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OPENSEQ.org
4Y0Y_6_inf_trimmed
Genes: A B A+B
Length: 214 49 263
Sequences: 14615 3016 168
Seq/Len: 68.29 61.55 0.64
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 0.18 0.17 0.02
2 0.20 0.19 0.03
5 0.21 0.20 0.05
10 0.22 0.21 0.11
20 0.23 0.21 0.21
100 0.25 0.23 0.50
∞ 0.28 0.24 0.64
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
69_K 17_Y 1.38 0.54 0.00
28_S 31_Y 1.07 0.30 0.00
100_V 4_P 1.05 0.29 0.00
139_K 41_F 0.99 0.25 0.00
43_K 43_S 0.94 0.22 0.00
76_Y 45_E 0.93 0.21 0.00
178_G 26_C 0.93 0.21 0.00
14_Y 48_M 0.92 0.20 0.00
190_I 38_R 0.90 0.20 0.00
173_C 39_N 0.89 0.19 0.00
186_K 29_F 0.89 0.19 0.00
35_V 13_R 0.87 0.18 0.00
163_A 43_S 0.86 0.17 0.00
209_V 19_Y 0.84 0.17 0.00
204_G 33_G 0.83 0.16 0.00
187_L 32_G 0.81 0.15 0.00
140_A 43_S 0.79 0.14 0.00
6_T 42_K 0.78 0.14 0.00
70_S 41_F 0.78 0.14 0.00
178_G 47_C 0.78 0.14 0.00
165_Y 43_S 0.77 0.14 0.00
195_S 43_S 0.77 0.14 0.00
88_I 18_F 0.76 0.13 0.00
25_C 33_G 0.75 0.13 0.00
187_L 12_A 0.75 0.13 0.00
105_L 45_E 0.74 0.13 0.00
110_A 41_F 0.74 0.13 0.00
24_F 18_F 0.74 0.12 0.00
173_C 47_C 0.73 0.12 0.00
38_A 6_Y 0.73 0.12 0.00
49_R 24_G 0.73 0.12 0.00
103_I 22_K 0.72 0.12 0.00
90_L 10_C 0.72 0.12 0.00
85_I 19_Y 0.72 0.12 0.00
88_I 24_G 0.72 0.12 0.00
105_L 39_N 0.71 0.12 0.00
10_N 31_Y 0.71 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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