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OPENSEQ.org
trib-akt_test
Genes: A B A+B
Length: 288 275 500
Sequences: 67552 67592 358
Seq/Len: 234.56 245.79 0.72
MirrorTree (Pazo et al. 2001) 0.25
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 0.10 0.10 0.09
2 0.13 0.12 0.15
5 0.17 0.16 0.28
10 0.20 0.20 0.41
20 0.24 0.24 0.64
100 0.32 0.31 1.00
∞ 0.34 0.34 1.05
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
176_S 194_G 1.39 0.58 0.00
235_T 135_L 1.11 0.36 0.00
210_L 36_Y 1.06 0.32 0.00
50_V 141_M 0.98 0.26 0.00
39_E 85_F 0.98 0.26 0.00
68_T 85_F 0.98 0.26 0.00
176_S 25_I 0.97 0.26 0.00
179_V 33_G 0.94 0.23 0.00
226_L 70_L 0.92 0.22 0.00
109_V 131_V 0.92 0.22 0.00
118_F 55_T 0.91 0.22 0.00
195_E 117_I 0.90 0.21 0.00
26_C 202_M 0.88 0.20 0.00
68_T 130_V 0.88 0.20 0.00
72_G 73_L 0.88 0.20 0.00
185_L 261_E 0.88 0.20 0.00
128_L 155_L 0.88 0.20 0.00
41_Y 239_L 0.88 0.20 0.00
187_G 205_G 0.88 0.20 0.00
151_A 141_M 0.86 0.19 0.00
21_G 124_L 0.85 0.18 0.00
49_H 215_E 0.84 0.18 0.00
26_C 233_G 0.84 0.18 0.00
51_A 105_F 0.83 0.17 0.00
24_Y 40_I 0.83 0.17 0.00
40_P 70_L 0.83 0.17 0.00
128_L 253_G 0.82 0.17 0.00
233_R 196_G 0.82 0.17 0.00
88_E 123_Y 0.82 0.17 0.00
166_S 121_L 0.82 0.17 0.00
231_A 59_N 0.82 0.17 0.00
49_H 205_G 0.82 0.17 0.00
39_E 70_L 0.81 0.17 0.00
185_L 218_F 0.81 0.17 0.00
204_R 150_I 0.81 0.17 0.00
184_M 202_M 0.81 0.16 0.00
100_L 121_L 0.81 0.16 0.00
26_C 204_C 0.81 0.16 0.00
32_Q 239_L 0.80 0.16 0.00
226_L 244_L 0.80 0.16 0.00
175_W 123_Y 0.80 0.16 0.00
129_V 72_A 0.79 0.15 0.00
13_Y 62_L 0.79 0.15 0.00
179_V 125_H 0.78 0.15 0.00
65_A 95_L 0.78 0.15 0.00
173_D 153_F 0.78 0.15 0.00
109_V 253_G 0.77 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)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.244), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
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