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OPENSEQ.org
sar-myd
Genes: A B A+B
Length: 300 146 427
Sequences: 7484 2190 112
Seq/Len: 24.95 15 0.26
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 0.04 0.09 0.01
2 0.04 0.10 0.01
5 0.05 0.12 0.02
10 0.06 0.13 0.02
20 0.07 0.14 0.04
100 0.13 0.14 0.13
∞ 0.22 0.17 0.25
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
189_L 118_L 1.45 0.35 0.00
144_L 128_N 1.43 0.34 0.00
74_V 28_M 1.30 0.27 0.00
30_T 74_S 1.25 0.24 0.00
160_A 73_V 1.24 0.24 0.00
19_L 74_S 1.23 0.23 0.00
167_L 123_V 1.22 0.23 0.00
60_N 17_Y 1.18 0.21 0.00
232_Q 62_I 1.16 0.20 0.00
149_F 74_S 1.15 0.20 0.00
252_T 105_I 1.15 0.20 0.00
235_G 32_L 1.15 0.20 0.00
111_A 38_R 1.12 0.19 0.00
189_L 71_V 1.09 0.17 0.00
78_L 103_I 1.09 0.17 0.00
264_L 15_I 1.08 0.17 0.00
283_A 79_Q 1.08 0.17 0.00
120_L 42_C 1.06 0.16 0.00
38_L 125_D 1.06 0.16 0.00
38_L 56_S 1.05 0.16 0.00
38_L 60_E 1.04 0.16 0.00
31_R 74_S 1.03 0.15 0.00
146_P 74_S 1.01 0.15 0.00
65_R 74_S 1.01 0.15 0.00
111_A 125_D 1.00 0.14 0.00
280_A 14_F 0.99 0.14 0.00
144_L 52_T 0.98 0.14 0.00
254_V 118_L 0.98 0.14 0.00
60_N 70_V 0.97 0.14 0.00
227_N 20_S 0.97 0.13 0.00
123_C 12_D 0.96 0.13 0.00
221_V 74_S 0.96 0.13 0.00
78_L 63_E 0.96 0.13 0.00
19_L 14_F 0.95 0.13 0.00
248_L 79_Q 0.95 0.13 0.00
258_I 72_V 0.95 0.13 0.00
63_K 100_K 0.93 0.12 0.00
144_L 122_T 0.93 0.12 0.00
135_M 105_I 0.92 0.12 0.00
264_L 32_L 0.92 0.12 0.00
240_C 89_F 0.92 0.12 0.00
144_L 72_V 0.91 0.12 0.00
72_R 119_R 0.91 0.12 0.00
216_D 105_I 0.90 0.11 0.00
50_V 54_V 0.89 0.11 0.00
81_M 58_A 0.89 0.11 0.00
74_V 30_R 0.89 0.11 0.00
19_L 16_C 0.89 0.11 0.00
152_E 126_Y 0.89 0.11 0.00
58_I 130_C 0.89 0.11 0.00
44_A 70_V 0.89 0.11 0.00
272_T 56_S 0.88 0.11 0.00
101_V 17_Y 0.88 0.11 0.00
148_A 66_C 0.88 0.11 0.00
217_L 116_S 0.88 0.11 0.00
161_C 41_L 0.87 0.11 0.00
284_L 77_Y 0.87 0.11 0.00
62_A 73_V 0.86 0.10 0.00
83_K 29_I 0.86 0.10 0.00
235_G 66_C 0.86 0.10 0.00
30_T 33_E 0.85 0.10 0.00
202_L 21_D 0.85 0.10 0.00
238_Y 25_V 0.85 0.10 0.00
286_L 116_S 0.84 0.10 0.00
55_L 71_V 0.84 0.10 0.00
74_V 12_D 0.84 0.10 0.00
55_L 67_R 0.84 0.10 0.00
78_L 70_V 0.84 0.10 0.00
144_L 54_V 0.84 0.10 0.00
103_Y 20_S 0.83 0.10 0.00
277_S 118_L 0.83 0.10 0.00
55_L 65_R 0.83 0.10 0.00
189_L 125_D 0.83 0.10 0.00
167_L 116_S 0.83 0.10 0.00
174_E 74_S 0.83 0.10 0.00
102_L 71_V 0.83 0.10 0.00
157_R 101_R 0.82 0.10 0.00
72_R 70_V 0.82 0.10 0.00
102_L 115_P 0.81 0.09 0.00
268_V 74_S 0.81 0.09 0.00
142_E 60_E 0.81 0.09 0.00
144_L 105_I 0.80 0.09 0.00
232_Q 14_F 0.80 0.09 0.00
260_A 77_Y 0.80 0.09 0.00
119_A 16_C 0.80 0.09 0.00
43_V 16_C 0.80 0.09 0.00
197_R 28_M 0.80 0.09 0.00
262_Q 69_M 0.80 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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