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OPENSEQ.org
RsfS-vs-L5
Genes: A B A+B
Length: 105 179 283
Sequences: 2682 2042 974
Seq/Len: 25.54 11.41 3.44
MirrorTree (Pazo et al. 2001) 0.64
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 0.01 0.09 0.00
2 0.01 0.09 0.00
5 0.01 0.09 0.00
10 0.01 0.09 0.00
20 0.01 0.09 0.01
100 0.01 0.09 0.36
∞ 0.01 0.09 3.43
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
11_I 24_S 1.15 0.83 0.09
47_H 117_L 1.01 0.70 0.06
27_V 166_G 0.93 0.61 0.04
39_I 4_L 0.93 0.60 0.04
86_I 2_A 0.92 0.59 0.04
76_D 173_F 0.91 0.58 0.04
94_S 93_G 0.90 0.57 0.04
46_R 38_M 0.88 0.54 0.04
31_S 130_M 0.87 0.53 0.04
90_M 157_T 0.87 0.53 0.04
47_H 78_K 0.87 0.53 0.04
18_K 78_K 0.84 0.49 0.03
90_M 83_Y 0.82 0.46 0.03
89_V 111_I 0.81 0.45 0.03
90_M 79_I 0.78 0.41 0.03
83_G 68_T 0.77 0.40 0.03
32_S 102_R 0.77 0.40 0.03
44_S 14_K 0.77 0.40 0.03
76_D 79_I 0.77 0.40 0.02
100_L 85_I 0.76 0.39 0.02
15_D 153_D 0.76 0.39 0.02
39_I 71_R 0.74 0.37 0.02
90_M 129_S 0.74 0.36 0.02
91_Q 154_I 0.74 0.36 0.02
37_M 61_S 0.73 0.35 0.02
47_H 97_W 0.73 0.35 0.02
81_D 62_G 0.73 0.35 0.02
103_L 129_S 0.72 0.34 0.02
27_V 32_E 0.71 0.33 0.02
48_V 132_V 0.69 0.31 0.02
30_K 130_M 0.69 0.31 0.02
79_V 152_L 0.69 0.31 0.02
26_D 103_L 0.68 0.29 0.02
68_G 71_R 0.67 0.29 0.02
40_C 155_T 0.67 0.29 0.02
60_R 175_F 0.67 0.28 0.02
75_A 154_I 0.67 0.28 0.02
38_I 94_E 0.66 0.28 0.02
102_K 142_D 0.66 0.28 0.02
70_E 3_K 0.66 0.27 0.02
61_A 12_V 0.66 0.27 0.02
90_M 135_Q 0.66 0.27 0.02
96_R 85_I 0.66 0.27 0.02
40_C 3_K 0.65 0.27 0.02
17_L 164_E 0.65 0.27 0.02
86_I 125_R 0.65 0.26 0.01
68_G 74_V 0.65 0.26 0.01
90_M 57_L 0.64 0.26 0.01
14_I 78_K 0.64 0.25 0.01
67_L 155_T 0.63 0.24 0.01
91_Q 35_T 0.63 0.24 0.01
38_I 106_I 0.62 0.24 0.01
90_M 172_A 0.62 0.24 0.01
55_V 157_T 0.62 0.24 0.01
103_L 98_E 0.62 0.24 0.01
16_D 76_G 0.61 0.23 0.01
37_M 166_G 0.61 0.23 0.01
37_M 93_G 0.61 0.23 0.01
47_H 12_V 0.61 0.23 0.01
61_A 115_R 0.61 0.23 0.01
72_E 58_A 0.61 0.22 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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