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OPENSEQ.org
PTPC2(aka AGAW)_AGAA
Genes: A B A+B
Length: 133 167 295
Sequences: 900 1654 306
Seq/Len: 6.77 9.9 1.04
MirrorTree (Pazo et al. 2001) 0.16
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 0.01 0.01
2 0.00 0.01 0.05
5 0.00 0.01 0.27
10 0.08 0.01 0.33
20 0.10 0.01 0.38
100 0.16 0.01 0.56
∞ 0.19 0.03 1.02
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_F 104_R 1.03 0.38 0.00
113_L 57_I 1.00 0.35 0.00
39_V 61_M 0.94 0.30 0.00
127_A 18_V 0.90 0.27 0.00
18_A 9_G 0.89 0.26 0.00
79_I 121_A 0.86 0.24 0.00
129_N 27_A 0.85 0.24 0.00
126_L 22_L 0.84 0.23 0.00
54_G 133_G 0.83 0.22 0.00
129_N 139_K 0.82 0.22 0.00
51_L 148_A 0.82 0.21 0.00
97_G 16_G 0.82 0.21 0.00
9_F 118_I 0.81 0.21 0.00
95_A 91_G 0.80 0.20 0.00
9_F 161_Q 0.77 0.18 0.00
60_W 54_I 0.76 0.18 0.00
58_L 155_V 0.76 0.18 0.00
33_V 14_E 0.75 0.17 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
0933 1.04 PTPC2(aka AGAW)_AGAA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done
0932 0.01 PTPC2(aka AGAW)_AGAA Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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