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OPENSEQ.org
JH2JH1
Genes: A B A+B
Length: 282 286 534
Sequences: 73023 70057 54
Seq/Len: 258.95 244.95 0.1
MirrorTree (Pazo et al. 2001) 0.39
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 0.11 0.11 0.02
2 0.13 0.13 0.03
5 0.17 0.17 0.05
10 0.21 0.20 0.07
20 0.25 0.24 0.10
100 0.32 0.31 0.16
∞ 0.34 0.33 0.17
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
172_G 93_L 1.66 0.26 0.00
52_K 93_L 1.65 0.26 0.00
149_N 150_D 1.58 0.23 0.00
102_F 90_Y 1.51 0.20 0.00
193_E 54_E 1.50 0.20 0.00
193_E 130_H 1.49 0.20 0.00
266_R 152_G 1.46 0.19 0.00
144_N 93_L 1.44 0.19 0.00
170_D 137_N 1.43 0.18 0.00
220_G 206_Y 1.40 0.17 0.00
100_V 88_L 1.35 0.16 0.00
172_G 54_E 1.34 0.16 0.00
105_L 93_L 1.33 0.15 0.00
52_K 54_E 1.33 0.15 0.00
192_P 179_P 1.33 0.15 0.00
172_G 152_G 1.33 0.15 0.00
52_K 152_G 1.31 0.15 0.00
128_L 112_Y 1.29 0.14 0.00
266_R 132_D 1.29 0.14 0.00
211_G 200_L 1.28 0.14 0.00
266_R 54_E 1.28 0.14 0.00
170_D 180_E 1.26 0.14 0.00
211_G 152_G 1.25 0.13 0.00
168_L 178_A 1.23 0.13 0.00
149_N 137_N 1.23 0.13 0.00
210_F 73_C 1.21 0.12 0.00
170_D 150_D 1.21 0.12 0.00
68_A 93_L 1.21 0.12 0.00
127_Q 127_R 1.21 0.12 0.00
193_E 132_D 1.20 0.12 0.00
266_R 93_L 1.20 0.12 0.00
193_E 150_D 1.19 0.12 0.00
191_P 178_A 1.17 0.12 0.00
146_C 134_A 1.17 0.12 0.00
81_V 123_L 1.17 0.12 0.00
136_E 134_A 1.16 0.11 0.00
193_E 38_K 1.15 0.11 0.00
146_C 150_D 1.14 0.11 0.00
179_P 84_I 1.14 0.11 0.00
206_D 192_D 1.14 0.11 0.00
193_E 93_L 1.14 0.11 0.00
170_D 93_L 1.14 0.11 0.00
208_W 194_W 1.13 0.11 0.00
32_K 146_V 1.13 0.11 0.00
136_E 148_I 1.13 0.11 0.00
151_L 147_K 1.12 0.11 0.00
144_N 54_E 1.11 0.10 0.00
214_L 200_L 1.11 0.10 0.00
95_L 122_Y 1.11 0.10 0.00
151_L 139_L 1.10 0.10 0.00
151_L 193_V 1.10 0.10 0.00
211_G 93_L 1.09 0.10 0.00
32_K 151_F 1.09 0.10 0.00
134_F 123_L 1.09 0.10 0.00
173_I 116_I 1.09 0.10 0.00
144_N 152_G 1.08 0.10 0.00
52_K 63_H 1.08 0.10 0.00
128_L 203_L 1.08 0.10 0.00
30_I 182_L 1.08 0.10 0.00
208_W 187_F 1.08 0.10 0.00
22_L 132_D 1.07 0.10 0.00
170_D 132_D 1.07 0.10 0.00
216_E 202_E 1.06 0.10 0.00
208_W 197_G 1.06 0.10 0.00
107_T 271_S 1.06 0.10 0.00
259_M 125_T 1.06 0.10 0.00
65_F 271_S 1.05 0.09 0.00
149_N 180_E 1.05 0.09 0.00
206_D 93_L 1.04 0.09 0.00
141_I 201_Y 1.03 0.09 0.00
268_S 271_S 1.03 0.09 0.00
219_S 205_T 1.02 0.09 0.00
125_A 193_V 1.02 0.09 0.00
172_G 132_D 1.02 0.09 0.00
98_E 195_S 1.01 0.09 0.00
151_L 130_H 1.01 0.09 0.00
52_K 132_D 1.01 0.09 0.00
75_L 120_M 1.01 0.09 0.00
197_N 276_A 1.01 0.09 0.00
142_H 195_S 1.00 0.09 0.00
23_G 93_L 1.00 0.09 0.00
32_K 138_I 1.00 0.09 0.00
72_M 58_L 1.00 0.09 0.00
142_H 122_Y 1.00 0.09 0.00
32_K 129_I 0.99 0.09 0.00
128_L 116_I 0.99 0.08 0.00
189_W 35_V 0.99 0.08 0.00
151_L 119_G 0.99 0.08 0.00
187_I 119_G 0.98 0.08 0.00
26_T 176_W 0.98 0.08 0.00
209_S 273_R 0.98 0.08 0.00
82_L 202_E 0.98 0.08 0.00
194_C 181_S 0.98 0.08 0.00
172_G 197_G 0.97 0.08 0.00
149_N 93_L 0.97 0.08 0.00
184_Q 85_M 0.97 0.08 0.00
52_K 197_G 0.97 0.08 0.00
22_L 55_I 0.96 0.08 0.00
143_G 131_R 0.96 0.08 0.00
149_N 151_F 0.96 0.08 0.00
105_L 258_M 0.95 0.08 0.00
71_M 195_S 0.95 0.08 0.00
205_T 176_W 0.95 0.08 0.00
166_I 36_A 0.95 0.08 0.00
266_R 137_N 0.95 0.08 0.00
58_H 87_Y 0.94 0.08 0.00
65_F 83_L 0.94 0.08 0.00
104_S 153_L 0.94 0.08 0.00
266_R 86_E 0.94 0.08 0.00
149_N 134_A 0.94 0.08 0.00
130_W 119_G 0.93 0.07 0.00
170_D 152_G 0.93 0.07 0.00
167_K 193_V 0.93 0.07 0.00
193_E 152_G 0.92 0.07 0.00
80_L 179_P 0.92 0.07 0.00
169_S 149_G 0.92 0.07 0.00
79_H 62_Q 0.92 0.07 0.00
94_I 267_N 0.92 0.07 0.00
156_E 148_I 0.92 0.07 0.00
206_D 180_E 0.92 0.07 0.00
140_L 123_L 0.92 0.07 0.00
38_V 140_V 0.92 0.07 0.00
54_L 147_K 0.92 0.07 0.00
129_A 53_R 0.92 0.07 0.00
100_V 208_E 0.92 0.07 0.00
210_F 196_F 0.92 0.07 0.00
140_L 124_G 0.91 0.07 0.00
191_P 45_E 0.91 0.07 0.00
88_V 84_I 0.91 0.07 0.00
211_G 58_L 0.91 0.07 0.00
266_R 150_D 0.91 0.07 0.00
104_S 13_K 0.90 0.07 0.00
53_V 85_M 0.90 0.07 0.00
246_P 138_I 0.90 0.07 0.00
189_W 150_D 0.90 0.07 0.00
171_P 93_L 0.90 0.07 0.00
105_L 36_A 0.90 0.07 0.00
74_K 116_I 0.90 0.07 0.00
209_S 258_M 0.90 0.07 0.00
142_H 12_G 0.90 0.07 0.00
80_L 244_L 0.90 0.07 0.00
132_M 55_I 0.90 0.07 0.00
132_M 120_M 0.89 0.07 0.00
105_L 152_G 0.89 0.07 0.00
193_E 195_S 0.89 0.07 0.00
166_I 119_G 0.89 0.07 0.00
132_M 148_I 0.89 0.07 0.00
22_L 145_R 0.89 0.07 0.00
167_K 274_D 0.89 0.07 0.00
166_I 115_Q 0.89 0.07 0.00
102_F 85_M 0.89 0.07 0.00
218_C 184_E 0.88 0.07 0.00
171_P 131_R 0.88 0.07 0.00
186_R 54_E 0.88 0.07 0.00
87_C 5_L 0.88 0.07 0.00
223_K 153_L 0.88 0.07 0.00
105_L 54_E 0.88 0.07 0.00
172_G 86_E 0.87 0.07 0.00
270_R 258_M 0.87 0.07 0.00
170_D 54_E 0.87 0.07 0.00
22_L 112_Y 0.87 0.07 0.00
142_H 93_L 0.87 0.07 0.00
206_D 197_G 0.87 0.07 0.00
97_Q 208_E 0.87 0.07 0.00
77_H 206_Y 0.87 0.07 0.00
272_I 44_T 0.87 0.07 0.00
212_T 12_G 0.86 0.07 0.00
132_M 117_C 0.86 0.07 0.00
156_E 115_Q 0.86 0.07 0.00
125_A 254_I 0.86 0.07 0.00
150_I 176_W 0.86 0.07 0.00
131_A 267_N 0.86 0.07 0.00
206_D 131_R 0.86 0.07 0.00
171_P 124_G 0.86 0.07 0.00
140_L 68_K 0.85 0.07 0.00
195_I 53_R 0.85 0.07 0.00
262_E 179_P 0.85 0.07 0.00
201_L 187_F 0.85 0.07 0.00
68_A 54_E 0.85 0.07 0.00
51_L 148_I 0.85 0.07 0.00
98_E 11_L 0.85 0.07 0.00
186_R 6_K 0.85 0.06 0.00
50_L 54_E 0.85 0.06 0.00
142_H 11_L 0.85 0.06 0.00
149_N 132_D 0.84 0.06 0.00
156_E 49_R 0.84 0.06 0.00
136_E 152_G 0.84 0.06 0.00
170_D 130_H 0.84 0.06 0.00
210_F 133_L 0.84 0.06 0.00
136_E 120_M 0.84 0.06 0.00
173_I 153_L 0.84 0.06 0.00
190_V 99_K 0.84 0.06 0.00
152_L 270_P 0.84 0.06 0.00
149_N 135_T 0.84 0.06 0.00
274_R 122_Y 0.84 0.06 0.00
18_F 7_F 0.84 0.06 0.00
195_I 155_K 0.84 0.06 0.00
50_L 130_H 0.84 0.06 0.00
134_F 249_G 0.84 0.06 0.00
69_A 38_K 0.84 0.06 0.00
78_K 82_K 0.84 0.06 0.00
123_E 86_E 0.83 0.06 0.00
209_S 195_S 0.83 0.06 0.00
193_E 192_D 0.83 0.06 0.00
229_D 56_E 0.83 0.06 0.00
270_R 200_L 0.83 0.06 0.00
96_V 148_I 0.83 0.06 0.00
96_V 138_I 0.83 0.06 0.00
136_E 124_G 0.83 0.06 0.00
206_D 152_G 0.83 0.06 0.00
272_I 127_R 0.82 0.06 0.00
148_K 37_V 0.82 0.06 0.00
208_W 149_G 0.82 0.06 0.00
67_E 85_M 0.82 0.06 0.00
83_N 61_L 0.82 0.06 0.00
108_Y 146_V 0.82 0.06 0.00
266_R 130_H 0.82 0.06 0.00
128_L 83_L 0.82 0.06 0.00
246_P 245_P 0.82 0.06 0.00
170_D 192_D 0.82 0.06 0.00
193_E 137_N 0.81 0.06 0.00
246_P 228_Q 0.81 0.06 0.00
68_A 152_G 0.81 0.06 0.00
140_L 151_F 0.81 0.06 0.00
70_S 147_K 0.81 0.06 0.00
38_V 234_L 0.81 0.06 0.00
103_G 200_L 0.81 0.06 0.00
122_L 270_P 0.80 0.06 0.00
274_R 61_L 0.80 0.06 0.00
130_W 88_L 0.80 0.06 0.00
71_M 201_Y 0.80 0.06 0.00
212_T 177_Y 0.80 0.06 0.00
67_E 95_D 0.80 0.06 0.00
171_P 180_E 0.80 0.06 0.00
22_L 152_G 0.80 0.06 0.00
191_P 130_H 0.80 0.06 0.00
23_G 182_L 0.80 0.06 0.00
67_E 97_L 0.80 0.06 0.00
170_D 134_A 0.80 0.06 0.00
191_P 137_N 0.80 0.06 0.00
268_S 6_K 0.80 0.06 0.00
250_E 57_I 0.79 0.06 0.00
98_E 66_I 0.79 0.06 0.00
191_P 103_R 0.79 0.06 0.00
225_L 277_L 0.79 0.06 0.00
75_L 269_R 0.79 0.06 0.00
186_R 93_L 0.79 0.06 0.00
21_S 61_L 0.79 0.06 0.00
140_L 266_V 0.79 0.06 0.00
265_F 140_V 0.79 0.06 0.00
91_D 168_E 0.79 0.06 0.00
63_E 154_T 0.79 0.06 0.00
96_V 55_I 0.79 0.06 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)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.232), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
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