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OPENSEQ.org
comp
Genes: A B A+B
Length: 63 69 128
Sequences: 296 88 61
Seq/Len: 4.7 1.28 0.48
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 0.00 0.01 0.05
2 0.01 0.01 0.05
5 0.01 0.01 0.06
10 0.01 0.01 0.07
20 0.01 0.01 0.09
100 0.02 0.01 0.19
∞ 0.09 0.11 0.46
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
52_E 7_D 1.27 0.38 0.00
52_E 32_L 1.21 0.34 0.00
36_V 8_W 1.15 0.29 0.00
63_M 17_S 1.00 0.21 0.00
32_L 42_S 0.94 0.18 0.00
5_K 8_W 0.90 0.17 0.00
54_T 56_L 0.88 0.15 0.00
46_A 60_V 0.87 0.15 0.00
32_L 52_T 0.86 0.15 0.00
56_K 4_T 0.85 0.14 0.00
34_V 66_K 0.85 0.14 0.00
61_R 63_S 0.82 0.14 0.00
24_T 14_R 0.81 0.13 0.00
34_V 19_E 0.80 0.13 0.00
34_V 60_V 0.78 0.12 0.00
32_L 14_R 0.77 0.12 0.00
52_E 33_T 0.76 0.11 0.00
55_R 62_A 0.76 0.11 0.00
32_L 9_L 0.76 0.11 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
8597 0.48 comp Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8596 0.48 comp Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8595 0.48 comp Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8583 0.02 comp Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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