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OPENSEQ.org
140-276
Genes: A B A+B
Length: 300 137 422
Sequences: 10053 2559 127
Seq/Len: 33.51 18.68 0.3
MirrorTree (Pazo et al. 2001) 0.05
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 0.05 0.08 0.02
2 0.05 0.09 0.02
5 0.07 0.10 0.04
10 0.08 0.11 0.05
20 0.12 0.12 0.07
100 0.21 0.13 0.17
∞ 0.28 0.16 0.29
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
38_L 2_F 1.47 0.40 0.00
58_I 65_S 1.43 0.37 0.00
81_M 60_M 1.33 0.31 0.00
264_L 23_L 1.26 0.27 0.00
38_L 6_I 1.09 0.19 0.00
188_P 108_I 1.09 0.19 0.00
58_I 7_C 1.07 0.18 0.00
224_L 7_C 1.06 0.18 0.00
101_V 67_D 1.05 0.17 0.00
273_N 96_I 1.03 0.17 0.00
172_E 94_I 1.01 0.16 0.00
54_G 60_M 1.00 0.16 0.00
231_A 15_F 0.99 0.15 0.00
107_R 95_P 0.98 0.15 0.00
78_L 8_Y 0.98 0.15 0.00
144_L 16_V 0.97 0.15 0.00
284_L 19_M 0.97 0.14 0.00
114_R 115_C 0.97 0.14 0.00
251_K 63_V 0.96 0.14 0.00
13_D 65_S 0.95 0.14 0.00
156_L 93_L 0.95 0.14 0.00
97_G 34_V 0.95 0.14 0.00
217_L 17_Q 0.94 0.14 0.00
111_A 68_Y 0.94 0.14 0.00
213_G 109_L 0.94 0.14 0.00
172_E 5_F 0.94 0.14 0.00
41_I 56_R 0.93 0.13 0.00
119_A 65_S 0.92 0.13 0.00
272_T 82_L 0.92 0.13 0.00
221_V 20_I 0.91 0.13 0.00
145_F 81_A 0.91 0.13 0.00
242_E 6_I 0.90 0.12 0.00
190_V 61_V 0.90 0.12 0.00
81_M 54_E 0.89 0.12 0.00
38_L 134_L 0.89 0.12 0.00
62_A 106_P 0.89 0.12 0.00
206_S 18_E 0.89 0.12 0.00
167_L 68_Y 0.89 0.12 0.00
186_V 105_F 0.88 0.12 0.00
157_R 72_K 0.88 0.12 0.00
222_P 11_S 0.88 0.12 0.00
57_V 65_S 0.88 0.12 0.00
15_G 16_V 0.88 0.12 0.00
26_P 8_Y 0.87 0.12 0.00
194_D 8_Y 0.87 0.12 0.00
242_E 57_C 0.87 0.12 0.00
62_A 8_Y 0.87 0.12 0.00
78_L 16_V 0.86 0.11 0.00
58_I 2_F 0.86 0.11 0.00
50_V 15_F 0.86 0.11 0.00
196_G 65_S 0.86 0.11 0.00
268_V 134_L 0.86 0.11 0.00
226_S 41_P 0.86 0.11 0.00
101_V 93_L 0.84 0.11 0.00
116_C 61_V 0.84 0.11 0.00
242_E 107_S 0.84 0.11 0.00
151_K 47_S 0.84 0.11 0.00
54_G 128_T 0.84 0.11 0.00
30_T 2_F 0.84 0.11 0.00
58_I 58_R 0.83 0.11 0.00
115_H 60_M 0.83 0.10 0.00
242_E 3_D 0.82 0.10 0.00
62_A 47_S 0.82 0.10 0.00
160_A 61_V 0.82 0.10 0.00
260_A 126_F 0.82 0.10 0.00
50_V 6_I 0.81 0.10 0.00
78_L 133_A 0.81 0.10 0.00
177_V 6_I 0.81 0.10 0.00
102_L 100_A 0.81 0.10 0.00
64_E 7_C 0.81 0.10 0.00
75_A 49_A 0.81 0.10 0.00
44_A 115_C 0.80 0.10 0.00
194_D 31_K 0.80 0.10 0.00
140_A 16_V 0.79 0.10 0.00
89_C 6_I 0.79 0.10 0.00
84_H 113_T 0.79 0.10 0.00
140_A 5_F 0.79 0.10 0.00
255_F 96_I 0.78 0.09 0.00
216_D 32_L 0.78 0.09 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
7549 0.3 140-276 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7540 0.28 140-276 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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