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OPENSEQ.org
L5-vs-S10
Genes: A B A+B
Length: 179 103 279
Sequences: 2042 1460 1282
Seq/Len: 11.41 14.17 4.59
MirrorTree (Pazo et al. 2001) 0.86
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 0.09 0.09 0.01
2 0.09 0.09 0.02
5 0.09 0.09 0.05
10 0.09 0.09 0.17
20 0.09 0.09 3.99
100 0.09 0.09 4.14
∞ 0.09 0.09 4.55
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
88_K 50_T 1.27 0.94 0.40
48_K 62_R 1.20 0.91 0.34
75_A 56_H 1.19 0.91 0.33
5_H 74_V 0.97 0.74 0.17
150_R 60_D 0.93 0.70 0.15
61_S 85_D 0.89 0.64 0.13
174_D 93_A 0.87 0.61 0.12
179_K 55_P 0.85 0.59 0.12
112_R 8_I 0.85 0.59 0.12
45_A 49_F 0.84 0.58 0.11
153_D 56_H 0.82 0.54 0.10
175_F 48_R 0.78 0.49 0.09
65_P 28_T 0.78 0.49 0.09
132_V 84_V 0.77 0.47 0.08
112_R 24_E 0.77 0.47 0.08
101_E 58_N 0.76 0.47 0.08
137_I 40_I 0.76 0.46 0.08
175_F 84_V 0.75 0.46 0.08
71_R 23_A 0.75 0.45 0.08
56_D 89_R 0.74 0.44 0.07
136_I 45_R 0.74 0.43 0.07
102_R 51_V 0.73 0.42 0.07
118_S 12_A 0.72 0.41 0.07
152_L 16_R 0.72 0.41 0.07
149_V 17_L 0.71 0.40 0.07
13_V 27_E 0.71 0.40 0.07
132_V 89_R 0.71 0.40 0.06
130_M 29_A 0.71 0.40 0.06
153_D 24_E 0.71 0.39 0.06
17_M 102_L 0.70 0.39 0.06
2_A 86_A 0.70 0.38 0.06
9_K 46_K 0.69 0.37 0.06
93_G 93_A 0.68 0.36 0.06
26_M 22_T 0.68 0.36 0.06
173_F 45_R 0.67 0.35 0.05
115_R 68_R 0.66 0.34 0.05
25_V 17_L 0.66 0.34 0.05
102_R 76_I 0.66 0.33 0.05
162_S 37_R 0.66 0.33 0.05
95_R 73_L 0.65 0.32 0.05
171_A 56_H 0.65 0.32 0.05
83_Y 65_Y 0.65 0.32 0.05
161_K 5_R 0.65 0.32 0.05
136_I 60_D 0.65 0.32 0.05
143_Y 12_A 0.65 0.32 0.05
76_G 65_Y 0.65 0.32 0.05
153_D 60_D 0.64 0.31 0.05
153_D 8_I 0.64 0.31 0.05
107_A 14_D 0.64 0.31 0.05
88_K 47_E 0.64 0.31 0.05
136_I 98_V 0.64 0.30 0.04
93_G 82_K 0.63 0.30 0.04
78_K 17_L 0.63 0.30 0.04
100_F 45_R 0.62 0.29 0.04
34_I 65_Y 0.62 0.29 0.04
49_L 37_R 0.62 0.29 0.04
157_T 65_Y 0.62 0.29 0.04
21_N 3_N 0.62 0.28 0.04
11_E 22_T 0.61 0.28 0.04
172_A 84_V 0.61 0.28 0.04
120_K 28_T 0.61 0.28 0.04
100_F 58_N 0.61 0.28 0.04
27_Q 102_L 0.61 0.28 0.04
152_L 90_L 0.61 0.27 0.04
57_L 53_I 0.61 0.27 0.04
121_S 70_H 0.61 0.27 0.04
100_F 51_V 0.61 0.27 0.04
46_D 51_V 0.60 0.27 0.04
61_S 11_K 0.60 0.26 0.04
72_K 58_N 0.60 0.26 0.04
179_K 23_A 0.60 0.26 0.04
157_T 61_A 0.60 0.26 0.04
111_I 54_S 0.60 0.26 0.04
2_A 35_Q 0.60 0.26 0.04
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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