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DOG1_AHG1 (A, 5-260) (B, 105-410)
Genes: A B A+B
Length: 256 306 521
Sequences: 387 4619 153
Seq/Len: 1.51 15.09 0.29
MirrorTree (Pazo et al. 2001) 0.03
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 0.12 0.04 0.01
2 0.12 0.05 0.01
5 0.13 0.05 0.01
10 0.13 0.06 0.01
20 0.13 0.06 0.01
100 0.14 0.08 0.07
∞ 0.29 0.15 0.27
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
230_G 303_V 1.15 0.21 0.00
202_A 152_L 1.14 0.21 0.00
172_D 303_V 1.10 0.19 0.00
133_S 26_N 1.02 0.16 0.00
163_V 130_A 0.98 0.15 0.00
70_S 228_L 0.97 0.14 0.00
179_A 248_A 0.93 0.13 0.00
52_I 204_R 0.92 0.13 0.00
167_Q 44_Y 0.91 0.12 0.00
247_W 176_I 0.90 0.12 0.00
234_L 64_V 0.88 0.12 0.00
137_L 237_D 0.87 0.11 0.00
90_G 12_G 0.87 0.11 0.00
239_K 248_A 0.86 0.11 0.00
55_F 224_G 0.86 0.11 0.00
87_I 163_N 0.83 0.10 0.00
218_L 135_L 0.83 0.10 0.00
147_V 135_L 0.83 0.10 0.00
171_A 176_I 0.83 0.10 0.00
198_K 183_V 0.82 0.10 0.00
30_A 134_V 0.82 0.10 0.00
52_I 239_L 0.82 0.10 0.00
49_G 142_V 0.81 0.10 0.00
214_R 152_L 0.81 0.10 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)
ID Seq/Len Name Options I_Prob Status
10605 0.11 DOG1_AHG1 (A, 5-260) (B, 105-410) Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10604 0.29 DOG1_AHG1 (A, 5-260) (B, 105-410) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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