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OPENSEQ.org
14avs49
Genes: A B A+B
Length: 125 424 528
Sequences: 8021 1152 179
Seq/Len: 64.17 2.72 0.34
MirrorTree (Pazo et al. 2001) 0.20
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 0.08 0.04 0.01
2 0.11 0.04 0.01
5 0.13 0.05 0.01
10 0.13 0.05 0.02
20 0.14 0.05 0.03
100 0.19 0.06 0.13
∞ 0.23 0.09 0.33
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
21_L 197_A 1.09 0.21 0.00
62_V 231_G 1.07 0.20 0.00
89_V 137_D 1.00 0.17 0.00
23_I 147_I 0.91 0.14 0.00
72_N 126_I 0.90 0.13 0.00
74_C 215_P 0.89 0.13 0.00
70_A 311_L 0.88 0.13 0.00
70_A 124_G 0.87 0.12 0.00
73_A 105_G 0.86 0.12 0.00
62_V 126_I 0.85 0.12 0.00
23_I 82_K 0.85 0.12 0.00
60_A 287_G 0.85 0.12 0.00
78_S 209_Q 0.85 0.12 0.00
42_Y 216_P 0.85 0.12 0.00
93_N 284_G 0.84 0.12 0.00
31_T 84_I 0.84 0.12 0.00
87_L 271_A 0.84 0.12 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 = 0.287), 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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