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OPENSEQ.org
PH_ZA
Genes: A B A+B
Length: 131 263 362
Sequences: 3764 522 193
Seq/Len: 28.73 1.98 0.53
MirrorTree (Pazo et al. 2001) 0.88
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 0.06 0.02 0.49
2 0.07 0.02 0.49
5 0.08 0.02 0.49
10 0.09 0.03 0.50
20 0.09 0.03 0.53
100 0.12 0.04 0.60
∞ 0.16 0.06 0.68
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
71_D 44_R 1.62 0.67 0.00
32_C 45_I 1.49 0.57 0.00
36_N 34_I 1.47 0.55 0.00
29_R 54_G 1.38 0.49 0.00
93_I 183_N 1.37 0.48 0.00
61_K 68_S 1.32 0.44 0.00
96_L 93_R 1.29 0.41 0.00
33_S 34_I 1.26 0.40 0.00
65_E 184_L 1.25 0.39 0.00
29_R 64_V 1.24 0.38 0.00
34_V 90_M 1.23 0.37 0.00
72_L 104_H 1.22 0.36 0.00
54_N 2_L 1.21 0.36 0.00
104_L 226_T 1.21 0.35 0.00
30_R 40_V 1.20 0.35 0.00
41_I 45_I 1.20 0.35 0.00
28_Q 73_M 1.19 0.34 0.00
104_L 50_L 1.19 0.34 0.00
90_V 34_I 1.18 0.34 0.00
77_R 104_H 1.17 0.33 0.00
79_Y 179_Q 1.17 0.33 0.00
13_K 180_N 1.17 0.33 0.00
75_H 44_R 1.14 0.31 0.00
51_A 179_Q 1.13 0.30 0.00
88_D 198_C 1.13 0.30 0.00
81_F 213_S 1.12 0.30 0.00
104_L 17_T 1.12 0.30 0.00
39_L 138_A 1.12 0.30 0.00
61_K 4_G 1.12 0.30 0.00
35_K 9_C 1.11 0.29 0.00
20_S 84_P 1.10 0.28 0.00
39_L 53_L 1.09 0.28 0.00
41_I 19_L 1.09 0.27 0.00
43_H 53_L 1.08 0.27 0.00
27_W 24_G 1.07 0.27 0.00
100_K 46_Q 1.06 0.26 0.00
34_V 176_F 1.06 0.26 0.00
18_K 4_G 1.06 0.26 0.00
76_N 117_K 1.05 0.25 0.00
77_R 195_L 1.04 0.25 0.00
29_R 175_D 1.04 0.25 0.00
56_L 56_S 1.02 0.24 0.00
32_C 175_D 1.02 0.23 0.00
48_R 124_A 1.02 0.23 0.00
81_F 44_R 1.02 0.23 0.00
57_T 208_K 1.01 0.23 0.00
12_K 86_P 1.01 0.23 0.00
61_K 71_D 1.01 0.23 0.00
10_S 166_A 1.01 0.23 0.00
13_K 21_T 1.00 0.23 0.00
32_C 44_R 1.00 0.23 0.00
105_T 227_A 1.00 0.22 0.00
97_T 37_E 1.00 0.22 0.00
47_N 117_K 1.00 0.22 0.00
77_R 54_G 0.99 0.22 0.00
71_D 208_K 0.99 0.22 0.00
20_S 176_F 0.99 0.22 0.00
34_V 17_T 0.99 0.22 0.00
58_C 105_R 0.99 0.22 0.00
88_D 213_S 0.98 0.21 0.00
70_F 20_S 0.98 0.21 0.00
38_I 17_T 0.98 0.21 0.00
81_F 175_D 0.98 0.21 0.00
19_K 136_V 0.98 0.21 0.00
18_K 83_K 0.97 0.21 0.00
55_L 195_L 0.97 0.21 0.00
84_E 196_H 0.97 0.21 0.00
107_A 135_Q 0.97 0.21 0.00
46_S 93_R 0.96 0.20 0.00
31_K 46_Q 0.96 0.20 0.00
59_Q 46_Q 0.96 0.20 0.00
52_K 60_L 0.96 0.20 0.00
36_N 187_Q 0.95 0.20 0.00
71_D 61_A 0.95 0.20 0.00
34_V 21_T 0.95 0.20 0.00
41_I 53_L 0.95 0.20 0.00
85_D 69_F 0.94 0.19 0.00
37_G 74_E 0.94 0.19 0.00
39_L 191_G 0.94 0.19 0.00
13_K 37_E 0.94 0.19 0.00
66_D 198_C 0.94 0.19 0.00
29_R 178_V 0.94 0.19 0.00
89_Y 214_K 0.94 0.19 0.00
41_I 188_T 0.93 0.19 0.00
89_Y 176_F 0.93 0.19 0.00
37_G 237_T 0.93 0.19 0.00
57_T 40_V 0.93 0.19 0.00
77_R 134_I 0.93 0.19 0.00
25_K 34_I 0.92 0.18 0.00
63_N 85_T 0.92 0.18 0.00
84_E 40_V 0.92 0.18 0.00
86_E 130_L 0.92 0.18 0.00
85_D 205_E 0.91 0.18 0.00
27_W 4_G 0.91 0.18 0.00
77_R 19_L 0.91 0.18 0.00
71_D 21_T 0.91 0.18 0.00
26_V 37_E 0.91 0.18 0.00
20_S 210_L 0.90 0.17 0.00
94_S 193_T 0.90 0.17 0.00
93_I 96_Y 0.90 0.17 0.00
71_D 56_S 0.90 0.17 0.00
25_K 94_K 0.89 0.17 0.00
37_G 26_L 0.89 0.17 0.00
20_S 93_R 0.89 0.17 0.00
41_I 239_C 0.89 0.17 0.00
100_K 239_C 0.89 0.17 0.00
24_R 208_K 0.88 0.17 0.00
104_L 197_Y 0.88 0.17 0.00
72_L 7_I 0.88 0.17 0.00
109_R 219_I 0.88 0.17 0.00
33_S 9_C 0.88 0.17 0.00
74_S 14_S 0.87 0.16 0.00
31_K 61_A 0.87 0.16 0.00
66_D 29_I 0.87 0.16 0.00
87_Q 218_D 0.87 0.16 0.00
79_Y 96_Y 0.87 0.16 0.00
96_L 236_A 0.87 0.16 0.00
103_A 130_L 0.86 0.16 0.00
75_H 213_S 0.86 0.16 0.00
104_L 32_S 0.86 0.16 0.00
24_R 179_Q 0.86 0.16 0.00
74_S 68_S 0.86 0.16 0.00
12_K 49_E 0.86 0.16 0.00
23_I 125_I 0.86 0.16 0.00
25_K 180_N 0.86 0.16 0.00
40_T 94_K 0.86 0.16 0.00
77_R 176_F 0.86 0.16 0.00
59_Q 137_Y 0.86 0.16 0.00
12_K 191_G 0.86 0.16 0.00
28_Q 94_K 0.86 0.16 0.00
49_Q 171_L 0.86 0.16 0.00
54_N 56_S 0.85 0.15 0.00
61_K 131_L 0.85 0.15 0.00
47_N 111_C 0.85 0.15 0.00
14_G 24_G 0.85 0.15 0.00
78_T 124_A 0.85 0.15 0.00
91_A 29_I 0.85 0.15 0.00
29_R 45_I 0.85 0.15 0.00
72_L 205_E 0.85 0.15 0.00
100_K 21_T 0.85 0.15 0.00
47_N 184_L 0.85 0.15 0.00
60_V 96_Y 0.84 0.15 0.00
53_L 131_L 0.84 0.15 0.00
66_D 12_G 0.84 0.15 0.00
97_T 61_A 0.84 0.15 0.00
28_Q 163_V 0.84 0.15 0.00
96_L 160_H 0.84 0.15 0.00
40_T 197_Y 0.83 0.15 0.00
31_K 37_E 0.83 0.15 0.00
51_A 177_L 0.83 0.15 0.00
78_T 122_L 0.83 0.15 0.00
10_S 156_E 0.83 0.14 0.00
89_Y 53_L 0.83 0.14 0.00
43_H 221_N 0.83 0.14 0.00
58_C 176_F 0.83 0.14 0.00
25_K 38_M 0.83 0.14 0.00
71_D 46_Q 0.83 0.14 0.00
62_P 25_I 0.83 0.14 0.00
36_N 185_D 0.83 0.14 0.00
105_T 242_L 0.83 0.14 0.00
57_T 198_C 0.82 0.14 0.00
32_C 185_D 0.82 0.14 0.00
31_K 217_V 0.82 0.14 0.00
19_K 64_V 0.82 0.14 0.00
49_Q 34_I 0.82 0.14 0.00
57_T 56_S 0.82 0.14 0.00
49_Q 80_P 0.82 0.14 0.00
100_K 19_L 0.82 0.14 0.00
96_L 48_L 0.82 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)
ID Seq/Len Name Options I_Prob Status
3220 0.58 PH_ZA Δgene:(0, 0) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
3219 0.53 PH_ZA Δgene:(0, 0) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3217 0.24 PH_ZA Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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