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OPENSEQ.org
L4-vs-S10
Genes: A B A+B
Length: 201 103 301
Sequences: 3177 1460 1854
Seq/Len: 15.81 14.17 6.16
MirrorTree (Pazo et al. 2001) 0.78
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 0.08 0.09 0.11
2 0.08 0.09 4.87
5 0.08 0.09 4.97
10 0.09 0.09 5.00
20 0.09 0.09 5.03
100 0.09 0.09 5.38
∞ 0.09 0.09 6.10
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
189_T 4_Q 1.01 0.85 0.03
70_S 58_N 0.95 0.79 0.03
41_Q 74_V 0.94 0.78 0.03
199_M 74_V 0.89 0.73 0.02
97_N 3_N 0.82 0.64 0.02
29_H 28_T 0.78 0.58 0.02
134_L 46_K 0.76 0.55 0.01
59_P 56_H 0.75 0.54 0.01
67_R 29_A 0.75 0.54 0.01
77_I 57_V 0.75 0.53 0.01
85_F 17_L 0.74 0.53 0.01
138_L 55_P 0.72 0.50 0.01
104_A 71_L 0.70 0.47 0.01
77_I 58_N 0.70 0.47 0.01
83_V 60_D 0.69 0.45 0.01
26_A 88_M 0.68 0.43 0.01
29_H 102_L 0.68 0.43 0.01
142_A 49_F 0.67 0.42 0.01
100_M 82_K 0.67 0.42 0.01
192_A 69_T 0.67 0.42 0.01
48_T 94_A 0.67 0.41 0.01
79_R 18_I 0.67 0.41 0.01
57_K 12_A 0.66 0.41 0.01
188_M 49_F 0.65 0.39 0.01
169_V 48_R 0.65 0.39 0.01
152_E 40_I 0.65 0.39 0.01
30_Q 88_M 0.63 0.37 0.01
28_V 30_K 0.63 0.36 0.01
198_E 70_H 0.63 0.36 0.01
155_E 36_V 0.63 0.36 0.01
41_Q 20_Q 0.63 0.36 0.01
54_G 13_F 0.63 0.35 0.01
161_A 37_R 0.62 0.35 0.01
86_A 47_E 0.62 0.34 0.01
172_A 102_L 0.61 0.34 0.01
129_P 21_A 0.61 0.34 0.01
103_G 40_I 0.61 0.34 0.01
31_V 45_R 0.61 0.33 0.01
80_S 93_A 0.60 0.32 0.01
9_Q 54_S 0.60 0.32 0.01
179_S 79_P 0.58 0.29 0.01
87_A 53_I 0.58 0.29 0.01
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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