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OPENSEQ.org
cI_A_E
Genes: A B A+B
Length: 613 147 725
Sequences: 2092 3696 1838
Seq/Len: 3.41 25.14 2.54
MirrorTree (Pazo et al. 2001) 0.89
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 0.00 0.01
2 0.00 0.00 0.06
5 0.00 0.00 0.99
10 0.00 0.00 1.61
20 0.00 0.00 2.29
100 0.00 0.01 2.36
∞ 0.01 0.01 2.42
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
388_A 125_W 0.90 0.47 0.00
437_F 106_F 0.88 0.45 0.00
192_L 103_A 0.88 0.45 0.00
174_T 87_A 0.87 0.44 0.00
244_A 82_A 0.86 0.43 0.00
548_V 107_I 0.83 0.40 0.00
176_V 121_G 0.82 0.38 0.00
354_L 87_A 0.81 0.37 0.00
78_N 109_V 0.80 0.37 0.00
163_N 52_S 0.78 0.34 0.00
489_S 107_I 0.77 0.33 0.00
10_L 114_L 0.77 0.33 0.00
104_S 114_L 0.77 0.33 0.00
92_V 109_V 0.76 0.32 0.00
394_A 124_D 0.76 0.32 0.00
225_G 86_F 0.74 0.30 0.00
384_A 87_A 0.74 0.30 0.00
95_V 17_A 0.73 0.29 0.00
149_C 58_G 0.72 0.28 0.00
102_Y 65_S 0.72 0.28 0.00
306_R 69_Y 0.71 0.27 0.00
260_T 73_M 0.71 0.27 0.00
507_L 33_G 0.71 0.27 0.00
85_S 31_L 0.71 0.27 0.00
293_L 103_A 0.71 0.27 0.00
298_A 47_N 0.70 0.26 0.00
318_Y 77_I 0.70 0.26 0.00
401_E 83_L 0.70 0.26 0.00
115_R 34_G 0.70 0.26 0.00
264_Y 67_K 0.70 0.26 0.00
502_V 24_I 0.70 0.26 0.00
400_D 113_G 0.69 0.26 0.00
117_F 26_L 0.69 0.25 0.00
514_G 17_A 0.68 0.24 0.00
189_Y 102_E 0.68 0.24 0.00
362_I 20_L 0.68 0.24 0.00
403_L 80_V 0.68 0.24 0.00
354_L 52_S 0.68 0.24 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)
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