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OPENSEQ.org
PopZ-R3-ChpT
Genes: A B A+B
Length: 79 225 280
Sequences: 178 269 77
Seq/Len: 2.25 1.2 0.28
MirrorTree (Pazo et al. 2001) 0.71
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.02
∞ 0.00 0.00 0.25
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
48_P 114_W 1.41 0.34 0.00
48_P 144_G 1.41 0.34 0.00
14_A 112_L 1.36 0.32 0.00
75_R 25_A 1.36 0.31 0.00
65_K 75_L 1.34 0.30 0.00
57_N 153_A 1.31 0.29 0.00
65_K 22_D 1.29 0.28 0.00
48_P 143_G 1.29 0.28 0.00
75_R 65_I 1.27 0.27 0.00
21_A 112_L 1.23 0.24 0.00
49_L 74_D 1.22 0.24 0.00
49_L 142_A 1.21 0.23 0.00
40_D 104_V 1.21 0.23 0.00
14_A 109_R 1.21 0.23 0.00
68_E 79_T 1.21 0.23 0.00
62_V 25_A 1.20 0.23 0.00
70_V 28_A 1.20 0.23 0.00
51_K 71_K 1.19 0.23 0.00
45_L 22_D 1.16 0.21 0.00
70_V 130_L 1.16 0.21 0.00
28_A 160_I 1.16 0.21 0.00
22_F 85_A 1.15 0.21 0.00
15_A 181_E 1.14 0.20 0.00
73_I 185_E 1.13 0.20 0.00
43_R 177_G 1.13 0.20 0.00
72_R 25_A 1.13 0.20 0.00
22_F 65_I 1.12 0.20 0.00
9_L 109_R 1.11 0.19 0.00
56_Q 195_A 1.10 0.19 0.00
62_V 44_S 1.09 0.18 0.00
22_F 36_I 1.09 0.18 0.00
73_I 75_L 1.09 0.18 0.00
37_T 51_D 1.08 0.18 0.00
62_V 78_F 1.08 0.18 0.00
14_A 148_V 1.08 0.18 0.00
37_T 105_F 1.07 0.17 0.00
49_L 46_L 1.07 0.17 0.00
9_L 180_G 1.06 0.17 0.00
18_A 196_Y 1.06 0.17 0.00
7_E 184_A 1.05 0.17 0.00
43_R 178_L 1.05 0.17 0.00
49_L 171_R 1.05 0.17 0.00
9_L 121_M 1.05 0.17 0.00
76_G 190_P 1.03 0.16 0.00
9_L 172_P 1.03 0.16 0.00
59_P 68_S 1.03 0.16 0.00
38_L 202_R 1.02 0.16 0.00
38_L 56_D 1.02 0.16 0.00
10_V 153_A 1.02 0.16 0.00
42_V 208_I 1.02 0.16 0.00
49_L 148_V 1.01 0.15 0.00
7_E 202_R 1.01 0.15 0.00
22_F 188_G 1.00 0.15 0.00
74_S 20_G 0.99 0.15 0.00
61_I 71_K 0.99 0.15 0.00
39_E 145_V 0.99 0.15 0.00
52_E 96_E 0.98 0.14 0.00
17_A 35_F 0.98 0.14 0.00
55_D 105_F 0.98 0.14 0.00
37_T 112_L 0.98 0.14 0.00
62_V 114_W 0.98 0.14 0.00
62_V 144_G 0.98 0.14 0.00
9_L 83_F 0.98 0.14 0.00
72_R 180_G 0.97 0.14 0.00
21_A 163_A 0.97 0.14 0.00
38_L 62_M 0.96 0.14 0.00
41_V 197_L 0.96 0.14 0.00
61_I 39_A 0.96 0.14 0.00
51_K 217_A 0.96 0.14 0.00
75_R 36_I 0.96 0.14 0.00
44_E 153_A 0.95 0.14 0.00
58_L 69_A 0.95 0.14 0.00
59_P 41_A 0.94 0.13 0.00
45_L 163_A 0.94 0.13 0.00
59_P 64_L 0.94 0.13 0.00
44_E 91_N 0.94 0.13 0.00
24_S 200_L 0.94 0.13 0.00
12_V 156_R 0.94 0.13 0.00
71_Q 72_L 0.94 0.13 0.00
67_E 155_G 0.94 0.13 0.00
11_G 132_I 0.93 0.13 0.00
15_A 104_V 0.93 0.13 0.00
38_L 221_A 0.93 0.13 0.00
21_A 77_Q 0.92 0.13 0.00
37_T 202_R 0.92 0.13 0.00
48_P 38_P 0.92 0.13 0.00
50_L 201_V 0.92 0.13 0.00
7_E 149_K 0.92 0.12 0.00
19_A 55_Q 0.92 0.12 0.00
70_V 30_R 0.92 0.12 0.00
19_A 217_A 0.91 0.12 0.00
73_I 48_L 0.91 0.12 0.00
6_A 135_I 0.91 0.12 0.00
62_V 123_K 0.91 0.12 0.00
46_L 131_N 0.91 0.12 0.00
49_L 121_M 0.91 0.12 0.00
14_A 132_I 0.91 0.12 0.00
61_I 184_A 0.90 0.12 0.00
44_E 202_R 0.90 0.12 0.00
16_S 192_V 0.90 0.12 0.00
22_F 191_W 0.90 0.12 0.00
47_R 70_R 0.89 0.12 0.00
75_R 61_A 0.89 0.12 0.00
51_K 67_S 0.89 0.12 0.00
70_V 201_V 0.89 0.12 0.00
76_G 196_Y 0.89 0.12 0.00
51_K 103_G 0.89 0.12 0.00
52_E 121_M 0.89 0.12 0.00
76_G 107_H 0.89 0.12 0.00
48_P 78_F 0.88 0.12 0.00
58_L 68_S 0.88 0.12 0.00
70_V 47_D 0.88 0.11 0.00
15_A 170_L 0.88 0.11 0.00
61_I 186_G 0.88 0.11 0.00
8_Q 151_V 0.87 0.11 0.00
64_T 75_L 0.87 0.11 0.00
6_A 56_D 0.87 0.11 0.00
20_S 74_D 0.87 0.11 0.00
9_L 146_A 0.87 0.11 0.00
37_T 108_V 0.87 0.11 0.00
44_E 161_A 0.86 0.11 0.00
55_D 208_I 0.86 0.11 0.00
21_A 96_E 0.86 0.11 0.00
46_L 49_L 0.86 0.11 0.00
7_E 59_D 0.86 0.11 0.00
77_R 135_I 0.85 0.11 0.00
62_V 143_G 0.85 0.10 0.00
37_T 103_G 0.85 0.10 0.00
66_V 68_S 0.85 0.10 0.00
9_L 212_I 0.85 0.10 0.00
22_F 42_I 0.85 0.10 0.00
14_A 105_F 0.84 0.10 0.00
10_V 127_R 0.84 0.10 0.00
18_A 107_H 0.84 0.10 0.00
22_F 61_A 0.84 0.10 0.00
53_W 32_C 0.84 0.10 0.00
53_W 33_H 0.84 0.10 0.00
53_W 80_R 0.84 0.10 0.00
69_E 32_C 0.84 0.10 0.00
69_E 33_H 0.84 0.10 0.00
69_E 80_R 0.84 0.10 0.00
34_D 122_N 0.84 0.10 0.00
65_K 113_D 0.84 0.10 0.00
41_V 26_M 0.84 0.10 0.00
42_V 138_S 0.83 0.10 0.00
61_I 167_R 0.83 0.10 0.00
61_I 195_A 0.83 0.10 0.00
70_V 39_A 0.83 0.10 0.00
76_G 66_A 0.83 0.10 0.00
38_L 28_A 0.83 0.10 0.00
48_P 83_F 0.83 0.10 0.00
75_R 193_Q 0.83 0.10 0.00
44_E 128_A 0.83 0.10 0.00
43_R 205_G 0.82 0.10 0.00
40_D 133_A 0.82 0.10 0.00
26_S 62_M 0.82 0.10 0.00
75_R 42_I 0.82 0.10 0.00
9_L 170_L 0.82 0.10 0.00
66_V 69_A 0.82 0.10 0.00
9_L 28_A 0.82 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
5991 0.28 PopZ-R3-ChpT Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5989 0 PopZ-R3-ChpT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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