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OPENSEQ.org
MopJ-DivK_dGene100
Genes: A B A+B
Length: 165 125 269
Sequences: 270 89670 181
Seq/Len: 1.64 717.36 0.67
MirrorTree (Pazo et al. 2001) 0.41
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 0.01 0.11 0.01
2 0.01 0.13 0.01
5 0.01 0.16 0.06
10 0.02 0.19 0.19
20 0.02 0.23 0.33
100 0.03 0.31 0.62
∞ 0.04 0.34 0.73
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
105_V 79_V 1.25 0.45 0.00
102_L 56_L 1.14 0.36 0.00
63_D 83_T 1.13 0.35 0.00
22_A 65_T 1.11 0.34 0.00
71_T 7_I 1.11 0.34 0.00
41_P 10_D 1.05 0.30 0.00
48_L 29_T 1.04 0.29 0.00
114_G 49_L 1.04 0.29 0.00
65_R 5_V 1.02 0.27 0.00
93_A 79_V 1.01 0.27 0.00
121_R 51_L 1.00 0.26 0.00
44_M 46_K 1.00 0.26 0.00
148_Y 11_N 0.97 0.24 0.00
145_I 4_K 0.96 0.24 0.00
26_S 56_L 0.95 0.23 0.00
152_V 56_L 0.94 0.22 0.00
87_G 77_I 0.94 0.22 0.00
106_V 51_L 0.92 0.21 0.00
133_L 61_G 0.91 0.21 0.00
151_V 123_Q 0.90 0.20 0.00
23_Y 8_V 0.89 0.20 0.00
135_L 114_E 0.89 0.19 0.00
66_L 38_A 0.88 0.19 0.00
24_W 6_L 0.88 0.19 0.00
115_V 56_L 0.88 0.19 0.00
73_L 79_V 0.88 0.19 0.00
38_D 70_E 0.87 0.19 0.00
41_P 61_G 0.87 0.19 0.00
138_N 47_P 0.87 0.19 0.00
34_P 22_L 0.87 0.18 0.00
102_L 35_G 0.85 0.18 0.00
80_E 7_I 0.85 0.18 0.00
51_V 38_A 0.83 0.17 0.00
54_I 50_I 0.83 0.17 0.00
114_G 37_S 0.82 0.16 0.00
45_K 29_T 0.82 0.16 0.00
13_A 56_L 0.82 0.16 0.00
127_S 49_L 0.82 0.16 0.00
143_D 7_I 0.82 0.16 0.00
65_R 112_F 0.82 0.16 0.00
59_G 121_E 0.81 0.16 0.00
143_D 50_I 0.81 0.16 0.00
37_V 37_S 0.81 0.16 0.00
98_W 31_Q 0.81 0.16 0.00
40_H 75_A 0.80 0.15 0.00
80_E 33_R 0.80 0.15 0.00
48_L 6_L 0.80 0.15 0.00
75_G 56_L 0.80 0.15 0.00
20_M 24_A 0.80 0.15 0.00
120_W 7_I 0.80 0.15 0.00
82_T 114_E 0.79 0.15 0.00
41_P 22_L 0.79 0.15 0.00
144_M 34_E 0.79 0.15 0.00
54_I 118_R 0.79 0.15 0.00
108_E 59_I 0.78 0.15 0.00
33_L 17_L 0.78 0.14 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
5825 0.67 MopJ-DivK_dGene100 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5824 0.36 MopJ-DivK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.15 Done - Shared
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