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OPENSEQ.org
Renyu
Genes: A B A+B
Length: 268 396 655
Sequences: 4509 12671 2721
Seq/Len: 16.82 32 4.15
MirrorTree (Pazo et al. 2001) 0.61
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 3.76
2 0.00 0.00 3.89
5 0.00 0.01 3.94
10 0.00 0.01 4.08
20 0.00 0.01 4.10
100 0.00 0.08 4.19
∞ 0.00 0.12 4.60
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
108_N 274_R 2.89 1.00 1.00
58_L 173_L 2.25 1.00 0.99
135_E 7_Y 2.19 1.00 0.99
103_A 277_I 1.90 1.00 0.98
107_F 282_K 1.71 0.99 0.96
79_A 290_D 1.62 0.99 0.95
78_P 290_D 1.37 0.95 0.87
77_T 290_D 1.35 0.95 0.86
134_E 21_M 1.29 0.93 0.83
107_F 277_I 1.27 0.93 0.81
65_Q 171_E 1.27 0.93 0.81
180_S 181_E 1.19 0.89 0.76
58_L 17_P 1.16 0.87 0.73
79_A 289_A 1.11 0.84 0.68
157_N 180_Y 0.88 0.60 0.41
137_A 5_N 0.86 0.58 0.39
157_N 19_I 0.86 0.57 0.38
54_F 293_I 0.78 0.46 0.28
227_G 82_G 0.77 0.45 0.27
159_D 22_P 0.73 0.40 0.23
177_L 19_I 0.68 0.34 0.19
58_L 278_Y 0.68 0.34 0.19
40_L 283_A 0.66 0.31 0.17
58_L 196_Y 0.65 0.30 0.16
180_S 19_I 0.65 0.30 0.16
215_S 338_L 0.65 0.30 0.16
58_L 169_C 0.65 0.29 0.16
163_L 22_P 0.64 0.29 0.16
89_R 97_A 0.63 0.28 0.14
134_E 25_N 0.62 0.27 0.14
65_Q 160_S 0.62 0.27 0.14
107_F 281_M 0.59 0.24 0.12
129_A 17_P 0.59 0.24 0.12
185_A 178_G 0.58 0.23 0.11
147_N 333_E 0.58 0.23 0.11
173_Y 199_I 0.58 0.23 0.11
138_P 282_K 0.58 0.23 0.11
107_F 15_Y 0.58 0.23 0.11
174_T 156_I 0.57 0.22 0.10
108_N 287_Q 0.57 0.21 0.10
198_E 329_D 0.56 0.21 0.10
205_A 329_D 0.56 0.21 0.10
68_N 257_G 0.56 0.21 0.10
180_S 122_S 0.56 0.21 0.10
163_L 261_I 0.56 0.20 0.10
135_E 190_A 0.55 0.20 0.09
210_Q 163_A 0.55 0.20 0.09
33_S 59_T 0.55 0.20 0.09
107_F 275_V 0.54 0.19 0.09
155_P 180_Y 0.54 0.19 0.09
123_V 52_A 0.54 0.19 0.09
42_D 66_A 0.53 0.19 0.08
241_I 121_A 0.53 0.19 0.08
227_G 120_L 0.53 0.18 0.08
80_Q 290_D 0.53 0.18 0.08
83_E 42_A 0.53 0.18 0.08
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
5880 3.11 1K7F Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
5329 4.15 Renyu Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 1.00 Done - Shared
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