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OPENSEQ.org
PopZ-R3-DivK
Genes: A B A+B
Length: 79 125 197
Sequences: 178 89670 159
Seq/Len: 2.25 717.36 0.81
MirrorTree (Pazo et al. 2001) 0.16
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 0.11 0.01
2 0.00 0.13 0.01
5 0.00 0.16 0.09
10 0.00 0.19 0.15
20 0.00 0.23 0.24
100 0.00 0.31 0.57
∞ 0.00 0.34 0.78
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
51_K 19_H 1.36 0.60 0.00
39_E 22_L 1.35 0.59 0.00
18_A 119_L 1.11 0.38 0.00
47_R 20_D 1.06 0.34 0.00
52_E 56_L 1.04 0.33 0.00
35_G 113_L 1.04 0.32 0.00
14_A 116_I 0.98 0.28 0.00
50_L 38_A 0.97 0.28 0.00
38_L 65_T 0.96 0.27 0.00
38_L 37_S 0.96 0.27 0.00
39_E 113_L 0.93 0.24 0.00
44_E 62_L 0.91 0.23 0.00
61_I 4_K 0.91 0.23 0.00
56_Q 63_E 0.91 0.23 0.00
70_V 64_V 0.89 0.22 0.00
73_I 34_E 0.87 0.21 0.00
44_E 38_A 0.86 0.21 0.00
74_S 115_T 0.86 0.20 0.00
17_A 23_E 0.85 0.20 0.00
9_L 23_E 0.84 0.20 0.00
44_E 120_L 0.83 0.19 0.00
38_L 98_G 0.83 0.19 0.00
46_L 51_L 0.83 0.19 0.00
74_S 114_E 0.83 0.19 0.00
8_Q 103_I 0.82 0.18 0.00
41_V 67_W 0.82 0.18 0.00
22_F 97_G 0.82 0.18 0.00
67_E 50_I 0.82 0.18 0.00
29_L 6_L 0.81 0.18 0.00
13_S 8_V 0.81 0.18 0.00
65_K 76_H 0.81 0.18 0.00
64_T 66_K 0.79 0.17 0.00
56_Q 77_I 0.79 0.17 0.00
66_V 61_G 0.79 0.17 0.00
15_A 114_E 0.78 0.16 0.00
49_L 35_G 0.78 0.16 0.00
21_A 24_A 0.77 0.16 0.00
13_S 56_L 0.77 0.16 0.00
12_V 39_L 0.77 0.16 0.00
35_G 11_N 0.77 0.16 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
5993 0.81 PopZ-R3-DivK Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5990 0.25 PopZ-R3-DivK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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