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OPENSEQ.org
166
Genes: A B A+B
Length: 195 180 355
Sequences: 1218 12105 157
Seq/Len: 6.25 67.25 0.44
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 0.04 0.05 0.03
2 0.04 0.06 0.05
5 0.05 0.07 0.11
10 0.05 0.09 0.22
20 0.05 0.12 0.42
100 0.07 0.22 1.14
∞ 0.10 0.28 1.87
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
75_V 30_T 1.39 0.44 0.00
156_K 83_N 1.27 0.35 0.00
158_G 19_I 1.25 0.34 0.00
181_R 91_V 1.17 0.29 0.00
167_R 157_T 1.14 0.27 0.00
83_H 22_V 1.14 0.27 0.00
163_V 60_I 1.13 0.27 0.00
87_D 159_A 1.12 0.26 0.00
64_Y 141_K 1.10 0.25 0.00
64_Y 99_V 1.09 0.25 0.00
189_N 94_N 1.00 0.20 0.00
79_F 131_N 0.99 0.19 0.00
15_M 30_T 0.99 0.19 0.00
130_S 123_F 0.95 0.18 0.00
184_Y 139_T 0.93 0.17 0.00
146_T 30_T 0.90 0.15 0.00
78_A 22_V 0.90 0.15 0.00
148_L 176_L 0.89 0.15 0.00
30_I 76_L 0.89 0.15 0.00
176_P 174_N 0.88 0.15 0.00
189_N 138_I 0.88 0.15 0.00
140_S 102_A 0.88 0.15 0.00
75_V 81_F 0.87 0.14 0.00
107_A 62_F 0.87 0.14 0.00
161_R 32_I 0.87 0.14 0.00
83_H 122_V 0.86 0.14 0.00
184_Y 142_L 0.86 0.14 0.00
194_I 118_A 0.85 0.14 0.00
127_V 35_K 0.84 0.14 0.00
97_F 87_L 0.82 0.13 0.00
87_D 170_D 0.80 0.12 0.00
184_Y 81_F 0.80 0.12 0.00
85_F 98_R 0.80 0.12 0.00
46_I 19_I 0.79 0.12 0.00
138_S 91_V 0.78 0.11 0.00
163_V 35_K 0.77 0.11 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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