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OPENSEQ.org
tv_complex_001
Genes: A B A+B
Length: 121 296 378
Sequences: 9880 55922 1985
Seq/Len: 81.65 188.93 5.25
MirrorTree (Pazo et al. 2001) 0.08
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 0.06 0.09 0.49
2 0.06 0.12 0.86
5 0.07 0.15 1.75
10 0.08 0.19 3.05
20 0.09 0.23 4.76
100 0.17 0.31 8.79
∞ 0.22 0.33 9.52
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
92_T 58_E 0.80 0.56 0.00
102_A 264_Q 0.72 0.44 0.00
98_E 220_R 0.65 0.36 0.00
9_E 35_F 0.64 0.34 0.00
91_E 211_V 0.64 0.34 0.00
103_I 242_F 0.63 0.32 0.00
103_I 76_L 0.63 0.32 0.00
93_P 82_P 0.60 0.29 0.00
68_P 252_S 0.60 0.29 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
14007 0 aktcomplex_tv Δgene:(1, 20) A:(1E-80, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
14002 5.25 tv_complex_001 Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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