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OPENSEQ.org
stbAB
Genes: A B A+B
Length: 196 112 301
Sequences: 2229 1636 847
Seq/Len: 11.37 14.61 2.81
MirrorTree (Pazo et al. 2001) 0.45
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 0.00 0.03 0.06
2 0.00 0.04 0.07
5 0.00 0.04 0.08
10 0.00 0.05 0.11
20 0.00 0.05 0.14
100 0.00 0.05 0.52
∞ 0.01 0.17 2.75
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
29_L 56_L 0.92 0.54 0.00
47_E 56_L 0.87 0.47 0.00
82_L 15_E 0.83 0.42 0.00
142_Q 4_V 0.83 0.42 0.00
102_L 59_L 0.79 0.37 0.00
39_E 96_V 0.78 0.37 0.00
83_Y 92_F 0.78 0.36 0.00
56_V 9_R 0.76 0.35 0.00
188_K 93_V 0.76 0.34 0.00
97_R 102_I 0.76 0.34 0.00
100_N 4_V 0.73 0.31 0.00
64_A 45_R 0.72 0.30 0.00
20_E 98_Q 0.72 0.30 0.00
168_Q 73_V 0.71 0.29 0.00
72_V 30_I 0.71 0.29 0.00
139_T 61_V 0.71 0.29 0.00
122_D 59_L 0.70 0.28 0.00
26_D 23_A 0.70 0.28 0.00
116_I 56_L 0.69 0.27 0.00
100_N 74_I 0.68 0.26 0.00
139_T 77_L 0.67 0.25 0.00
55_Q 74_I 0.66 0.24 0.00
133_C 36_F 0.65 0.23 0.00
183_L 14_D 0.64 0.22 0.00
168_Q 77_L 0.63 0.22 0.00
5_L 93_V 0.63 0.21 0.00
180_F 112_I 0.63 0.21 0.00
27_W 77_L 0.62 0.20 0.00
98_L 59_L 0.61 0.20 0.00
9_T 86_I 0.60 0.19 0.00
116_I 12_K 0.60 0.19 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
0350 0.2 stbAB Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2013_03) Killed
0349 0.67 stbAB Δgene:(1, 100) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 0.01 Done
0348 0.62 stbAB Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0347 0.72 stbAB Δgene:(1, 100) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2013_03) 0.00 Done
0346 0.53 stbAB Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed
0345 3.16 stbAB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0344 2.81 stbAB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0343 0.14 stbAB Δgene:(1, 20) A:(1E-40, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
0342 0.15 stbAB Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
0341 0.15 stbAB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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