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OPENSEQ.org
TSAB_RIMI
Genes: A B A+B
Length: 231 148 373
Sequences: 3099 2778 1917
Seq/Len: 13.42 18.77 5.14
MirrorTree (Pazo et al. 2001) 0.59
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 0.04 3.88
2 0.00 0.04 3.94
5 0.00 0.04 3.94
10 0.00 0.04 3.95
20 0.00 0.04 3.95
100 0.00 0.05 4.05
∞ 0.00 0.06 5.06
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
100_Q 76_Q 0.91 0.70 0.01
46_L 36_Q 0.79 0.53 0.01
37_R 60_V 0.76 0.50 0.01
203_A 75_Y 0.75 0.49 0.00
203_A 90_D 0.68 0.38 0.00
71_V 97_V 0.67 0.38 0.00
148_I 21_R 0.67 0.37 0.00
74_G 73_P 0.67 0.37 0.00
162_T 70_A 0.66 0.36 0.00
74_G 23_H 0.64 0.34 0.00
92_V 13_P 0.64 0.33 0.00
17_L 118_L 0.63 0.32 0.00
94_T 116_E 0.63 0.32 0.00
47_T 66_L 0.63 0.32 0.00
80_G 35_N 0.62 0.31 0.00
91_G 41_L 0.62 0.31 0.00
75_I 35_N 0.61 0.30 0.00
28_E 71_V 0.61 0.30 0.00
192_E 110_A 0.61 0.29 0.00
52_S 78_Q 0.61 0.29 0.00
44_D 46_T 0.61 0.29 0.00
198_A 142_M 0.61 0.29 0.00
62_G 52_A 0.61 0.29 0.00
40_P 52_A 0.61 0.29 0.00
218_L 142_M 0.61 0.29 0.00
50_G 86_E 0.60 0.28 0.00
92_V 26_P 0.60 0.28 0.00
39_L 25_F 0.60 0.28 0.00
96_M 28_S 0.59 0.28 0.00
164_G 85_L 0.59 0.27 0.00
164_G 120_F 0.59 0.27 0.00
24_N 121_N 0.59 0.27 0.00
168_Q 84_L 0.58 0.26 0.00
197_I 34_S 0.58 0.26 0.00
163_V 101_W 0.58 0.26 0.00
100_Q 29_E 0.58 0.26 0.00
59_L 71_V 0.58 0.26 0.00
43_Q 69_I 0.57 0.25 0.00
23_V 76_Q 0.57 0.25 0.00
172_D 121_N 0.57 0.25 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
2712 5.14 TSAB_RIMI Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.01 Done
2189 10.66 yeaz-rimi Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
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