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OPENSEQ.org
3uos_H_I
Genes: A B A+B
Length: 165 142 290
Sequences: 2373 1997 1784
Seq/Len: 14.38 14.06 6.15
MirrorTree (Pazo et al. 2001) 0.66
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 0.09 0.09 0.05
2 0.09 0.09 5.01
5 0.09 0.09 5.58
10 0.09 0.09 5.72
20 0.09 0.09 5.81
100 0.09 0.09 5.89
∞ 0.09 0.09 6.15
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
46_R 119_G 1.62 0.99 0.92
46_R 120_A 1.38 0.98 0.83
36_D 58_V 0.83 0.65 0.29
15_V 77_A 0.77 0.57 0.23
43_K 120_A 0.72 0.49 0.19
77_V 44_A 0.71 0.48 0.18
109_K 60_T 0.70 0.47 0.17
82_I 106_L 0.66 0.40 0.14
134_E 31_Q 0.66 0.40 0.14
129_L 66_S 0.65 0.38 0.13
99_F 39_C 0.64 0.37 0.13
40_E 66_S 0.64 0.37 0.13
75_A 80_L 0.64 0.37 0.13
38_M 77_A 0.62 0.35 0.12
59_L 89_G 0.62 0.35 0.12
160_D 138_L 0.62 0.35 0.12
117_L 84_A 0.61 0.33 0.11
69_F 58_V 0.60 0.32 0.10
111_A 31_Q 0.60 0.32 0.10
144_K 61_V 0.58 0.30 0.10
59_L 37_E 0.58 0.29 0.09
60_L 31_Q 0.58 0.29 0.09
139_L 65_R 0.57 0.28 0.09
61_R 70_V 0.57 0.28 0.09
49_G 33_V 0.56 0.28 0.09
67_T 21_S 0.56 0.27 0.08
46_R 121_D 0.56 0.27 0.08
158_V 42_F 0.56 0.27 0.08
141_A 88_S 0.56 0.27 0.08
107_E 66_S 0.56 0.27 0.08
81_L 73_T 0.55 0.26 0.08
39_T 120_A 0.55 0.26 0.08
79_P 101_I 0.55 0.26 0.08
33_V 99_G 0.55 0.26 0.08
7_D 47_D 0.55 0.26 0.08
91_A 19_N 0.55 0.26 0.08
16_S 24_V 0.55 0.25 0.08
51_Y 118_T 0.54 0.25 0.08
121_S 111_Q 0.54 0.25 0.08
117_L 45_K 0.53 0.24 0.07
68_P 140_V 0.53 0.24 0.07
67_T 58_V 0.53 0.23 0.07
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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