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OPENSEQ.org
stbAB
Genes: A B A+B
Length: 196 112 301
Sequences: 2841 1967 951
Seq/Len: 14.49 17.56 3.16
MirrorTree (Pazo et al. 2001) 0.45
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 0.02 0.07
2 0.00 0.03 0.08
5 0.00 0.03 0.08
10 0.00 0.03 0.12
20 0.00 0.03 0.16
100 0.00 0.04 0.60
∞ 0.01 0.11 3.09
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
9_T 7_I 0.79 0.40 0.00
47_E 56_L 0.77 0.38 0.00
64_A 45_R 0.77 0.38 0.00
56_V 9_R 0.76 0.37 0.00
5_L 57_Q 0.71 0.31 0.00
102_L 60_K 0.71 0.31 0.00
116_I 56_L 0.70 0.30 0.00
9_T 86_I 0.69 0.29 0.00
5_L 93_V 0.68 0.28 0.00
62_E 28_M 0.66 0.26 0.00
183_L 14_D 0.66 0.26 0.00
104_N 65_V 0.65 0.25 0.00
159_R 59_L 0.65 0.25 0.00
44_T 78_T 0.65 0.25 0.00
158_Y 15_E 0.62 0.23 0.00
7_V 42_Q 0.62 0.22 0.00
44_T 21_V 0.62 0.22 0.00
50_C 28_M 0.61 0.22 0.00
28_E 97_D 0.60 0.20 0.00
21_Y 110_E 0.60 0.20 0.00
126_A 17_K 0.59 0.20 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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