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OPENSEQ.org
2qba_K_D
Genes: A B A+B
Length: 123 209 331
Sequences: 1712 2894 1680
Seq/Len: 13.92 13.85 5.08
MirrorTree (Pazo et al. 2001) 0.85
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 0.00
2 0.09 0.09 0.00
5 0.09 0.09 0.05
10 0.09 0.09 4.70
20 0.09 0.09 5.06
100 0.09 0.09 5.17
∞ 0.10 0.09 5.49
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
68_G 122_V 0.97 0.77 0.02
93_Q 129_T 0.89 0.68 0.01
84_C 104_V 0.84 0.60 0.01
72_P 20_V 0.81 0.57 0.01
122_V 145_S 0.81 0.57 0.01
86_L 151_T 0.78 0.52 0.01
31_R 43_D 0.75 0.48 0.01
51_K 164_Q 0.74 0.47 0.01
70_R 109_V 0.74 0.47 0.01
14_S 141_R 0.72 0.44 0.01
91_S 77_R 0.71 0.42 0.01
115_I 109_V 0.71 0.42 0.01
84_C 1_M 0.70 0.41 0.01
93_Q 131_D 0.70 0.41 0.01
84_C 21_S 0.70 0.41 0.01
41_I 133_T 0.70 0.41 0.01
68_G 129_T 0.69 0.40 0.01
42_T 14_I 0.69 0.39 0.01
38_I 119_A 0.68 0.38 0.01
14_S 1_M 0.68 0.38 0.01
41_I 3_G 0.68 0.38 0.01
66_K 190_K 0.67 0.37 0.01
51_K 132_A 0.67 0.37 0.01
17_R 96_I 0.67 0.37 0.01
99_I 96_I 0.66 0.36 0.01
52_V 112_T 0.66 0.36 0.01
93_Q 151_T 0.66 0.36 0.01
31_R 111_G 0.66 0.35 0.01
7_M 111_G 0.66 0.35 0.01
19_V 206_A 0.65 0.34 0.01
115_I 83_R 0.64 0.33 0.01
76_V 13_R 0.64 0.33 0.01
117_S 134_H 0.64 0.33 0.01
77_I 206_A 0.63 0.32 0.01
35_V 23_P 0.63 0.32 0.01
70_R 192_A 0.63 0.32 0.01
43_I 91_T 0.63 0.32 0.01
61_V 177_V 0.62 0.31 0.01
4_E 35_T 0.62 0.31 0.01
105_R 11_M 0.62 0.30 0.01
55_G 173_Q 0.62 0.30 0.01
78_R 151_T 0.62 0.30 0.01
51_K 184_R 0.61 0.30 0.01
51_K 160_K 0.61 0.30 0.01
89_N 77_R 0.61 0.30 0.01
39_I 145_S 0.61 0.30 0.01
116_I 149_N 0.61 0.29 0.01
89_N 53_G 0.61 0.29 0.01
42_T 151_T 0.61 0.29 0.01
68_G 201_L 0.60 0.29 0.01
58_L 125_W 0.60 0.29 0.01
116_I 164_Q 0.60 0.29 0.01
104_T 150_Q 0.60 0.28 0.01
62_V 168_E 0.60 0.28 0.01
35_V 50_V 0.59 0.27 0.01
60_A 147_G 0.59 0.27 0.01
29_H 113_S 0.59 0.27 0.01
19_V 62_K 0.59 0.27 0.01
89_N 133_T 0.58 0.26 0.01
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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