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OPENSEQ.org
4Y0Y_4_20
Genes: A B A+B
Length: 216 51 267
Sequences: 14869 3157 54
Seq/Len: 68.84 61.9 0.2
MirrorTree (Pazo et al. 2001) 0.12
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 0.18 0.19 0.02
2 0.19 0.20 0.03
5 0.20 0.22 0.04
10 0.21 0.23 0.10
20 0.22 0.23 0.20
100 0.24 0.24 0.52
∞ 0.28 0.26 0.68
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
173_C 47_C 1.31 0.23 0.00
14_Y 36_A 1.26 0.21 0.00
182_V 4_P 1.18 0.18 0.00
120_G 37_K 1.11 0.15 0.00
7_C 17_Y 1.10 0.15 0.00
181_V 40_N 1.08 0.14 0.00
30_I 31_Y 1.05 0.14 0.00
65_I 27_Q 1.05 0.14 0.00
88_I 8_G 1.05 0.14 0.00
173_C 51_C 1.04 0.14 0.00
35_V 21_A 1.04 0.13 0.00
72_V 43_S 1.03 0.13 0.00
159_N 19_Y 1.02 0.13 0.00
161_F 17_Y 1.02 0.13 0.00
120_G 47_C 1.02 0.13 0.00
180_P 33_G 1.00 0.12 0.00
97_N 17_Y 0.99 0.12 0.00
196_G 31_Y 0.99 0.12 0.00
136_K 17_Y 0.98 0.12 0.00
110_A 40_N 0.98 0.12 0.00
187_L 28_T 0.98 0.12 0.00
191_V 16_R 0.97 0.12 0.00
178_G 26_C 0.97 0.12 0.00
178_G 39_N 0.97 0.12 0.00
121_W 31_Y 0.96 0.11 0.00
107_T 20_N 0.95 0.11 0.00
189_G 26_C 0.95 0.11 0.00
189_G 39_N 0.95 0.11 0.00
166_L 19_Y 0.95 0.11 0.00
92_S 19_Y 0.94 0.11 0.00
93_A 8_G 0.94 0.11 0.00
187_L 19_Y 0.94 0.11 0.00
209_V 20_N 0.92 0.10 0.00
65_I 35_R 0.92 0.10 0.00
173_C 26_C 0.92 0.10 0.00
173_C 39_N 0.92 0.10 0.00
23_H 40_N 0.89 0.10 0.00
163_A 10_C 0.89 0.10 0.00
70_S 32_G 0.89 0.10 0.00
151_A 24_G 0.88 0.10 0.00
25_C 26_C 0.88 0.10 0.00
25_C 39_N 0.88 0.10 0.00
87_L 45_E 0.87 0.09 0.00
212_Y 4_P 0.86 0.09 0.00
143_L 20_N 0.86 0.09 0.00
144_S 5_P 0.85 0.09 0.00
61_N 19_Y 0.85 0.09 0.00
198_A 19_Y 0.85 0.09 0.00
48_V 30_V 0.85 0.09 0.00
122_G 47_C 0.84 0.09 0.00
164_G 1_C 0.84 0.09 0.00
150_S 32_G 0.84 0.09 0.00
56_N 29_F 0.84 0.09 0.00
178_G 33_G 0.84 0.09 0.00
154_G 37_K 0.84 0.09 0.00
116_C 6_Y 0.84 0.09 0.00
6_T 17_Y 0.84 0.09 0.00
95_S 46_D 0.83 0.09 0.00
106_P 33_G 0.83 0.09 0.00
84_D 47_C 0.83 0.09 0.00
41_C 26_C 0.83 0.09 0.00
41_C 39_N 0.83 0.09 0.00
35_V 32_G 0.83 0.09 0.00
162_C 26_C 0.83 0.09 0.00
162_C 39_N 0.83 0.09 0.00
205_V 9_P 0.83 0.09 0.00
113_G 17_Y 0.83 0.09 0.00
69_K 17_Y 0.82 0.08 0.00
197_C 47_C 0.82 0.08 0.00
170_K 22_K 0.82 0.08 0.00
74_P 32_G 0.82 0.08 0.00
190_I 17_Y 0.82 0.08 0.00
101_A 18_F 0.81 0.08 0.00
66_S 17_Y 0.81 0.08 0.00
180_P 8_G 0.81 0.08 0.00
170_K 5_P 0.81 0.08 0.00
142_I 40_N 0.81 0.08 0.00
148_C 26_C 0.80 0.08 0.00
148_C 39_N 0.80 0.08 0.00
92_S 24_G 0.80 0.08 0.00
95_S 18_F 0.80 0.08 0.00
166_L 37_K 0.80 0.08 0.00
11_T 18_F 0.79 0.08 0.00
48_V 3_E 0.79 0.08 0.00
207_T 44_A 0.79 0.08 0.00
86_M 7_T 0.79 0.08 0.00
199_Q 43_S 0.79 0.08 0.00
173_C 29_F 0.78 0.08 0.00
181_V 9_P 0.78 0.08 0.00
178_G 47_C 0.78 0.08 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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