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OPENSEQ.org
PH_ZA
Genes: A B A+B
Length: 131 263 377
Sequences: 934 448 90
Seq/Len: 7.13 1.7 0.24
MirrorTree (Pazo et al. 2001) 0.91
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 0.04 0.03 0.23
2 0.04 0.04 0.23
5 0.05 0.04 0.23
10 0.05 0.04 0.23
20 0.05 0.04 0.25
100 0.06 0.05 0.27
∞ 0.08 0.07 0.32
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
86_E 60_L 1.87 0.59 0.00
77_R 54_G 1.62 0.44 0.00
96_L 93_R 1.60 0.42 0.00
19_K 185_D 1.55 0.39 0.00
36_N 34_I 1.53 0.38 0.00
65_E 29_I 1.41 0.31 0.00
96_L 160_H 1.41 0.31 0.00
34_V 90_M 1.40 0.30 0.00
43_H 53_L 1.34 0.27 0.00
87_Q 218_D 1.29 0.25 0.00
104_L 226_T 1.28 0.24 0.00
35_K 158_A 1.28 0.24 0.00
19_K 202_S 1.27 0.24 0.00
93_I 187_Q 1.23 0.22 0.00
47_N 213_S 1.22 0.22 0.00
9_G 171_L 1.21 0.21 0.00
29_R 106_F 1.19 0.21 0.00
69_S 105_R 1.19 0.20 0.00
104_L 200_M 1.18 0.20 0.00
77_R 19_L 1.18 0.20 0.00
62_P 75_A 1.16 0.19 0.00
49_Q 233_R 1.16 0.19 0.00
60_V 23_L 1.15 0.19 0.00
60_V 138_A 1.14 0.18 0.00
100_K 46_Q 1.12 0.18 0.00
81_F 54_G 1.11 0.17 0.00
27_W 24_G 1.11 0.17 0.00
72_L 199_S 1.11 0.17 0.00
71_D 37_E 1.10 0.17 0.00
84_E 21_T 1.10 0.17 0.00
6_K 93_R 1.10 0.17 0.00
86_E 7_I 1.09 0.17 0.00
96_L 138_A 1.09 0.17 0.00
101_E 199_S 1.08 0.17 0.00
104_L 229_D 1.08 0.17 0.00
97_T 212_R 1.08 0.16 0.00
67_K 111_C 1.07 0.16 0.00
86_E 83_K 1.07 0.16 0.00
103_A 243_L 1.07 0.16 0.00
26_V 239_C 1.06 0.16 0.00
116_E 169_T 1.06 0.16 0.00
73_I 99_A 1.05 0.15 0.00
25_K 21_T 1.05 0.15 0.00
88_D 42_I 1.05 0.15 0.00
45_T 219_I 1.05 0.15 0.00
103_A 50_L 1.04 0.15 0.00
75_H 54_G 1.04 0.15 0.00
65_E 184_L 1.04 0.15 0.00
13_K 21_T 1.04 0.15 0.00
54_N 174_V 1.03 0.15 0.00
99_S 84_P 1.03 0.14 0.00
17_L 108_R 1.03 0.14 0.00
90_V 34_I 1.01 0.14 0.00
35_K 9_C 1.01 0.14 0.00
41_I 239_C 1.00 0.14 0.00
75_H 27_T 1.00 0.14 0.00
10_S 215_P 1.00 0.14 0.00
104_L 160_H 1.00 0.14 0.00
41_I 45_I 1.00 0.14 0.00
84_E 50_L 1.00 0.14 0.00
100_K 182_G 1.00 0.14 0.00
25_K 180_N 1.00 0.14 0.00
39_L 24_G 0.99 0.14 0.00
41_I 44_R 0.99 0.14 0.00
42_S 53_L 0.99 0.13 0.00
32_C 54_G 0.99 0.13 0.00
25_K 84_P 0.99 0.13 0.00
84_E 32_S 0.98 0.13 0.00
20_S 193_T 0.98 0.13 0.00
82_Q 29_I 0.98 0.13 0.00
89_Y 225_E 0.98 0.13 0.00
104_L 50_L 0.97 0.13 0.00
35_K 72_I 0.97 0.13 0.00
62_P 216_T 0.97 0.13 0.00
35_K 34_I 0.97 0.13 0.00
38_I 17_T 0.96 0.13 0.00
72_L 133_L 0.96 0.13 0.00
51_A 177_L 0.96 0.12 0.00
55_L 211_L 0.96 0.12 0.00
54_N 96_Y 0.96 0.12 0.00
5_N 129_D 0.95 0.12 0.00
43_H 176_F 0.95 0.12 0.00
56_L 226_T 0.95 0.12 0.00
74_S 9_C 0.95 0.12 0.00
102_E 93_R 0.95 0.12 0.00
93_I 79_S 0.95 0.12 0.00
74_S 212_R 0.95 0.12 0.00
5_N 214_K 0.94 0.12 0.00
89_Y 221_N 0.94 0.12 0.00
29_R 178_V 0.94 0.12 0.00
124_K 12_G 0.94 0.12 0.00
111_E 230_I 0.94 0.12 0.00
35_K 98_T 0.93 0.12 0.00
110_G 220_V 0.93 0.12 0.00
126_I 198_C 0.93 0.12 0.00
71_D 61_A 0.93 0.12 0.00
102_E 128_R 0.93 0.12 0.00
67_K 236_A 0.93 0.12 0.00
116_E 222_Q 0.93 0.12 0.00
71_D 56_S 0.93 0.12 0.00
61_K 62_K 0.93 0.12 0.00
42_S 210_L 0.93 0.12 0.00
126_I 169_T 0.93 0.12 0.00
34_V 157_T 0.93 0.12 0.00
86_E 72_I 0.93 0.12 0.00
127_I 3_P 0.92 0.12 0.00
72_L 236_A 0.92 0.12 0.00
74_S 74_E 0.92 0.12 0.00
53_L 104_H 0.92 0.12 0.00
83_A 195_L 0.92 0.11 0.00
32_C 44_R 0.91 0.11 0.00
43_H 130_L 0.91 0.11 0.00
89_Y 216_T 0.91 0.11 0.00
96_L 83_K 0.91 0.11 0.00
56_L 56_S 0.91 0.11 0.00
81_F 44_R 0.91 0.11 0.00
57_T 86_P 0.91 0.11 0.00
28_Q 15_E 0.91 0.11 0.00
19_K 204_P 0.91 0.11 0.00
49_Q 77_L 0.91 0.11 0.00
61_K 210_L 0.90 0.11 0.00
7_E 136_V 0.90 0.11 0.00
100_K 44_R 0.90 0.11 0.00
93_I 86_P 0.90 0.11 0.00
13_K 45_I 0.90 0.11 0.00
44_A 179_Q 0.90 0.11 0.00
6_K 210_L 0.90 0.11 0.00
73_I 218_D 0.90 0.11 0.00
99_S 83_K 0.89 0.11 0.00
125_A 45_I 0.89 0.11 0.00
41_I 46_Q 0.89 0.11 0.00
20_S 84_P 0.89 0.11 0.00
79_Y 179_Q 0.89 0.11 0.00
117_N 162_A 0.89 0.11 0.00
25_K 72_I 0.89 0.11 0.00
71_D 207_L 0.88 0.11 0.00
73_I 212_R 0.88 0.10 0.00
83_A 24_G 0.88 0.10 0.00
44_A 123_E 0.88 0.10 0.00
74_S 83_K 0.88 0.10 0.00
104_L 17_T 0.88 0.10 0.00
118_S 220_V 0.88 0.10 0.00
117_N 169_T 0.88 0.10 0.00
55_L 195_L 0.88 0.10 0.00
15_Y 65_G 0.88 0.10 0.00
102_E 216_T 0.88 0.10 0.00
90_V 227_A 0.87 0.10 0.00
75_H 213_S 0.87 0.10 0.00
125_A 65_G 0.87 0.10 0.00
58_C 176_F 0.87 0.10 0.00
14_G 18_W 0.87 0.10 0.00
14_G 28_C 0.87 0.10 0.00
14_G 31_C 0.87 0.10 0.00
14_G 33_G 0.87 0.10 0.00
14_G 35_H 0.87 0.10 0.00
14_G 36_R 0.87 0.10 0.00
14_G 43_S 0.87 0.10 0.00
14_G 47_S 0.87 0.10 0.00
14_G 51_D 0.87 0.10 0.00
16_L 18_W 0.87 0.10 0.00
16_L 28_C 0.87 0.10 0.00
16_L 31_C 0.87 0.10 0.00
16_L 33_G 0.87 0.10 0.00
16_L 35_H 0.87 0.10 0.00
16_L 36_R 0.87 0.10 0.00
16_L 43_S 0.87 0.10 0.00
16_L 47_S 0.87 0.10 0.00
16_L 51_D 0.87 0.10 0.00
70_F 18_W 0.87 0.10 0.00
70_F 28_C 0.87 0.10 0.00
70_F 31_C 0.87 0.10 0.00
70_F 33_G 0.87 0.10 0.00
70_F 35_H 0.87 0.10 0.00
70_F 36_R 0.87 0.10 0.00
70_F 43_S 0.87 0.10 0.00
70_F 47_S 0.87 0.10 0.00
70_F 51_D 0.87 0.10 0.00
92_W 18_W 0.87 0.10 0.00
92_W 28_C 0.87 0.10 0.00
92_W 31_C 0.87 0.10 0.00
92_W 33_G 0.87 0.10 0.00
92_W 35_H 0.87 0.10 0.00
92_W 36_R 0.87 0.10 0.00
92_W 43_S 0.87 0.10 0.00
92_W 47_S 0.87 0.10 0.00
92_W 51_D 0.87 0.10 0.00
55_L 48_L 0.86 0.10 0.00
20_S 123_E 0.86 0.10 0.00
22_G 208_K 0.86 0.10 0.00
119_L 169_T 0.86 0.10 0.00
54_N 56_S 0.86 0.10 0.00
74_S 41_H 0.86 0.10 0.00
84_E 26_L 0.86 0.10 0.00
24_R 21_T 0.86 0.10 0.00
114_A 230_I 0.86 0.10 0.00
77_R 134_I 0.86 0.10 0.00
36_N 220_V 0.86 0.10 0.00
103_A 49_E 0.86 0.10 0.00
2_L 38_M 0.85 0.10 0.00
51_A 125_I 0.85 0.10 0.00
57_T 198_C 0.85 0.10 0.00
100_K 45_I 0.85 0.10 0.00
9_G 88_S 0.85 0.10 0.00
61_K 58_L 0.85 0.10 0.00
38_I 9_C 0.84 0.10 0.00
99_S 163_V 0.84 0.10 0.00
56_L 71_D 0.84 0.10 0.00
31_K 96_Y 0.84 0.10 0.00
103_A 61_A 0.84 0.10 0.00
54_N 123_E 0.84 0.10 0.00
19_K 4_G 0.84 0.10 0.00
103_A 136_V 0.84 0.10 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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