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OPENSEQ.org
2oza_A_B
Genes: A B A+B
Length: 328 282 531
Sequences: 8769 41823 604
Seq/Len: 26.73 148.31 1.14
MirrorTree (Pazo et al. 2001) 0.10
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 0.10
2 0.06 0.10 0.15
5 0.06 0.14 0.33
10 0.08 0.17 0.56
20 0.11 0.21 0.99
100 0.21 0.30 2.65
∞ 0.28 0.33 3.68
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
184_W 181_W 1.27 0.63 0.00
178_N 159_L 1.20 0.55 0.00
155_L 26_L 1.18 0.54 0.00
128_G 52_Q 0.99 0.36 0.00
269_D 188_Y 0.94 0.31 0.00
285_F 139_A 0.93 0.31 0.00
70_K 167_A 0.90 0.29 0.00
142_L 139_A 0.90 0.29 0.00
138_I 182_S 0.89 0.28 0.00
204_D 225_K 0.89 0.28 0.00
269_D 96_C 0.88 0.27 0.00
157_I 157_A 0.87 0.26 0.00
264_K 74_V 0.86 0.26 0.00
216_V 129_A 0.86 0.25 0.00
187_G 241_P 0.84 0.24 0.00
157_I 148_L 0.84 0.24 0.00
262_L 243_I 0.81 0.22 0.00
262_L 167_A 0.80 0.22 0.00
72_E 93_V 0.80 0.21 0.00
181_V 159_L 0.80 0.21 0.00
76_G 161_L 0.80 0.21 0.00
18_E 26_L 0.78 0.20 0.00
278_Q 233_T 0.78 0.20 0.00
235_Y 26_L 0.77 0.20 0.00
269_D 211_E 0.77 0.20 0.00
125_I 108_D 0.76 0.19 0.00
33_F 50_M 0.76 0.19 0.00
187_G 68_S 0.76 0.19 0.00
212_I 174_Y 0.76 0.19 0.00
217_G 181_W 0.76 0.19 0.00
78_L 126_I 0.75 0.18 0.00
278_Q 221_R 0.75 0.18 0.00
138_I 166_F 0.75 0.18 0.00
105_N 182_S 0.75 0.18 0.00
186_V 236_E 0.74 0.18 0.00
100_M 75_R 0.74 0.18 0.00
156_K 19_Y 0.72 0.17 0.00
63_L 205_P 0.72 0.17 0.00
138_I 167_A 0.72 0.17 0.00
118_V 235_T 0.72 0.17 0.00
275_T 55_P 0.72 0.17 0.00
216_V 50_M 0.71 0.16 0.00
194_L 19_Y 0.71 0.16 0.00
126_L 215_E 0.71 0.16 0.00
272_K 66_R 0.71 0.16 0.00
79_D 156_N 0.71 0.16 0.00
177_Y 71_P 0.71 0.16 0.00
184_W 224_L 0.70 0.16 0.00
93_V 128_E 0.70 0.16 0.00
93_V 188_Y 0.70 0.16 0.00
44_K 60_E 0.70 0.15 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)
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