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OPENSEQ.org
C2-Ta
Genes: A B A+B
Length: 334 439 731
Sequences: 14390 1037 240
Seq/Len: 43.08 2.36 0.33
MirrorTree (Pazo et al. 2001) -0.01
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 0.06 0.02
2 0.06 0.06 0.04
5 0.09 0.06 0.08
10 0.13 0.07 0.18
20 0.19 0.07 0.31
100 0.31 0.10 0.77
∞ 0.35 0.18 0.99
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
113_E 122_I 1.29 0.31 0.00
316_E 5_I 1.02 0.17 0.00
69_L 374_A 1.01 0.17 0.00
298_D 381_T 0.98 0.16 0.00
165_H 7_I 0.94 0.14 0.00
127_L 40_K 0.92 0.14 0.00
307_D 124_K 0.90 0.13 0.00
87_L 171_I 0.89 0.13 0.00
307_D 287_S 0.87 0.12 0.00
316_E 190_T 0.86 0.12 0.00
300_L 137_V 0.86 0.12 0.00
36_D 7_I 0.86 0.12 0.00
153_H 185_Y 0.86 0.12 0.00
163_I 7_I 0.85 0.12 0.00
316_E 147_S 0.85 0.12 0.00
95_T 7_I 0.84 0.11 0.00
172_L 220_E 0.84 0.11 0.00
158_P 53_F 0.83 0.11 0.00
172_L 365_G 0.82 0.11 0.00
172_L 372_Q 0.82 0.11 0.00
172_L 65_A 0.82 0.11 0.00
133_R 124_K 0.81 0.11 0.00
303_L 137_V 0.81 0.10 0.00
135_Y 87_F 0.80 0.10 0.00
81_I 340_S 0.80 0.10 0.00
127_L 153_L 0.79 0.10 0.00
44_L 374_A 0.79 0.10 0.00
65_V 425_M 0.79 0.10 0.00
220_M 7_I 0.79 0.10 0.00
164_D 75_I 0.79 0.10 0.00
189_V 171_I 0.78 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)
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