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OPENSEQ.org
MopJ-DivLHK
Genes: A B A+B
Length: 165 249 387
Sequences: 270 83656 128
Seq/Len: 1.64 335.97 0.33
MirrorTree (Pazo et al. 2001) 0.80
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
47_L 168_E 1.52 0.46 0.00
86_I 168_E 1.49 0.43 0.00
102_L 148_A 1.43 0.39 0.00
148_Y 229_T 1.38 0.36 0.00
112_G 116_G 1.34 0.34 0.00
149_D 220_L 1.29 0.31 0.00
68_L 148_A 1.27 0.29 0.00
108_E 229_T 1.26 0.29 0.00
53_L 171_L 1.23 0.27 0.00
82_T 152_T 1.23 0.27 0.00
145_I 211_V 1.21 0.26 0.00
39_L 33_R 1.18 0.24 0.00
46_R 124_E 1.17 0.24 0.00
46_R 101_L 1.16 0.23 0.00
17_H 54_E 1.15 0.23 0.00
110_R 145_V 1.14 0.23 0.00
123_A 31_E 1.11 0.21 0.00
77_Y 81_A 1.08 0.20 0.00
69_A 180_V 1.07 0.20 0.00
87_G 211_V 1.07 0.19 0.00
41_P 177_G 1.06 0.19 0.00
41_P 201_G 1.06 0.19 0.00
41_P 203_G 1.06 0.19 0.00
122_G 188_I 1.06 0.19 0.00
39_L 82_Q 1.06 0.19 0.00
29_R 111_D 1.06 0.19 0.00
134_P 227_G 1.05 0.18 0.00
68_L 86_G 1.04 0.18 0.00
108_E 159_T 1.03 0.18 0.00
105_V 103_N 1.03 0.18 0.00
54_I 156_G 1.02 0.17 0.00
20_M 104_A 1.01 0.17 0.00
142_V 33_R 1.01 0.17 0.00
102_L 131_R 1.01 0.17 0.00
42_A 135_K 1.01 0.17 0.00
12_T 231_T 1.01 0.17 0.00
149_D 81_A 1.00 0.17 0.00
66_L 132_G 0.99 0.16 0.00
46_R 123_C 0.99 0.16 0.00
109_R 152_T 0.99 0.16 0.00
28_R 171_L 0.99 0.16 0.00
9_A 109_L 0.99 0.16 0.00
71_T 114_L 0.98 0.16 0.00
123_A 212_E 0.97 0.15 0.00
71_T 152_T 0.97 0.15 0.00
116_H 23_D 0.97 0.15 0.00
105_V 221_E 0.97 0.15 0.00
141_D 105_Q 0.97 0.15 0.00
71_T 128_G 0.97 0.15 0.00
107_D 68_T 0.97 0.15 0.00
71_T 106_E 0.97 0.15 0.00
36_R 234_L 0.97 0.15 0.00
151_V 156_G 0.96 0.15 0.00
149_D 96_R 0.96 0.15 0.00
93_A 126_D 0.96 0.15 0.00
80_E 100_L 0.95 0.15 0.00
25_A 141_L 0.95 0.15 0.00
10_S 122_E 0.95 0.15 0.00
126_M 149_L 0.94 0.14 0.00
29_R 85_A 0.94 0.14 0.00
41_P 147_N 0.94 0.14 0.00
143_D 75_D 0.94 0.14 0.00
12_T 47_E 0.94 0.14 0.00
34_P 82_Q 0.94 0.14 0.00
142_V 165_A 0.94 0.14 0.00
117_S 115_G 0.94 0.14 0.00
63_D 14_L 0.93 0.14 0.00
51_V 191_R 0.93 0.14 0.00
68_L 218_V 0.93 0.14 0.00
144_M 160_L 0.93 0.14 0.00
15_R 47_E 0.92 0.14 0.00
96_D 99_D 0.92 0.14 0.00
41_P 175_D 0.92 0.14 0.00
106_V 196_D 0.92 0.14 0.00
49_P 92_I 0.92 0.14 0.00
92_A 113_Q 0.92 0.14 0.00
113_V 33_R 0.92 0.14 0.00
92_A 76_D 0.92 0.14 0.00
20_M 81_A 0.91 0.14 0.00
136_A 39_I 0.91 0.14 0.00
18_Q 160_L 0.91 0.13 0.00
57_V 149_L 0.91 0.13 0.00
82_T 55_R 0.91 0.13 0.00
69_A 82_Q 0.90 0.13 0.00
49_P 181_P 0.90 0.13 0.00
127_S 16_E 0.90 0.13 0.00
101_E 231_T 0.90 0.13 0.00
117_S 101_L 0.90 0.13 0.00
94_A 145_V 0.90 0.13 0.00
39_L 18_E 0.90 0.13 0.00
91_N 211_V 0.90 0.13 0.00
19_E 65_A 0.89 0.13 0.00
88_D 226_N 0.89 0.13 0.00
140_K 214_H 0.89 0.13 0.00
93_A 134_G 0.89 0.13 0.00
139_G 171_L 0.89 0.13 0.00
70_G 177_G 0.89 0.13 0.00
70_G 201_G 0.89 0.13 0.00
70_G 203_G 0.89 0.13 0.00
139_G 148_A 0.89 0.13 0.00
105_V 106_E 0.89 0.13 0.00
115_V 122_E 0.89 0.13 0.00
117_S 92_I 0.89 0.13 0.00
112_G 94_D 0.88 0.13 0.00
30_G 211_V 0.88 0.13 0.00
89_V 220_L 0.88 0.13 0.00
19_E 185_Q 0.88 0.13 0.00
55_D 210_L 0.88 0.12 0.00
35_A 220_L 0.88 0.12 0.00
71_T 160_L 0.88 0.12 0.00
89_V 86_G 0.88 0.12 0.00
108_E 111_D 0.88 0.12 0.00
105_V 125_E 0.88 0.12 0.00
49_P 236_E 0.88 0.12 0.00
81_I 148_A 0.88 0.12 0.00
143_D 105_Q 0.88 0.12 0.00
78_G 32_L 0.87 0.12 0.00
112_G 145_V 0.87 0.12 0.00
112_G 232_C 0.87 0.12 0.00
33_L 64_R 0.87 0.12 0.00
50_T 134_G 0.87 0.12 0.00
9_A 183_H 0.87 0.12 0.00
68_L 49_A 0.87 0.12 0.00
8_S 171_L 0.87 0.12 0.00
142_V 115_G 0.87 0.12 0.00
140_K 200_P 0.86 0.12 0.00
122_G 114_L 0.86 0.12 0.00
41_P 30_Y 0.86 0.12 0.00
41_P 227_G 0.86 0.12 0.00
134_P 177_G 0.86 0.12 0.00
134_P 201_G 0.86 0.12 0.00
134_P 203_G 0.86 0.12 0.00
11_A 169_V 0.86 0.12 0.00
55_D 200_P 0.86 0.12 0.00
53_L 149_L 0.86 0.12 0.00
117_S 96_R 0.86 0.12 0.00
98_W 149_L 0.86 0.12 0.00
8_S 92_I 0.86 0.12 0.00
68_L 123_C 0.86 0.12 0.00
105_V 68_T 0.85 0.12 0.00
99_R 171_L 0.85 0.12 0.00
92_A 116_G 0.85 0.12 0.00
109_R 223_E 0.85 0.12 0.00
26_S 173_V 0.85 0.12 0.00
105_V 98_S 0.85 0.12 0.00
150_A 39_I 0.84 0.11 0.00
20_M 197_R 0.84 0.11 0.00
114_G 39_I 0.84 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
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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