177_P 0.90 0.17 0.00
37_I 103_L 0.89 0.17 0.00
25_E 147_L 0.89 0.17 0.00
26_D 90_N 0.88 0.16 0.00
6_F 161_C 0.87 0.16 0.00
4_L 30_L 0.86 0.15 0.00
8_Y 80_D 0.86 0.15 0.00
9_D 132_Y 0.86 0.15 0.00
25_E 125_I 0.86 0.15 0.00
30_I 144_D 0.85 0.15 0.00
31_E 100_I 0.84 0.15 0.00
8_Y 25_A 0.84 0.15 0.00
28_D 29_W 0.84 0.15 0.00
8_Y 21_F 0.83 0.14 0.00
3_S 157_N 0.83 0.14 0.00
5_R 32_D 0.82 0.14 0.00
18_T 56_F 0.82 0.14 0.00
13_I 137_S 0.82 0.14 0.00
19_P 52_F 0.81 0.14 0.00
13_I 32_D 0.81 0.13 0.00
4_L 53_N 0.80 0.13 0.00
21_D 14_I 0.80 0.13 0.00
26_D 24_L 0.80 0.13 0.00
12_R 119_N 0.79 0.13 0.00
16_D 76_K 0.79 0.13 0.00
13_I 64_G 0.78 0.12 0.00
13_I 111_V 0.78 0.12 0.00
13_I 102_D 0.78 0.12 0.00
39_G 112_D 0.78 0.12 0.00
2_D 25_A 0.77 0.12 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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