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OPENSEQ.org
h3_sirt_coevolutoon
Genes: A B A+B
Length: 268 136 394
Sequences: 3707 688 194
Seq/Len: 13.83 5.06 0.49
MirrorTree (Pazo et al. 2001) 0.13
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 0.02 0.06 0.01
2 0.02 0.06 0.02
5 0.03 0.07 0.04
10 0.03 0.08 0.04
20 0.03 0.08 0.06
100 0.05 0.10 0.20
∞ 0.11 0.12 0.48
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
255_I 55_Y 1.08 0.26 0.00
22_C 75_I 0.97 0.20 0.00
103_D 43_R 0.93 0.18 0.00
95_C 55_Y 0.91 0.17 0.00
162_P 90_V 0.89 0.16 0.00
25_I 90_V 0.86 0.15 0.00
243_F 125_I 0.86 0.15 0.00
174_A 97_C 0.85 0.15 0.00
255_I 103_G 0.85 0.15 0.00
46_D 55_Y 0.85 0.14 0.00
250_D 42_Y 0.84 0.14 0.00
235_R 38_K 0.84 0.14 0.00
186_N 131_I 0.83 0.14 0.00
202_V 121_M 0.83 0.14 0.00
102_S 72_M 0.83 0.14 0.00
129_I 90_V 0.82 0.14 0.00
92_P 96_A 0.82 0.14 0.00
244_D 90_V 0.81 0.13 0.00
144_K 96_A 0.81 0.13 0.00
104_K 131_I 0.79 0.12 0.00
205_L 111_C 0.79 0.12 0.00
236_E 125_I 0.78 0.12 0.00
207_V 31_P 0.78 0.12 0.00
33_V 90_V 0.77 0.12 0.00
35_V 87_S 0.76 0.12 0.00
56_F 31_P 0.75 0.11 0.00
94_L 55_Y 0.75 0.11 0.00
83_K 55_Y 0.74 0.11 0.00
129_I 111_C 0.74 0.11 0.00
244_D 131_I 0.74 0.11 0.00
103_D 90_V 0.73 0.11 0.00
238_L 103_G 0.73 0.11 0.00
200_D 88_S 0.72 0.10 0.00
243_F 42_Y 0.72 0.10 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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