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OPENSEQ.org
4Y0Y_6_inf
Genes: A B A+B
Length: 216 51 267
Sequences: 14703 2987 172
Seq/Len: 68.07 58.57 0.64
MirrorTree (Pazo et al. 2001) -0.00
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 0.17 0.17 0.02
2 0.19 0.19 0.03
5 0.20 0.21 0.04
10 0.21 0.21 0.10
20 0.22 0.21 0.20
100 0.24 0.23 0.50
∞ 0.27 0.25 0.64
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
69_K 17_Y 1.22 0.41 0.00
88_I 18_F 1.20 0.39 0.00
161_F 17_Y 1.18 0.38 0.00
124_T 45_E 1.08 0.31 0.00
28_S 31_Y 1.07 0.30 0.00
76_Y 45_E 1.04 0.28 0.00
178_G 26_C 0.99 0.25 0.00
173_C 39_N 0.95 0.23 0.00
139_K 41_F 0.95 0.22 0.00
100_V 4_P 0.95 0.22 0.00
64_F 41_F 0.90 0.20 0.00
187_L 12_A 0.90 0.20 0.00
178_G 47_C 0.89 0.19 0.00
31_N 19_Y 0.89 0.19 0.00
212_Y 22_K 0.88 0.19 0.00
178_G 51_C 0.87 0.18 0.00
14_Y 48_M 0.84 0.17 0.00
48_V 37_K 0.84 0.17 0.00
72_V 49_R 0.82 0.16 0.00
197_C 17_Y 0.81 0.15 0.00
14_Y 36_A 0.80 0.15 0.00
14_Y 37_K 0.80 0.15 0.00
35_V 13_R 0.79 0.14 0.00
93_A 20_N 0.77 0.14 0.00
27_G 16_R 0.77 0.14 0.00
43_K 43_S 0.76 0.13 0.00
198_A 19_Y 0.75 0.13 0.00
142_I 5_P 0.75 0.13 0.00
138_L 42_K 0.74 0.13 0.00
187_L 27_Q 0.74 0.13 0.00
35_V 10_C 0.74 0.13 0.00
103_I 28_T 0.73 0.12 0.00
105_L 45_E 0.73 0.12 0.00
29_L 49_R 0.73 0.12 0.00
46_I 19_Y 0.73 0.12 0.00
14_Y 29_F 0.72 0.12 0.00
135_L 45_E 0.72 0.12 0.00
201_N 4_P 0.72 0.12 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)
ID Seq/Len Name Options I_Prob Status
11600 0.58 4Y0Y_10_inf Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11597 0.64 4Y0Y_6_inf Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11596 0.67 4Y0Y_4_inf Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11594 0.68 4Y0Y_2_inf Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11564 0.2 4Y0Y_4_20 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11545 0.19 4Y0Y_10_20 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11478 0.2 4Y0Y_6_20 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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