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OPENSEQ.org
MopJ-DivLHK_dGene100
Genes: A B A+B
Length: 165 249 381
Sequences: 270 83656 191
Seq/Len: 1.64 335.97 0.5
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 0.04 0.01
2 0.01 0.07 0.02
5 0.01 0.11 0.21
10 0.02 0.14 0.27
20 0.02 0.18 0.31
100 0.03 0.28 0.46
∞ 0.04 0.32 0.56
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
53_L 171_L 1.49 0.55 0.00
39_L 33_R 1.38 0.47 0.00
102_L 148_A 1.29 0.41 0.00
86_I 168_E 1.28 0.40 0.00
148_Y 229_T 1.20 0.34 0.00
31_A 104_A 1.19 0.33 0.00
47_L 168_E 1.14 0.30 0.00
94_A 145_V 1.11 0.28 0.00
68_L 21_K 1.10 0.27 0.00
95_V 213_L 1.09 0.27 0.00
68_L 148_A 1.06 0.25 0.00
145_I 211_V 1.05 0.24 0.00
29_R 113_Q 1.04 0.24 0.00
89_V 86_G 1.03 0.23 0.00
149_D 15_A 1.03 0.23 0.00
112_G 116_G 1.02 0.23 0.00
150_A 39_I 1.01 0.22 0.00
32_S 105_Q 1.00 0.22 0.00
91_N 211_V 0.98 0.21 0.00
53_L 149_L 0.98 0.20 0.00
38_D 161_S 0.98 0.20 0.00
54_I 156_G 0.95 0.19 0.00
49_P 181_P 0.95 0.19 0.00
80_E 100_L 0.95 0.19 0.00
82_T 152_T 0.94 0.18 0.00
55_D 200_P 0.94 0.18 0.00
99_R 171_L 0.94 0.18 0.00
29_R 231_T 0.92 0.18 0.00
68_L 164_R 0.92 0.18 0.00
110_R 145_V 0.92 0.18 0.00
46_R 124_E 0.91 0.17 0.00
80_E 137_L 0.91 0.17 0.00
29_R 85_A 0.91 0.17 0.00
113_V 33_R 0.90 0.17 0.00
28_R 171_L 0.90 0.17 0.00
108_E 229_T 0.90 0.17 0.00
45_K 16_E 0.90 0.17 0.00
25_A 171_L 0.90 0.17 0.00
142_V 33_R 0.89 0.16 0.00
68_L 218_V 0.89 0.16 0.00
17_H 54_E 0.88 0.16 0.00
146_L 207_V 0.88 0.16 0.00
144_M 160_L 0.88 0.16 0.00
54_I 119_L 0.87 0.16 0.00
64_Y 90_L 0.87 0.15 0.00
122_G 114_L 0.87 0.15 0.00
133_L 133_D 0.86 0.15 0.00
149_D 96_R 0.86 0.15 0.00
10_S 94_D 0.86 0.15 0.00
143_D 75_D 0.86 0.15 0.00
39_L 82_Q 0.86 0.15 0.00
79_R 190_D 0.85 0.15 0.00
43_S 160_L 0.85 0.15 0.00
63_D 71_A 0.85 0.15 0.00
105_V 103_N 0.84 0.14 0.00
84_R 188_I 0.84 0.14 0.00
108_E 231_T 0.84 0.14 0.00
104_K 183_H 0.84 0.14 0.00
11_A 138_A 0.84 0.14 0.00
85_L 208_K 0.83 0.14 0.00
19_E 185_Q 0.83 0.14 0.00
20_M 104_A 0.83 0.14 0.00
143_D 97_V 0.83 0.14 0.00
10_S 156_G 0.83 0.14 0.00
41_P 177_G 0.83 0.14 0.00
41_P 201_G 0.83 0.14 0.00
41_P 203_G 0.83 0.14 0.00
106_V 158_V 0.83 0.14 0.00
114_G 103_N 0.82 0.14 0.00
90_Y 221_E 0.82 0.14 0.00
37_V 169_V 0.82 0.14 0.00
66_L 132_G 0.82 0.14 0.00
44_M 130_I 0.82 0.14 0.00
44_M 81_A 0.82 0.14 0.00
33_L 142_D 0.82 0.14 0.00
112_G 232_C 0.81 0.13 0.00
43_S 91_E 0.81 0.13 0.00
133_L 38_T 0.81 0.13 0.00
118_L 130_I 0.81 0.13 0.00
75_G 115_G 0.81 0.13 0.00
12_T 47_E 0.81 0.13 0.00
77_Y 81_A 0.80 0.13 0.00
62_R 145_V 0.80 0.13 0.00
107_D 149_L 0.80 0.13 0.00
30_G 125_E 0.80 0.13 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
5826 0.5 MopJ-DivLHK_dGene100 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5823 0.33 MopJ-DivLHK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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