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OPENSEQ.org
K1-C2
Genes: A B A+B
Length: 333 334 624
Sequences: 3770 14390 651
Seq/Len: 11.32 43.08 1.04
MirrorTree (Pazo et al. 2001) 0.07
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 0.02 0.04 0.07
2 0.03 0.06 0.15
5 0.04 0.09 0.32
10 0.05 0.13 0.58
20 0.07 0.19 0.98
100 0.14 0.31 2.51
∞ 0.24 0.35 3.06
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
295_V 84_L 1.03 0.37 0.00
281_I 58_I 0.90 0.27 0.00
222_K 322_Y 0.87 0.25 0.00
221_G 41_V 0.82 0.21 0.00
301_S 198_G 0.82 0.21 0.00
55_E 84_L 0.80 0.20 0.00
131_F 60_N 0.79 0.20 0.00
163_G 224_M 0.78 0.19 0.00
29_F 44_L 0.77 0.19 0.00
57_V 137_Y 0.75 0.17 0.00
271_V 150_G 0.75 0.17 0.00
245_D 127_L 0.75 0.17 0.00
113_N 143_L 0.74 0.17 0.00
112_F 167_H 0.74 0.17 0.00
138_I 285_H 0.73 0.16 0.00
189_A 216_S 0.73 0.16 0.00
237_T 103_P 0.72 0.16 0.00
190_V 44_L 0.72 0.16 0.00
290_A 110_L 0.72 0.16 0.00
137_K 93_I 0.71 0.15 0.00
271_V 212_L 0.71 0.15 0.00
69_V 185_Q 0.71 0.15 0.00
281_I 252_D 0.71 0.15 0.00
125_H 44_L 0.70 0.15 0.00
51_S 300_L 0.70 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)
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