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OPENSEQ.org
L1-vs-RfsS
Genes: A B A+B
Length: 234 105 329
Sequences: 3196 2682 1117
Seq/Len: 13.66 25.54 3.4
MirrorTree (Pazo et al. 2001) 0.57
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 0.01 0.00
2 0.09 0.01 0.00
5 0.09 0.01 0.00
10 0.09 0.01 0.01
20 0.09 0.01 0.06
100 0.09 0.01 0.32
∞ 0.10 0.01 3.29
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
215_S 18_K 1.11 0.79 0.05
124_V 16_D 1.02 0.70 0.04
99_D 60_R 0.94 0.61 0.03
165_N 25_L 0.87 0.52 0.02
161_V 82_L 0.83 0.48 0.02
45_A 55_V 0.82 0.47 0.02
225_D 66_P 0.81 0.45 0.02
65_L 97_L 0.81 0.44 0.02
161_V 46_R 0.76 0.39 0.02
185_L 47_H 0.76 0.39 0.02
23_I 96_R 0.75 0.37 0.01
153_V 32_S 0.73 0.35 0.01
155_N 76_D 0.73 0.35 0.01
129_Q 90_M 0.73 0.35 0.01
74_R 51_I 0.73 0.35 0.01
22_D 92_E 0.72 0.34 0.01
117_S 17_L 0.72 0.34 0.01
73_V 14_I 0.71 0.32 0.01
198_K 55_V 0.70 0.32 0.01
43_D 43_T 0.70 0.31 0.01
130_V 42_G 0.70 0.31 0.01
46_V 87_V 0.69 0.31 0.01
62_A 94_S 0.69 0.30 0.01
42_V 22_I 0.67 0.28 0.01
74_R 55_V 0.67 0.28 0.01
207_V 49_M 0.66 0.28 0.01
209_I 80_V 0.65 0.26 0.01
45_A 82_L 0.65 0.26 0.01
160_Q 41_T 0.65 0.26 0.01
94_L 92_E 0.65 0.26 0.01
76_A 15_D 0.65 0.26 0.01
155_N 82_L 0.65 0.26 0.01
106_K 26_D 0.65 0.26 0.01
25_E 22_I 0.64 0.26 0.01
185_L 21_D 0.64 0.26 0.01
180_F 70_E 0.64 0.25 0.01
214_I 10_V 0.64 0.25 0.01
103_Q 19_G 0.64 0.25 0.01
62_A 37_M 0.64 0.25 0.01
108_E 37_M 0.63 0.24 0.01
204_A 16_D 0.63 0.24 0.01
5_T 33_I 0.63 0.24 0.01
127_L 79_V 0.62 0.24 0.01
150_A 16_D 0.62 0.23 0.01
106_K 73_N 0.61 0.22 0.01
114_V 103_L 0.61 0.22 0.01
123_V 53_D 0.61 0.22 0.01
148_N 84_D 0.61 0.22 0.01
198_K 14_I 0.61 0.22 0.01
204_A 38_I 0.61 0.22 0.01
120_A 90_M 0.60 0.22 0.01
219_G 31_S 0.60 0.22 0.01
214_I 68_G 0.60 0.22 0.01
222_V 12_D 0.60 0.22 0.01
175_I 85_V 0.60 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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