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OPENSEQ.org
PopZ-R3-SpmX-L
Genes: A B A+B
Length: 79 155 222
Sequences: 178 1316 57
Seq/Len: 2.25 8.49 0.26
MirrorTree (Pazo et al. 2001) 0.27
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.00
100 0.00 0.02 0.06
∞ 0.00 0.10 0.24
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
55_D 108_E 1.23 0.23 0.00
5_V 120_M 1.21 0.23 0.00
29_L 11_A 1.19 0.21 0.00
39_E 29_P 1.17 0.20 0.00
14_A 94_L 1.13 0.19 0.00
43_R 57_L 1.09 0.18 0.00
59_P 69_V 1.09 0.17 0.00
40_D 137_V 1.08 0.17 0.00
23_G 90_F 1.07 0.17 0.00
7_E 113_Q 1.04 0.16 0.00
51_K 35_V 1.03 0.15 0.00
65_K 26_A 1.02 0.15 0.00
15_A 35_V 0.98 0.14 0.00
60_R 135_A 0.96 0.13 0.00
9_L 148_L 0.96 0.13 0.00
10_V 115_A 0.96 0.13 0.00
37_T 57_L 0.96 0.13 0.00
39_E 148_L 0.94 0.13 0.00
25_L 138_R 0.94 0.13 0.00
21_A 33_W 0.93 0.12 0.00
36_R 55_E 0.92 0.12 0.00
39_E 56_A 0.92 0.12 0.00
73_I 33_W 0.92 0.12 0.00
10_V 9_R 0.89 0.11 0.00
46_L 40_T 0.89 0.11 0.00
55_D 16_K 0.88 0.11 0.00
42_V 119_E 0.88 0.11 0.00
66_V 87_C 0.88 0.11 0.00
67_E 122_R 0.88 0.11 0.00
40_D 110_S 0.88 0.11 0.00
9_L 51_E 0.87 0.11 0.00
46_L 15_I 0.86 0.11 0.00
21_A 78_N 0.86 0.10 0.00
25_L 25_A 0.85 0.10 0.00
58_L 36_G 0.85 0.10 0.00
6_A 113_Q 0.85 0.10 0.00
37_T 31_G 0.84 0.10 0.00
61_I 18_F 0.84 0.10 0.00
43_R 106_I 0.84 0.10 0.00
53_W 19_E 0.83 0.10 0.00
53_W 38_G 0.83 0.10 0.00
53_W 139_R 0.83 0.10 0.00
69_E 19_E 0.83 0.10 0.00
69_E 38_G 0.83 0.10 0.00
69_E 139_R 0.83 0.10 0.00
66_V 62_L 0.83 0.10 0.00
74_S 62_L 0.83 0.10 0.00
41_V 122_R 0.82 0.10 0.00
18_A 32_R 0.82 0.09 0.00
12_V 94_L 0.82 0.09 0.00
38_L 116_C 0.81 0.09 0.00
75_R 46_G 0.81 0.09 0.00
39_E 84_A 0.81 0.09 0.00
28_A 50_S 0.81 0.09 0.00
10_V 86_V 0.81 0.09 0.00
71_Q 122_R 0.81 0.09 0.00
38_L 28_L 0.81 0.09 0.00
65_K 43_A 0.80 0.09 0.00
17_A 124_A 0.80 0.09 0.00
73_I 41_L 0.80 0.09 0.00
47_R 135_A 0.80 0.09 0.00
12_V 17_R 0.80 0.09 0.00
76_G 123_K 0.80 0.09 0.00
57_N 95_D 0.79 0.09 0.00
77_R 133_I 0.79 0.09 0.00
37_T 56_A 0.79 0.09 0.00
51_K 24_K 0.79 0.09 0.00
14_A 11_A 0.79 0.09 0.00
9_L 75_T 0.78 0.09 0.00
37_T 109_G 0.78 0.09 0.00
37_T 142_A 0.78 0.09 0.00
44_E 122_R 0.77 0.09 0.00
70_V 26_A 0.77 0.09 0.00
73_I 103_L 0.77 0.09 0.00
52_E 102_V 0.77 0.09 0.00
26_S 73_T 0.77 0.08 0.00
19_A 146_L 0.77 0.08 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
5992 0.26 PopZ-R3-SpmX-L Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5988 0 PopZ-R3-SpmX-L Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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