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OPENSEQ.org
fdxiscx
Genes: A B A+B
Length: 111 66 176
Sequences: 5243 320 228
Seq/Len: 47.23 4.85 1.3
MirrorTree (Pazo et al. 2001) 0.56
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.00 1.27
2 0.04 0.00 1.29
5 0.05 0.00 1.25
10 0.05 0.00 1.29
20 0.06 0.00 1.31
100 0.08 0.00 1.35
∞ 0.13 0.00 1.60
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
67_E 48_A 1.44 0.79 0.04
44_K 40_E 1.42 0.78 0.04
44_K 19_Y 1.25 0.65 0.02
9_H 19_Y 1.21 0.61 0.02
108_A 17_D 1.21 0.61 0.02
3_K 58_L 1.10 0.51 0.01
5_V 13_E 1.09 0.49 0.01
70_D 60_V 1.08 0.48 0.01
105_I 60_V 1.08 0.48 0.01
3_K 36_I 1.06 0.47 0.01
96_L 35_W 1.03 0.43 0.01
29_D 18_A 0.98 0.39 0.01
55_V 14_A 0.98 0.39 0.01
25_E 41_D 0.96 0.37 0.01
31_A 63_D 0.96 0.36 0.01
107_H 63_D 0.94 0.35 0.01
19_L 62_L 0.93 0.34 0.01
24_G 36_I 0.93 0.34 0.01
21_A 41_D 0.92 0.33 0.01
35_G 46_P 0.91 0.32 0.01
63_P 62_L 0.90 0.31 0.01
109_R 14_A 0.89 0.30 0.01
35_G 49_S 0.89 0.30 0.01
95_D 40_E 0.87 0.29 0.01
53_C 3_L 0.87 0.29 0.01
45_S 53_I 0.87 0.29 0.01
14_P 24_P 0.87 0.28 0.01
107_H 17_D 0.87 0.28 0.01
15_D 27_V 0.87 0.28 0.01
35_G 50_N 0.86 0.28 0.01
3_K 66_E 0.86 0.28 0.01
73_L 44_D 0.85 0.27 0.01
33_R 41_D 0.84 0.27 0.01
107_H 13_E 0.84 0.26 0.01
109_R 40_E 0.83 0.26 0.01
75_K 63_D 0.83 0.25 0.01
91_V 47_Q 0.82 0.25 0.01
57_E 6_T 0.81 0.24 0.01
104_T 52_K 0.81 0.24 0.01
43_E 53_I 0.81 0.24 0.01
66_S 14_A 0.81 0.24 0.01
65_S 13_E 0.80 0.24 0.01
6_I 1_M 0.80 0.24 0.01
105_I 50_N 0.80 0.23 0.01
104_T 35_W 0.80 0.23 0.01
53_C 47_Q 0.80 0.23 0.01
12_L 28_R 0.79 0.23 0.01
26_T 58_L 0.79 0.23 0.01
70_D 50_N 0.79 0.22 0.01
15_D 63_D 0.78 0.22 0.01
23_S 28_R 0.78 0.22 0.01
65_S 8_S 0.78 0.22 0.01
5_V 37_C 0.78 0.22 0.01
54_I 8_S 0.78 0.22 0.01
17_A 10_E 0.77 0.21 0.01
72_M 25_K 0.77 0.21 0.01
29_D 27_V 0.76 0.21 0.01
28_L 1_M 0.76 0.21 0.01
21_A 34_Q 0.76 0.20 0.01
66_S 22_L 0.76 0.20 0.01
109_R 63_D 0.75 0.20 0.01
95_D 11_I 0.75 0.20 0.01
33_R 10_E 0.74 0.19 0.00
60_D 9_R 0.73 0.19 0.00
95_D 33_H 0.73 0.19 0.00
97_V 35_W 0.73 0.18 0.00
108_A 3_L 0.73 0.18 0.00
60_D 19_Y 0.72 0.18 0.00
97_V 31_D 0.72 0.18 0.00
30_A 30_T 0.71 0.18 0.00
30_A 33_H 0.71 0.17 0.00
70_D 48_A 0.71 0.17 0.00
31_A 59_L 0.71 0.17 0.00
15_D 21_D 0.70 0.17 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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