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OPENSEQ.org
PH_ZA
Genes: A B A+B
Length: 117 277 365
Sequences: 6799 391 213
Seq/Len: 58.11 1.41 0.58
MirrorTree (Pazo et al. 2001) 0.89
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 0.08 0.02 0.54
2 0.10 0.03 0.55
5 0.13 0.03 0.56
10 0.13 0.03 0.57
20 0.14 0.03 0.59
100 0.18 0.04 0.64
∞ 0.22 0.06 0.71
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
93_I 197_N 1.95 0.87 0.21
33_S 48_I 1.64 0.71 0.10
29_R 68_G 1.51 0.61 0.07
71_D 58_R 1.48 0.60 0.06
13_K 35_T 1.43 0.55 0.05
61_K 18_G 1.41 0.54 0.05
41_I 59_I 1.39 0.52 0.05
29_R 78_V 1.38 0.51 0.04
32_C 59_I 1.37 0.50 0.04
104_L 46_S 1.33 0.47 0.04
104_L 64_L 1.27 0.42 0.03
36_N 48_I 1.26 0.42 0.03
30_R 54_V 1.22 0.39 0.03
81_F 58_R 1.22 0.39 0.03
71_D 75_A 1.22 0.39 0.03
28_Q 87_M 1.20 0.37 0.02
81_F 227_S 1.19 0.36 0.02
77_R 190_F 1.18 0.36 0.02
64_A 216_S 1.17 0.35 0.02
75_H 58_R 1.15 0.34 0.02
93_I 110_Y 1.13 0.32 0.02
68_K 69_T 1.11 0.31 0.02
78_T 138_A 1.11 0.31 0.02
81_F 189_D 1.11 0.31 0.02
57_T 222_K 1.11 0.31 0.02
54_N 70_S 1.10 0.30 0.02
72_L 21_I 1.10 0.30 0.02
19_K 110_Y 1.10 0.30 0.02
61_K 82_S 1.09 0.30 0.02
79_Y 193_Q 1.08 0.29 0.02
31_K 75_A 1.08 0.29 0.02
37_G 40_L 1.07 0.28 0.02
100_K 60_Q 1.07 0.28 0.02
41_I 33_L 1.06 0.28 0.01
72_L 150_V 1.06 0.27 0.01
41_I 67_L 1.05 0.27 0.01
20_S 14_Q 1.05 0.27 0.01
71_D 222_K 1.04 0.26 0.01
100_K 111_I 1.03 0.26 0.01
57_T 54_V 1.03 0.25 0.01
66_D 43_I 1.02 0.25 0.01
71_D 70_S 1.02 0.25 0.01
105_T 143_D 1.02 0.25 0.01
26_V 51_E 1.01 0.24 0.01
94_S 10_I 1.01 0.24 0.01
71_D 35_T 1.00 0.24 0.01
88_D 212_C 1.00 0.24 0.01
43_H 67_L 1.00 0.24 0.01
70_F 34_S 1.00 0.24 0.01
37_G 88_E 1.00 0.23 0.01
90_V 150_V 0.99 0.23 0.01
61_K 106_V 0.99 0.23 0.01
55_L 120_F 0.99 0.23 0.01
63_N 16_L 0.98 0.23 0.01
89_Y 228_K 0.98 0.23 0.01
19_K 150_V 0.98 0.23 0.01
13_K 97_K 0.98 0.23 0.01
13_K 194_N 0.97 0.22 0.01
40_T 148_I 0.97 0.22 0.01
18_K 18_G 0.97 0.22 0.01
12_K 100_P 0.97 0.22 0.01
39_L 152_A 0.97 0.22 0.01
27_W 224_L 0.97 0.22 0.01
28_Q 177_V 0.97 0.22 0.01
96_L 97_K 0.96 0.21 0.01
109_R 13_V 0.96 0.21 0.01
25_K 52_M 0.96 0.21 0.01
61_K 85_D 0.96 0.21 0.01
75_H 68_G 0.96 0.21 0.01
57_T 70_S 0.96 0.21 0.01
58_C 119_R 0.95 0.21 0.01
84_E 54_V 0.95 0.21 0.01
34_V 35_T 0.95 0.21 0.01
59_Q 60_Q 0.95 0.21 0.01
77_R 68_G 0.94 0.21 0.01
52_K 74_L 0.94 0.21 0.01
56_L 223_L 0.94 0.20 0.01
68_K 24_D 0.94 0.20 0.01
89_Y 190_F 0.94 0.20 0.01
104_L 31_T 0.94 0.20 0.01
48_R 243_D 0.94 0.20 0.01
32_C 189_D 0.93 0.20 0.01
73_I 232_D 0.93 0.20 0.01
54_N 188_V 0.93 0.20 0.01
48_R 138_A 0.93 0.20 0.01
100_K 253_C 0.93 0.20 0.01
29_R 58_R 0.93 0.20 0.01
103_A 144_L 0.93 0.20 0.01
31_K 60_Q 0.93 0.20 0.01
84_E 210_H 0.92 0.20 0.01
41_I 253_C 0.92 0.19 0.01
29_R 192_V 0.92 0.19 0.01
93_I 16_L 0.92 0.19 0.01
51_A 193_Q 0.92 0.19 0.01
15_Y 79_G 0.92 0.19 0.01
29_R 189_D 0.91 0.19 0.01
41_I 202_T 0.91 0.19 0.01
35_K 172_A 0.91 0.19 0.01
77_R 51_E 0.91 0.19 0.01
37_G 240_T 0.91 0.19 0.01
93_I 81_N 0.91 0.19 0.01
105_T 241_A 0.91 0.19 0.01
73_I 10_I 0.90 0.19 0.01
85_D 157_L 0.90 0.18 0.01
37_G 251_T 0.90 0.18 0.01
84_E 118_H 0.90 0.18 0.01
104_L 240_T 0.90 0.18 0.01
34_V 104_M 0.90 0.18 0.01
74_S 23_C 0.90 0.18 0.01
32_C 68_G 0.90 0.18 0.01
81_F 68_G 0.89 0.18 0.01
78_T 128_S 0.89 0.18 0.01
92_W 45_C 0.89 0.18 0.01
92_W 49_H 0.89 0.18 0.01
56_L 24_D 0.89 0.18 0.01
38_I 31_T 0.89 0.18 0.01
25_K 48_I 0.89 0.18 0.01
10_S 27_S 0.88 0.18 0.01
72_L 152_A 0.88 0.17 0.01
65_E 198_L 0.88 0.17 0.01
79_Y 52_M 0.87 0.17 0.01
55_L 209_L 0.87 0.17 0.01
89_Y 230_T 0.87 0.17 0.01
34_V 190_F 0.87 0.17 0.01
100_K 196_G 0.87 0.17 0.01
104_L 174_H 0.86 0.17 0.01
45_T 239_E 0.86 0.17 0.01
51_A 191_L 0.86 0.17 0.01
13_K 51_E 0.86 0.17 0.01
110_G 142_R 0.86 0.16 0.01
69_S 43_I 0.85 0.16 0.01
85_D 83_F 0.85 0.16 0.01
78_T 216_S 0.85 0.16 0.01
49_Q 241_A 0.85 0.16 0.01
90_V 48_I 0.85 0.16 0.01
22_G 156_E 0.85 0.16 0.01
58_C 35_T 0.85 0.16 0.01
77_R 148_I 0.85 0.16 0.01
35_K 23_C 0.84 0.16 0.01
65_E 21_I 0.84 0.16 0.01
56_L 154_G 0.84 0.16 0.01
97_T 51_E 0.84 0.16 0.01
31_K 212_C 0.83 0.15 0.01
55_L 114_K 0.83 0.15 0.01
12_K 28_S 0.83 0.15 0.01
99_S 76_K 0.83 0.15 0.01
37_G 173_L 0.83 0.15 0.01
56_L 70_S 0.82 0.15 0.01
74_S 82_S 0.82 0.15 0.01
54_N 137_E 0.82 0.15 0.01
47_N 202_T 0.82 0.15 0.01
97_T 154_G 0.82 0.15 0.01
93_I 234_V 0.82 0.15 0.01
25_K 197_N 0.82 0.15 0.01
10_S 170_E 0.82 0.15 0.01
36_N 120_F 0.82 0.15 0.01
26_V 222_K 0.81 0.15 0.01
39_L 205_G 0.81 0.15 0.01
33_S 56_I 0.81 0.15 0.01
59_Q 206_N 0.81 0.15 0.01
25_K 108_K 0.81 0.14 0.01
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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