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OPENSEQ.org
mxij_spa24
Genes: A B A+B
Length: 241 216 391
Sequences: 340 1404 246
Seq/Len: 1.41 6.5 0.63
MirrorTree (Pazo et al. 2001) 0.78
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 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.09
10 0.01 0.00 0.32
20 0.01 0.01 0.54
100 0.02 0.01 0.56
∞ 0.05 0.08 0.61
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
98_S 178_M 1.71 0.77 0.02
132_S 158_Y 1.60 0.70 0.02
175_S 106_H 1.59 0.70 0.02
131_V 67_I 1.48 0.62 0.01
131_V 167_V 1.45 0.59 0.01
17_G 173_L 1.39 0.54 0.01
18_C 103_L 1.39 0.54 0.01
116_Q 22_A 1.37 0.53 0.01
174_F 174_A 1.36 0.52 0.01
69_A 45_Q 1.35 0.52 0.01
98_S 41_L 1.35 0.51 0.01
150_I 180_M 1.32 0.49 0.01
17_G 50_M 1.29 0.46 0.01
182_I 11_L 1.29 0.46 0.01
28_L 175_L 1.25 0.43 0.01
135_L 27_Y 1.25 0.43 0.01
35_E 63_V 1.22 0.41 0.01
49_K 64_M 1.22 0.41 0.01
166_I 175_L 1.21 0.40 0.01
153_Y 152_K 1.20 0.39 0.01
164_S 180_M 1.19 0.38 0.01
131_V 37_V 1.18 0.37 0.01
33_A 57_L 1.17 0.37 0.01
85_D 171_I 1.17 0.37 0.01
167_K 103_L 1.15 0.36 0.01
36_I 32_I 1.15 0.35 0.01
115_E 11_L 1.15 0.35 0.01
148_S 72_Y 1.15 0.35 0.01
175_S 189_I 1.15 0.35 0.01
176_D 48_S 1.14 0.35 0.01
172_N 114_F 1.14 0.35 0.01
111_E 17_L 1.14 0.34 0.01
117_S 206_A 1.13 0.34 0.01
173_T 55_I 1.13 0.34 0.01
36_I 163_V 1.13 0.34 0.00
133_Y 135_L 1.12 0.34 0.00
121_I 193_L 1.12 0.33 0.00
34_N 29_K 1.09 0.31 0.00
25_I 189_I 1.09 0.31 0.00
118_L 7_L 1.09 0.31 0.00
18_C 29_K 1.09 0.31 0.00
133_Y 180_M 1.09 0.31 0.00
121_I 10_T 1.08 0.31 0.00
49_K 102_Y 1.08 0.30 0.00
166_I 168_I 1.07 0.30 0.00
31_R 152_K 1.07 0.30 0.00
104_A 160_P 1.07 0.29 0.00
182_I 134_S 1.06 0.29 0.00
63_K 109_L 1.06 0.29 0.00
97_S 211_Y 1.06 0.29 0.00
158_E 163_V 1.06 0.29 0.00
180_E 7_L 1.06 0.29 0.00
136_E 27_Y 1.05 0.28 0.00
113_R 62_F 1.04 0.28 0.00
95_L 114_F 1.04 0.28 0.00
98_S 181_S 1.04 0.28 0.00
25_I 103_L 1.04 0.28 0.00
59_V 163_V 1.04 0.28 0.00
177_V 48_S 1.04 0.27 0.00
11_L 129_E 1.03 0.27 0.00
44_N 119_E 1.03 0.27 0.00
86_I 22_A 1.03 0.27 0.00
76_Y 189_I 1.03 0.27 0.00
105_R 191_L 1.02 0.26 0.00
114_L 209_E 1.02 0.26 0.00
91_P 134_S 1.01 0.26 0.00
183_S 185_I 1.01 0.26 0.00
181_N 88_I 1.01 0.26 0.00
82_E 198_D 1.01 0.26 0.00
151_A 168_I 1.01 0.26 0.00
135_L 186_S 1.01 0.26 0.00
67_A 168_I 1.00 0.25 0.00
49_K 173_L 1.00 0.25 0.00
173_T 195_V 1.00 0.25 0.00
8_I 72_Y 1.00 0.25 0.00
119_V 39_N 1.00 0.25 0.00
56_G 62_F 1.00 0.25 0.00
59_V 63_V 1.00 0.25 0.00
105_R 53_N 1.00 0.25 0.00
36_I 175_L 1.00 0.25 0.00
130_H 155_F 1.00 0.25 0.00
93_D 27_Y 1.00 0.25 0.00
167_K 19_F 0.99 0.24 0.00
131_V 185_I 0.99 0.24 0.00
184_V 39_N 0.99 0.24 0.00
152_I 196_A 0.98 0.24 0.00
121_I 155_F 0.97 0.23 0.00
101_A 189_I 0.97 0.23 0.00
119_V 133_Y 0.97 0.23 0.00
135_L 179_M 0.97 0.23 0.00
98_S 179_M 0.97 0.23 0.00
101_A 142_Y 0.97 0.23 0.00
30_Q 36_M 0.97 0.23 0.00
59_V 164_V 0.96 0.23 0.00
25_I 63_V 0.96 0.23 0.00
94_S 102_Y 0.95 0.22 0.00
135_L 177_M 0.95 0.22 0.00
131_V 146_E 0.95 0.22 0.00
69_A 36_M 0.95 0.22 0.00
146_H 61_L 0.95 0.22 0.00
166_I 11_L 0.95 0.22 0.00
30_Q 170_S 0.95 0.22 0.00
96_V 58_I 0.95 0.22 0.00
180_E 108_D 0.95 0.22 0.00
187_T 211_Y 0.95 0.22 0.00
99_P 203_L 0.94 0.22 0.00
185_I 60_A 0.94 0.22 0.00
54_K 144_L 0.94 0.21 0.00
59_V 135_L 0.94 0.21 0.00
98_S 139_L 0.94 0.21 0.00
134_D 34_F 0.94 0.21 0.00
53_G 164_V 0.94 0.21 0.00
23_E 117_R 0.94 0.21 0.00
9_L 128_A 0.93 0.21 0.00
165_N 41_L 0.93 0.21 0.00
182_I 7_L 0.93 0.21 0.00
11_L 62_F 0.93 0.21 0.00
109_A 193_L 0.93 0.21 0.00
159_S 37_V 0.93 0.21 0.00
155_S 48_S 0.93 0.21 0.00
175_S 111_L 0.93 0.21 0.00
99_P 50_M 0.92 0.21 0.00
37_I 145_S 0.92 0.21 0.00
89_M 149_D 0.92 0.20 0.00
19_E 70_A 0.92 0.20 0.00
139_N 41_L 0.92 0.20 0.00
86_I 48_S 0.92 0.20 0.00
53_G 53_N 0.92 0.20 0.00
152_I 26_C 0.92 0.20 0.00
91_P 99_Y 0.92 0.20 0.00
169_F 175_L 0.92 0.20 0.00
26_S 159_L 0.92 0.20 0.00
24_L 145_S 0.92 0.20 0.00
47_A 133_Y 0.91 0.20 0.00
186_L 58_I 0.91 0.20 0.00
162_L 178_M 0.91 0.20 0.00
151_A 143_A 0.91 0.20 0.00
27_N 208_I 0.91 0.20 0.00
185_I 169_S 0.91 0.20 0.00
158_E 197_L 0.91 0.20 0.00
24_L 7_L 0.91 0.20 0.00
11_L 141_A 0.90 0.19 0.00
45_I 17_L 0.90 0.19 0.00
112_Q 39_N 0.90 0.19 0.00
171_K 152_K 0.90 0.19 0.00
8_I 90_R 0.90 0.19 0.00
63_K 67_I 0.90 0.19 0.00
151_A 186_S 0.90 0.19 0.00
130_H 146_E 0.90 0.19 0.00
32_Q 178_M 0.90 0.19 0.00
187_T 43_L 0.89 0.19 0.00
130_H 206_A 0.89 0.19 0.00
99_P 114_F 0.89 0.19 0.00
47_A 100_K 0.89 0.19 0.00
23_E 209_E 0.89 0.19 0.00
120_S 32_I 0.89 0.19 0.00
53_G 27_Y 0.89 0.19 0.00
159_S 189_I 0.89 0.19 0.00
96_V 22_A 0.88 0.18 0.00
177_V 98_E 0.88 0.18 0.00
102_E 153_I 0.88 0.18 0.00
10_F 145_S 0.88 0.18 0.00
95_L 20_L 0.88 0.18 0.00
113_R 17_L 0.87 0.18 0.00
162_L 27_Y 0.87 0.18 0.00
8_I 101_Q 0.87 0.18 0.00
54_K 108_D 0.87 0.18 0.00
56_G 21_V 0.87 0.18 0.00
62_E 93_D 0.87 0.18 0.00
30_Q 29_K 0.87 0.18 0.00
56_G 143_A 0.87 0.18 0.00
172_N 160_P 0.87 0.18 0.00
107_Y 130_N 0.87 0.18 0.00
15_L 49_N 0.87 0.18 0.00
36_I 103_L 0.86 0.18 0.00
137_E 205_K 0.86 0.18 0.00
108_S 175_L 0.86 0.18 0.00
25_I 32_I 0.86 0.18 0.00
38_S 163_V 0.86 0.17 0.00
110_I 34_F 0.86 0.17 0.00
152_I 65_K 0.86 0.17 0.00
92_T 62_F 0.86 0.17 0.00
105_R 155_F 0.86 0.17 0.00
185_I 160_P 0.86 0.17 0.00
57_I 37_V 0.86 0.17 0.00
183_S 88_I 0.86 0.17 0.00
118_L 50_M 0.86 0.17 0.00
57_I 51_T 0.85 0.17 0.00
32_Q 146_E 0.85 0.17 0.00
104_A 159_L 0.85 0.17 0.00
184_V 22_A 0.85 0.17 0.00
24_L 138_L 0.85 0.17 0.00
92_T 102_Y 0.85 0.17 0.00
126_S 159_L 0.85 0.17 0.00
153_Y 185_I 0.85 0.17 0.00
166_I 55_I 0.85 0.17 0.00
122_G 134_S 0.85 0.17 0.00
110_I 60_A 0.85 0.17 0.00
173_T 157_L 0.85 0.17 0.00
18_C 19_F 0.85 0.17 0.00
70_V 118_S 0.85 0.17 0.00
94_S 206_A 0.85 0.17 0.00
112_Q 44_Q 0.85 0.17 0.00
36_I 67_I 0.84 0.17 0.00
113_R 155_F 0.84 0.17 0.00
173_T 37_V 0.84 0.17 0.00
80_N 156_Y 0.84 0.17 0.00
9_L 87_D 0.84 0.17 0.00
117_S 155_F 0.84 0.17 0.00
77_D 203_L 0.84 0.17 0.00
49_K 29_K 0.84 0.17 0.00
11_L 133_Y 0.84 0.16 0.00
57_I 180_M 0.84 0.16 0.00
173_T 58_I 0.84 0.16 0.00
174_F 186_S 0.83 0.16 0.00
96_V 117_R 0.83 0.16 0.00
94_S 155_F 0.83 0.16 0.00
128_K 155_F 0.83 0.16 0.00
75_M 34_F 0.83 0.16 0.00
96_V 115_F 0.83 0.16 0.00
162_L 158_Y 0.83 0.16 0.00
89_M 128_A 0.83 0.16 0.00
10_F 93_D 0.83 0.16 0.00
177_V 162_V 0.83 0.16 0.00
57_I 53_N 0.83 0.16 0.00
45_I 143_A 0.83 0.16 0.00
109_A 168_I 0.83 0.16 0.00
109_A 169_S 0.83 0.16 0.00
12_L 92_S 0.83 0.16 0.00
143_K 157_L 0.82 0.16 0.00
186_L 159_L 0.82 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
8982 6.14 mxij spa24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.16 Done
7087 7.04 mxij_spa24 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.46 Done
6868 0.52 jp Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done - Shared
6862 mxij_spa24_jackhammer Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) Running
6829 0.63 mxij_spa24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done
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