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OPENSEQ.org
MopJ-DivK
Genes: A B A+B
Length: 165 125 269
Sequences: 270 89670 97
Seq/Len: 1.64 717.36 0.36
MirrorTree (Pazo et al. 2001) 0.61
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 2.08 0.82 0.15
131_L 31_Q 1.61 0.54 0.04
71_T 7_I 1.37 0.38 0.02
13_A 56_L 1.36 0.37 0.02
44_M 46_K 1.20 0.27 0.01
74_Y 4_K 1.19 0.27 0.01
115_V 56_L 1.19 0.27 0.01
87_G 77_I 1.18 0.26 0.01
66_L 123_Q 1.17 0.25 0.01
154_A 56_L 1.16 0.25 0.01
73_L 79_V 1.16 0.25 0.01
34_P 61_G 1.15 0.24 0.01
55_D 37_S 1.14 0.24 0.01
98_W 91_E 1.13 0.23 0.01
66_L 38_A 1.11 0.23 0.01
8_S 30_L 1.10 0.22 0.01
151_V 123_Q 1.08 0.21 0.01
9_A 33_R 1.08 0.21 0.01
67_R 15_M 1.07 0.21 0.01
39_L 77_I 1.07 0.21 0.01
44_M 19_H 1.07 0.21 0.01
41_P 61_G 1.06 0.20 0.01
48_L 6_L 1.06 0.20 0.01
41_P 10_D 1.06 0.20 0.01
102_L 12_E 1.06 0.20 0.01
87_G 91_E 1.05 0.20 0.01
58_G 83_T 1.05 0.20 0.01
134_P 61_G 1.04 0.19 0.01
131_L 42_A 1.02 0.18 0.01
18_Q 4_K 1.02 0.18 0.01
106_V 83_T 1.01 0.18 0.01
155_A 79_V 1.01 0.18 0.01
15_R 7_I 1.00 0.17 0.01
139_G 83_T 1.00 0.17 0.01
56_V 83_T 0.99 0.17 0.01
30_G 49_L 0.98 0.17 0.01
97_Y 68_L 0.97 0.16 0.01
133_L 15_M 0.97 0.16 0.01
24_W 6_L 0.96 0.16 0.01
123_A 41_I 0.96 0.16 0.01
32_S 76_H 0.95 0.16 0.01
52_S 83_T 0.94 0.15 0.01
86_I 7_I 0.94 0.15 0.01
104_K 64_V 0.94 0.15 0.01
130_W 19_H 0.94 0.15 0.01
55_D 13_L 0.94 0.15 0.01
26_S 7_I 0.94 0.15 0.01
66_L 19_H 0.93 0.15 0.01
48_L 29_T 0.93 0.15 0.01
53_L 46_K 0.93 0.15 0.00
19_E 72_D 0.93 0.15 0.00
30_G 7_I 0.92 0.15 0.00
9_A 30_L 0.92 0.14 0.00
106_V 51_L 0.92 0.14 0.00
48_L 53_D 0.92 0.14 0.00
106_V 103_I 0.91 0.14 0.00
53_L 17_L 0.90 0.14 0.00
53_L 77_I 0.90 0.14 0.00
10_S 58_E 0.90 0.14 0.00
10_S 110_V 0.89 0.14 0.00
8_S 91_E 0.89 0.14 0.00
19_E 76_H 0.89 0.13 0.00
103_D 58_E 0.88 0.13 0.00
75_G 46_K 0.88 0.13 0.00
149_D 83_T 0.88 0.13 0.00
8_S 19_H 0.88 0.13 0.00
101_E 7_I 0.87 0.13 0.00
66_L 83_T 0.87 0.13 0.00
132_R 15_M 0.86 0.13 0.00
18_Q 49_L 0.86 0.12 0.00
143_D 50_I 0.85 0.12 0.00
13_A 118_R 0.85 0.12 0.00
112_G 118_R 0.85 0.12 0.00
142_V 37_S 0.85 0.12 0.00
156_A 80_V 0.85 0.12 0.00
129_L 64_V 0.84 0.12 0.00
10_S 72_D 0.84 0.12 0.00
150_A 5_V 0.84 0.12 0.00
108_E 31_Q 0.83 0.12 0.00
131_L 41_I 0.83 0.12 0.00
102_L 56_L 0.83 0.12 0.00
8_S 76_H 0.82 0.11 0.00
38_D 70_E 0.82 0.11 0.00
27_L 22_L 0.82 0.11 0.00
15_R 123_Q 0.81 0.11 0.00
48_L 10_D 0.81 0.11 0.00
54_I 118_R 0.81 0.11 0.00
91_N 23_E 0.81 0.11 0.00
96_D 56_L 0.80 0.11 0.00
22_A 56_L 0.80 0.11 0.00
29_R 49_L 0.80 0.11 0.00
49_P 70_E 0.80 0.11 0.00
19_E 62_L 0.80 0.11 0.00
95_V 16_K 0.80 0.11 0.00
106_V 11_N 0.80 0.11 0.00
87_G 79_V 0.80 0.11 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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