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OPENSEQ.org
L4-vs-RsfS
Genes: A B A+B
Length: 201 105 305
Sequences: 3177 2682 1102
Seq/Len: 15.81 25.54 3.61
MirrorTree (Pazo et al. 2001) 0.66
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 0.01 0.00
2 0.08 0.01 0.00
5 0.08 0.01 0.01
10 0.09 0.01 0.01
20 0.09 0.01 0.05
100 0.09 0.01 0.40
∞ 0.09 0.01 3.60
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
110_S 103_L 0.99 0.69 0.01
83_V 86_I 0.97 0.67 0.01
106_K 34_T 0.89 0.57 0.01
57_K 17_L 0.87 0.55 0.01
112_L 90_M 0.86 0.53 0.01
117_R 68_G 0.79 0.43 0.01
180_L 19_G 0.77 0.41 0.01
97_N 14_I 0.77 0.41 0.01
13_T 2_Q 0.73 0.37 0.01
13_T 86_I 0.72 0.35 0.01
160_A 103_L 0.72 0.35 0.01
175_I 74_S 0.72 0.35 0.01
108_I 90_M 0.71 0.35 0.01
170_R 28_Q 0.71 0.34 0.01
13_T 89_V 0.71 0.34 0.01
103_G 90_M 0.70 0.33 0.01
55_S 94_S 0.70 0.33 0.01
132_K 78_I 0.70 0.32 0.01
118_L 28_Q 0.69 0.32 0.01
97_N 51_I 0.68 0.31 0.01
178_V 59_S 0.68 0.30 0.00
72_S 33_I 0.67 0.30 0.00
30_Q 26_D 0.67 0.29 0.00
16_E 86_I 0.67 0.29 0.00
179_S 89_V 0.66 0.29 0.00
53_T 105_S 0.66 0.28 0.00
116_D 30_K 0.66 0.28 0.00
180_L 53_D 0.65 0.27 0.00
125_S 78_I 0.65 0.27 0.00
97_N 76_D 0.64 0.27 0.00
47_K 26_D 0.64 0.26 0.00
175_I 27_V 0.63 0.26 0.00
22_D 47_H 0.63 0.25 0.00
175_I 54_H 0.63 0.25 0.00
5_L 19_G 0.62 0.25 0.00
196_V 27_V 0.62 0.24 0.00
153_L 21_D 0.62 0.24 0.00
195_Q 38_I 0.62 0.24 0.00
23_F 47_H 0.61 0.24 0.00
28_V 101_E 0.61 0.24 0.00
161_A 55_V 0.61 0.24 0.00
91_D 97_L 0.61 0.23 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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