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OPENSEQ.org
h3_sirt_coevolutoon
Genes: A B A+B
Length: 268 136 394
Sequences: 9875 911 347
Seq/Len: 36.85 6.7 0.88
MirrorTree (Pazo et al. 2001) 0.10
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 0.06 0.02
2 0.01 0.07 0.03
5 0.01 0.09 0.05
10 0.01 0.10 0.07
20 0.01 0.11 0.11
100 0.02 0.12 0.35
∞ 0.04 0.15 0.86
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
57_P 96_A 1.03 0.34 0.00
25_I 113_I 1.02 0.33 0.00
69_E 55_Y 0.98 0.30 0.00
23_K 111_C 0.98 0.29 0.00
136_A 103_G 0.94 0.27 0.00
35_V 87_S 0.94 0.27 0.00
33_V 111_C 0.92 0.26 0.00
255_I 55_Y 0.86 0.22 0.00
136_A 111_C 0.85 0.21 0.00
236_E 125_I 0.84 0.20 0.00
50_A 125_I 0.83 0.20 0.00
205_L 91_M 0.82 0.19 0.00
205_L 43_R 0.82 0.19 0.00
144_K 90_V 0.81 0.18 0.00
239_P 96_A 0.78 0.17 0.00
77_P 111_C 0.76 0.16 0.00
130_Q 43_R 0.76 0.16 0.00
95_C 122_P 0.75 0.15 0.00
190_Q 90_V 0.74 0.15 0.00
176_M 72_M 0.72 0.14 0.00
258_L 43_R 0.72 0.14 0.00
202_V 97_C 0.72 0.14 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
9516 0.88 h3_sirt_coevolutoon Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9515 0.49 h3_sirt_coevolutoon Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9514 0.06 h3_sirt_coevolutoon Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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