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OPENSEQ.org
sar-myd
Genes: A B A+B
Length: 300 146 427
Sequences: 10053 2190 121
Seq/Len: 33.51 15 0.28
MirrorTree (Pazo et al. 2001) 0.03
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 0.09 0.01
2 0.05 0.10 0.02
5 0.07 0.12 0.03
10 0.08 0.13 0.04
20 0.12 0.14 0.06
100 0.21 0.14 0.16
∞ 0.28 0.17 0.27
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
81_M 69_M 1.35 0.31 0.00
38_L 11_F 1.22 0.24 0.00
58_I 16_C 1.21 0.24 0.00
101_V 76_D 1.20 0.23 0.00
264_L 32_L 1.11 0.19 0.00
167_L 77_Y 1.06 0.17 0.00
188_P 117_I 1.06 0.17 0.00
284_L 28_M 1.06 0.17 0.00
58_I 91_L 1.05 0.17 0.00
78_L 17_Y 1.04 0.16 0.00
156_L 102_L 1.03 0.16 0.00
221_V 29_I 1.03 0.16 0.00
190_V 51_G 1.02 0.16 0.00
217_L 26_Q 1.01 0.15 0.00
62_A 56_S 1.01 0.15 0.00
111_A 77_Y 1.00 0.15 0.00
58_I 74_S 1.00 0.15 0.00
119_A 74_S 0.99 0.15 0.00
67_P 47_D 0.99 0.15 0.00
172_E 14_F 0.98 0.14 0.00
213_G 118_L 0.97 0.14 0.00
186_V 114_F 0.96 0.14 0.00
242_E 66_C 0.95 0.13 0.00
242_E 116_S 0.95 0.13 0.00
157_R 81_K 0.94 0.13 0.00
26_P 101_R 0.94 0.13 0.00
74_V 115_P 0.93 0.13 0.00
101_V 86_Q 0.93 0.13 0.00
215_D 45_D 0.93 0.13 0.00
144_L 25_V 0.93 0.13 0.00
271_S 13_A 0.92 0.13 0.00
160_A 70_V 0.92 0.12 0.00
145_F 90_A 0.91 0.12 0.00
13_D 74_S 0.90 0.12 0.00
97_G 43_V 0.89 0.12 0.00
242_E 105_I 0.89 0.12 0.00
140_A 14_F 0.89 0.12 0.00
41_I 65_R 0.88 0.11 0.00
65_R 30_R 0.87 0.11 0.00
114_R 124_C 0.86 0.11 0.00
186_V 95_P 0.86 0.11 0.00
182_T 101_R 0.85 0.11 0.00
35_A 15_I 0.85 0.11 0.00
47_R 26_Q 0.84 0.10 0.00
122_N 14_F 0.84 0.10 0.00
62_A 13_A 0.84 0.10 0.00
59_L 118_L 0.84 0.10 0.00
54_G 69_M 0.83 0.10 0.00
142_E 142_A 0.83 0.10 0.00
62_A 115_P 0.83 0.10 0.00
191_A 29_I 0.83 0.10 0.00
55_L 25_V 0.82 0.10 0.00
231_A 24_F 0.82 0.10 0.00
156_L 94_S 0.82 0.10 0.00
182_T 60_E 0.82 0.10 0.00
49_R 74_S 0.82 0.10 0.00
156_L 110_M 0.82 0.10 0.00
222_P 20_S 0.82 0.10 0.00
38_L 15_I 0.81 0.10 0.00
116_C 70_V 0.81 0.10 0.00
264_L 33_E 0.81 0.10 0.00
102_L 77_Y 0.81 0.10 0.00
120_L 108_K 0.81 0.10 0.00
182_T 102_L 0.81 0.10 0.00
112_L 55_W 0.81 0.10 0.00
147_L 47_D 0.80 0.10 0.00
220_L 79_Q 0.80 0.10 0.00
107_R 104_P 0.80 0.10 0.00
251_K 72_V 0.80 0.09 0.00
62_A 17_Y 0.80 0.09 0.00
272_T 91_L 0.80 0.09 0.00
58_I 67_R 0.80 0.09 0.00
140_A 25_V 0.80 0.09 0.00
198_F 21_D 0.80 0.09 0.00
38_L 143_L 0.80 0.09 0.00
120_L 90_A 0.80 0.09 0.00
167_L 68_R 0.80 0.09 0.00
276_K 16_C 0.80 0.09 0.00
121_G 56_S 0.79 0.09 0.00
160_A 128_N 0.79 0.09 0.00
132_Q 108_K 0.79 0.09 0.00
78_L 76_D 0.79 0.09 0.00
217_L 84_D 0.79 0.09 0.00
196_G 74_S 0.79 0.09 0.00
34_A 103_I 0.79 0.09 0.00
35_A 65_R 0.78 0.09 0.00
268_V 143_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
7528 0.26 sar-myd Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7527 0.28 sar-myd Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7526 0.01 sar-myd Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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