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OPENSEQ.org
3rpf_A_D
Genes: A B A+B
Length: 143 63 204
Sequences: 63 65 63
Seq/Len: 0.44 1.03 0.31
MirrorTree (Pazo et al. 2001) 0.50
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 0.00 0.31
2 0.01 0.00 0.31
5 0.01 0.00 0.31
10 0.01 0.00 0.31
20 0.01 0.00 0.31
100 0.01 0.00 0.31
∞ 0.01 0.00 0.31
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
14_E 54_I 1.73 0.58 0.00
3_L 56_L 1.69 0.55 0.00
86_Q 47_P 1.48 0.41 0.00
105_E 20_R 1.45 0.40 0.00
75_K 38_I 1.38 0.35 0.00
78_S 50_D 1.38 0.35 0.00
8_G 48_L 1.34 0.32 0.00
132_E 43_H 1.31 0.30 0.00
132_E 1_V 1.29 0.30 0.00
21_E 56_L 1.29 0.30 0.00
75_K 29_L 1.27 0.28 0.00
70_L 45_I 1.24 0.27 0.00
74_L 36_C 1.23 0.26 0.00
6_I 1_V 1.23 0.26 0.00
140_S 56_L 1.22 0.26 0.00
43_N 45_I 1.21 0.25 0.00
85_G 36_C 1.20 0.25 0.00
94_G 4_R 1.18 0.24 0.00
18_A 1_V 1.17 0.23 0.00
11_D 53_V 1.17 0.23 0.00
42_D 45_I 1.16 0.23 0.00
98_K 29_L 1.15 0.22 0.00
98_K 20_R 1.15 0.22 0.00
132_E 14_F 1.15 0.22 0.00
126_K 21_A 1.15 0.22 0.00
42_D 55_S 1.12 0.21 0.00
142_L 25_E 1.12 0.21 0.00
45_Q 44_L 1.12 0.21 0.00
108_I 45_I 1.12 0.21 0.00
126_K 30_K 1.11 0.20 0.00
125_N 56_L 1.11 0.20 0.00
79_L 15_F 1.09 0.20 0.00
55_L 19_L 1.09 0.20 0.00
55_L 55_S 1.08 0.19 0.00
66_K 39_A 1.05 0.18 0.00
46_G 19_L 1.04 0.17 0.00
58_T 44_L 1.04 0.17 0.00
114_N 56_L 1.03 0.17 0.00
5_I 15_F 1.03 0.17 0.00
123_I 12_E 1.01 0.16 0.00
126_K 13_N 1.01 0.16 0.00
71_G 55_S 1.01 0.16 0.00
91_C 16_I 0.99 0.16 0.00
137_L 16_I 0.99 0.15 0.00
37_I 20_R 0.98 0.15 0.00
93_S 26_K 0.98 0.15 0.00
138_K 16_I 0.95 0.14 0.00
17_K 56_L 0.95 0.14 0.00
20_Q 35_V 0.93 0.14 0.00
70_L 19_L 0.93 0.14 0.00
74_L 38_I 0.92 0.13 0.00
22_E 55_S 0.92 0.13 0.00
124_H 1_V 0.91 0.13 0.00
135_H 20_R 0.90 0.13 0.00
131_K 19_L 0.90 0.13 0.00
42_D 29_L 0.90 0.13 0.00
106_N 53_V 0.88 0.12 0.00
91_C 34_G 0.87 0.12 0.00
108_I 11_E 0.87 0.12 0.00
139_G 48_L 0.87 0.12 0.00
54_A 6_F 0.87 0.12 0.00
74_L 15_F 0.86 0.12 0.00
14_E 16_I 0.86 0.12 0.00
44_I 42_D 0.86 0.12 0.00
96_N 20_R 0.86 0.12 0.00
28_F 44_L 0.86 0.11 0.00
58_T 43_H 0.86 0.11 0.00
90_L 13_N 0.86 0.11 0.00
128_I 31_E 0.86 0.11 0.00
98_K 35_V 0.85 0.11 0.00
104_Y 9_I 0.85 0.11 0.00
55_L 40_L 0.85 0.11 0.00
104_Y 11_E 0.84 0.11 0.00
26_K 29_L 0.84 0.11 0.00
11_D 49_K 0.84 0.11 0.00
18_A 3_V 0.83 0.11 0.00
70_L 25_E 0.83 0.11 0.00
19_Y 6_F 0.83 0.11 0.00
135_H 55_S 0.83 0.11 0.00
75_K 50_D 0.83 0.11 0.00
31_F 22_I 0.83 0.11 0.00
50_D 42_D 0.83 0.11 0.00
92_V 43_H 0.82 0.10 0.00
12_T 39_A 0.82 0.10 0.00
32_C 11_E 0.81 0.10 0.00
9_A 47_P 0.81 0.10 0.00
57_K 54_I 0.81 0.10 0.00
72_V 28_G 0.81 0.10 0.00
7_Q 24_Q 0.80 0.10 0.00
136_P 35_V 0.80 0.10 0.00
6_I 13_N 0.80 0.10 0.00
83_L 11_E 0.80 0.10 0.00
98_K 30_K 0.80 0.10 0.00
79_L 29_L 0.80 0.10 0.00
21_E 17_K 0.79 0.10 0.00
89_F 3_V 0.79 0.10 0.00
38_V 35_V 0.79 0.10 0.00
37_I 49_K 0.79 0.10 0.00
64_H 25_E 0.79 0.10 0.00
114_N 3_V 0.79 0.10 0.00
9_A 50_D 0.78 0.10 0.00
86_Q 11_E 0.78 0.10 0.00
21_E 18_E 0.78 0.10 0.00
25_A 31_E 0.78 0.10 0.00
84_I 12_E 0.78 0.09 0.00
74_L 24_Q 0.78 0.09 0.00
74_L 19_L 0.77 0.09 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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