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OPENSEQ.org
uaf30 hht1 (A, 110-200)
Genes: A B A+B
Length: 91 136 224
Sequences: 1141 712 120
Seq/Len: 12.54 5.24 0.54
MirrorTree (Pazo et al. 2001) -0.02
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 0.03 0.05 0.01
2 0.03 0.06 0.01
5 0.03 0.07 0.02
10 0.03 0.08 0.03
20 0.04 0.08 0.06
100 0.04 0.09 0.16
∞ 0.07 0.12 0.53
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
50_N 55_F 1.90 0.83 0.10
24_L 96_S 1.33 0.46 0.02
24_L 90_I 1.21 0.36 0.01
36_V 103_S 1.12 0.30 0.01
82_S 81_T 1.00 0.23 0.01
22_A 91_G 0.95 0.20 0.01
36_V 23_S 0.89 0.17 0.00
25_L 131_L 0.84 0.15 0.00
41_A 55_F 0.81 0.14 0.00
75_E 55_F 0.81 0.14 0.00
42_Y 94_Q 0.80 0.13 0.00
22_A 42_Y 0.77 0.12 0.00
17_L 54_R 0.77 0.12 0.00
53_N 42_Y 0.77 0.12 0.00
66_I 60_E 0.77 0.12 0.00
29_E 54_R 0.76 0.12 0.00
70_S 79_F 0.76 0.12 0.00
67_L 27_R 0.74 0.12 0.00
38_R 103_S 0.73 0.11 0.00
26_G 96_S 0.73 0.11 0.00
24_L 97_V 0.73 0.11 0.00
55_K 54_R 0.73 0.11 0.00
59_C 33_T 0.72 0.11 0.00
70_S 55_F 0.72 0.11 0.00
90_I 55_F 0.71 0.11 0.00
59_C 36_V 0.71 0.11 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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