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OPENSEQ.org
cgc
Genes: A B A+B
Length: 105 220 308
Sequences: 1542 2033 189
Seq/Len: 14.69 9.24 0.61
MirrorTree (Pazo et al. 2001) 0.51
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 0.07 0.00 0.11
2 0.07 0.00 0.13
5 0.07 0.00 0.25
10 0.07 0.00 0.54
20 0.07 0.01 0.58
100 0.07 0.01 0.75
∞ 0.11 0.02 2.13
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
17_M 153_R 1.69 0.75 0.01
17_M 61_C 1.38 0.53 0.01
26_V 85_A 1.37 0.52 0.01
31_F 12_V 1.35 0.51 0.01
17_M 136_L 1.33 0.49 0.01
9_V 114_Q 1.30 0.47 0.01
35_L 80_G 1.29 0.45 0.01
9_V 129_V 1.15 0.35 0.00
62_E 100_T 1.11 0.32 0.00
24_I 10_G 1.09 0.30 0.00
82_S 168_I 1.09 0.30 0.00
12_F 166_S 1.09 0.30 0.00
35_L 153_R 1.06 0.28 0.00
32_V 62_R 1.06 0.28 0.00
33_P 160_L 1.04 0.27 0.00
71_S 169_F 1.04 0.27 0.00
26_V 53_S 1.03 0.26 0.00
94_G 61_C 1.02 0.26 0.00
78_S 103_L 1.02 0.26 0.00
81_I 100_T 1.01 0.25 0.00
19_I 185_G 1.00 0.24 0.00
31_F 122_I 0.98 0.23 0.00
75_L 199_A 0.98 0.23 0.00
66_T 202_P 0.98 0.23 0.00
41_A 100_T 0.96 0.22 0.00
89_Y 138_L 0.95 0.22 0.00
60_L 53_S 0.95 0.22 0.00
12_F 68_I 0.94 0.21 0.00
81_I 202_P 0.92 0.20 0.00
18_L 138_L 0.92 0.20 0.00
56_S 145_L 0.91 0.20 0.00
44_D 84_L 0.90 0.19 0.00
71_S 53_S 0.90 0.19 0.00
76_V 96_L 0.89 0.19 0.00
33_P 202_P 0.89 0.19 0.00
17_M 43_L 0.89 0.19 0.00
26_V 211_I 0.89 0.19 0.00
33_P 163_A 0.89 0.18 0.00
22_L 180_I 0.88 0.18 0.00
26_V 83_F 0.88 0.18 0.00
91_A 54_Q 0.88 0.18 0.00
40_D 98_L 0.88 0.18 0.00
12_F 75_F 0.88 0.18 0.00
18_L 148_F 0.87 0.18 0.00
11_A 161_F 0.86 0.17 0.00
37_K 154_I 0.85 0.17 0.00
87_D 116_P 0.85 0.17 0.00
41_A 45_P 0.85 0.17 0.00
35_L 154_I 0.85 0.17 0.00
34_N 104_T 0.85 0.17 0.00
65_N 54_Q 0.85 0.17 0.00
25_S 204_L 0.85 0.17 0.00
52_K 212_I 0.85 0.17 0.00
41_A 85_A 0.84 0.16 0.00
95_K 130_T 0.84 0.16 0.00
11_A 166_S 0.84 0.16 0.00
78_S 99_L 0.84 0.16 0.00
95_K 6_F 0.84 0.16 0.00
96_H 43_L 0.83 0.16 0.00
54_V 123_F 0.83 0.16 0.00
17_M 75_F 0.83 0.16 0.00
16_E 109_D 0.83 0.16 0.00
16_E 155_G 0.83 0.16 0.00
16_E 157_G 0.83 0.16 0.00
16_E 158_D 0.83 0.16 0.00
61_Y 4_L 0.82 0.15 0.00
32_V 3_H 0.82 0.15 0.00
11_A 201_V 0.82 0.15 0.00
34_N 96_L 0.82 0.15 0.00
8_K 58_L 0.82 0.15 0.00
57_Q 86_T 0.82 0.15 0.00
24_I 198_L 0.81 0.15 0.00
32_V 165_C 0.81 0.15 0.00
24_I 80_G 0.81 0.15 0.00
21_L 29_I 0.81 0.15 0.00
60_L 80_G 0.80 0.15 0.00
70_A 126_M 0.80 0.15 0.00
31_F 74_F 0.79 0.14 0.00
58_A 127_L 0.79 0.14 0.00
81_I 111_R 0.79 0.14 0.00
20_V 135_L 0.79 0.14 0.00
70_A 65_G 0.79 0.14 0.00
12_F 23_R 0.79 0.14 0.00
61_Y 170_S 0.78 0.14 0.00
91_A 53_S 0.78 0.14 0.00
30_L 194_K 0.78 0.14 0.00
81_I 86_T 0.78 0.14 0.00
18_L 151_N 0.78 0.14 0.00
54_V 215_K 0.78 0.14 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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