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OPENSEQ.org
3A0R_AB
Genes: A B A+B
Length: 334 116 444
Sequences: 27670 89405 13047
Seq/Len: 82.84 770.73 29.39
MirrorTree (Pazo et al. 2001) 0.91
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 0.10 21.00
2 0.06 0.13 22.70
5 0.07 0.16 24.51
10 0.09 0.19 26.63
20 0.11 0.23 28.99
100 0.19 0.32 34.95
∞ 0.25 0.34 36.75
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
140_T 13_I 1.42 1.00 0.78
161_K 15_E 1.38 0.99 0.75
169_E 12_N 1.33 0.99 0.72
144_G 16_L 1.29 0.99 0.68
165_I 15_E 1.07 0.95 0.47
152_H 23_E 1.01 0.93 0.41
168_N 12_N 0.94 0.89 0.33
147_M 104_F 0.92 0.87 0.31
147_M 103_N 0.91 0.86 0.30
151_K 23_E 0.84 0.80 0.23
162_Y 19_E 0.72 0.63 0.14
158_T 22_Q 0.71 0.63 0.14
145_F 16_L 0.66 0.53 0.11
158_T 19_E 0.63 0.49 0.10
141_I 12_N 0.61 0.45 0.08
171_S 103_N 0.60 0.44 0.08
151_K 105_D 0.55 0.36 0.06
140_T 102_F 0.55 0.36 0.06
165_I 12_N 0.55 0.35 0.06
148_R 19_E 0.54 0.34 0.06
172_R 10_E 0.52 0.31 0.05
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
10439 29.39 3A0R_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.78 Done - Shared
1369 4.22 3a0r_A_B Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2013_03) 0.91 Done - Shared
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