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OPENSEQ.org
proteasome ab6
Genes: A B A+B
Length: 244 202 438
Sequences: 2994 3744 2991
Seq/Len: 12.27 18.53 6.83
MirrorTree (Pazo et al. 2001) 0.98
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.05 6.71
2 0.05 0.06 6.71
5 0.07 0.07 6.71
10 0.08 0.08 6.71
20 0.09 0.09 6.71
100 0.13 0.13 6.71
∞ 0.21 0.18 6.71
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
144_E 105_P 4.69 1.00 1.00
184_K 145_E 4.43 1.00 1.00
44_K 9_D 4.42 1.00 1.00
222_E 182_S 4.36 1.00 1.00
191_E 150_E 4.36 1.00 1.00
195_E 154_Q 4.33 1.00 1.00
146_Q 107_E 4.33 1.00 1.00
189_T 148_T 4.30 1.00 1.00
107_E 73_P 4.28 1.00 1.00
187_D 146_G 4.24 1.00 1.00
73_E 39_D 4.18 1.00 1.00
221_V 181_E 4.10 1.00 1.00
70_K 36_P 4.07 1.00 1.00
194_V 153_L 3.98 1.00 1.00
190_F 149_K 3.97 1.00 1.00
183_K 144_R 3.89 1.00 1.00
111_D 77_H 3.88 1.00 1.00
192_Q 151_E 3.86 1.00 1.00
142_I 103_W 3.83 1.00 1.00
216_V 176_L 3.79 1.00 1.00
220_T 180_A 3.79 1.00 1.00
103_K 69_E 3.77 1.00 1.00
105_G 71_N 3.72 1.00 1.00
101_K 67_S 3.69 1.00 1.00
199_T 158_N 3.69 1.00 1.00
77_C 43_C 3.68 1.00 1.00
188_W 147_M 3.67 1.00 1.00
42_R 7_Q 3.65 1.00 1.00
139_L 100_I 3.63 1.00 1.00
95_Y 61_Y 3.62 1.00 1.00
123_V 89_R 3.62 1.00 1.00
117_I 83_F 3.61 1.00 1.00
75_I 41_I 3.60 1.00 1.00
120_I 86_M 3.58 1.00 1.00
163_K 124_S 3.58 1.00 1.00
181_K 142_T 3.53 1.00 1.00
91_Q 57_D 3.52 1.00 1.00
45_D 10_G 3.52 1.00 1.00
74_N 40_R 3.51 1.00 1.00
149_Q 110_Q 3.50 1.00 1.00
115_K 81_S 3.50 1.00 1.00
218_V 178_A 3.49 1.00 1.00
223_N 183_G 3.49 1.00 1.00
41_V 6_V 3.47 1.00 1.00
92_R 58_A 3.47 1.00 1.00
230_T 190_L 3.46 1.00 1.00
232_A 192_D 3.46 1.00 1.00
165_T 126_A 3.46 1.00 1.00
202_S 161_A 3.46 1.00 1.00
108_I 74_P 3.45 1.00 1.00
198_I 157_A 3.44 1.00 1.00
71_I 37_I 3.43 1.00 1.00
110_V 76_V 3.42 1.00 1.00
109_P 75_L 3.41 1.00 1.00
68_L 34_L 3.40 1.00 1.00
160_C 121_V 3.40 1.00 1.00
214_I 174_I 3.37 1.00 1.00
39_V 4_M 3.34 1.00 1.00
106_Y 72_E 3.33 1.00 1.00
90_V 56_A 3.32 1.00 1.00
112_M 78_T 3.32 1.00 1.00
64_T 30_V 3.31 1.00 1.00
119_D 85_E 3.30 1.00 1.00
159_Y 120_M 3.29 1.00 1.00
49_I 14_L 3.29 1.00 1.00
116_R 82_L 3.27 1.00 1.00
180_K 141_A 3.26 1.00 1.00
219_V 179_I 3.25 1.00 1.00
88_S 54_A 3.24 1.00 1.00
102_Y 68_I 3.24 1.00 1.00
99_N 65_F 3.24 1.00 1.00
69_F 35_T 3.24 1.00 1.00
55_V 20_T 3.20 1.00 1.00
56_P 21_T 3.20 1.00 1.00
172_T 133_S 3.20 1.00 1.00
182_V 143_Y 3.19 1.00 1.00
66_T 32_D 3.19 1.00 1.00
217_G 177_A 3.18 1.00 1.00
98_A 64_G 3.18 1.00 1.00
161_G 122_R 3.18 1.00 1.00
177_F 138_Y 3.18 1.00 1.00
151_Y 112_Y 3.16 1.00 1.00
231_E 191_G 3.13 1.00 1.00
140_I 101_A 3.13 1.00 1.00
228_I 188_V 3.13 1.00 1.00
197_A 156_T 3.11 1.00 1.00
97_A 63_L 3.08 1.00 1.00
62_S 28_N 3.07 1.00 1.00
203_T 162_L 3.07 1.00 1.00
48_V 13_V 3.07 1.00 1.00
200_C 159_A 3.06 1.00 1.00
229_L 189_L 3.04 1.00 1.00
153_C 114_V 3.03 1.00 1.00
166_A 127_I 3.00 1.00 1.00
38_S 3_I 2.99 1.00 1.00
137_M 98_I 2.99 1.00 1.00
236_A 196_K 2.99 1.00 1.00
63_S 29_R 2.99 1.00 1.00
173_E 134_Y 2.99 1.00 1.00
96_E 62_Q 2.98 1.00 1.00
235_D 195_P 2.98 1.00 1.00
58_K 24_S 2.96 1.00 1.00
51_T 16_A 2.96 1.00 1.00
175_T 136_Y 2.96 1.00 1.00
114_C 80_A 2.96 1.00 1.00
147_G 108_G 2.95 1.00 1.00
135_C 96_A 2.95 1.00 1.00
65_V 31_T 2.95 1.00 1.00
167_A 128_G 2.94 1.00 1.00
47_A 12_V 2.93 1.00 1.00
94_R 60_T 2.92 1.00 1.00
118_A 84_K 2.91 1.00 1.00
158_Y 119_M 2.91 1.00 1.00
212_S 172_G 2.89 1.00 1.00
171_Q 132_S 2.89 1.00 1.00
57_D 22_T 2.88 1.00 1.00
152_K 113_S 2.88 1.00 1.00
78_V 44_C 2.87 1.00 1.00
234_I 194_I 2.86 1.00 1.00
148_P 109_G 2.86 1.00 1.00
93_A 59_V 2.85 1.00 1.00
205_L 164_M 2.85 1.00 1.00
43_G 8_F 2.84 1.00 1.00
100_W 66_H 2.84 1.00 1.00
72_T 38_H 2.81 1.00 1.00
76_G 42_F 2.81 1.00 1.00
138_I 99_I 2.80 1.00 1.00
233_E 193_Q 2.78 1.00 1.00
113_L 79_A 2.78 1.00 1.00
104_Y 70_L 2.78 1.00 1.00
206_S 165_E 2.77 1.00 1.00
50_V 15_G 2.76 1.00 1.00
196_T 155_F 2.75 1.00 1.00
193_T 152_C 2.73 1.00 1.00
89_Q 55_V 2.73 1.00 1.00
79_M 45_R 2.72 1.00 1.00
239_V 199_V 2.69 1.00 1.00
121_S 87_C 2.66 1.00 1.00
176_S 137_G 2.66 1.00 1.00
60_L 26_I 2.62 1.00 1.00
61_D 27_A 2.60 1.00 1.00
227_R 187_Q 2.60 1.00 1.00
83_T 49_A 2.59 1.00 1.00
204_V 163_A 2.58 1.00 1.00
145_E 106_Q 2.57 1.00 1.00
201_L 160_L 2.57 1.00 1.00
213_E 173_V 2.55 1.00 1.00
150_V 111_V 2.53 1.00 1.00
86_S 52_T 2.53 1.00 1.00
237_H 197_F 2.52 1.00 1.00
80_T 46_S 2.51 1.00 1.00
84_A 50_A 2.50 1.00 1.00
53_K 18_S 2.46 1.00 1.00
225_K 185_E 2.45 1.00 1.00
136_C 97_G 2.44 1.00 1.00
174_S 135_I 2.44 1.00 1.00
133_L 94_L 2.41 1.00 1.00
162_F 123_Q 2.34 1.00 1.00
124_Y 90_Y 2.34 1.00 1.00
82_M 48_S 2.33 1.00 1.00
215_E 175_R 2.32 1.00 1.00
87_R 53_Q 2.32 1.00 1.00
207_I 166_R 2.29 1.00 1.00
164_A 125_F 2.27 1.00 0.99
178_L 139_V 2.26 1.00 0.99
169_V 130_S 2.25 1.00 0.99
240_A 200_A 2.13 1.00 0.99
40_A 5_A 2.11 1.00 0.99
143_D 104_D 2.10 1.00 0.99
59_L 25_Y 2.09 1.00 0.99
238_L 198_A 2.01 1.00 0.99
224_P 184_V 1.96 1.00 0.99
46_C 11_G 1.96 1.00 0.99
54_K 19_R 1.94 1.00 0.99
156_A 117_G 1.93 1.00 0.99
170_K 131_G 1.92 1.00 0.98
155_P 116_M 1.89 1.00 0.98
37_T 2_T 1.78 1.00 0.98
209_F 168_G 1.76 1.00 0.97
154_D 115_P 1.73 1.00 0.97
134_G 95_M 1.71 1.00 0.97
226_F 186_R 1.71 1.00 0.97
210_K 170_S 1.59 1.00 0.95
179_E 140_D 1.55 0.99 0.94
241_L 201_T 1.52 0.99 0.94
126_Q 92_E 1.51 0.99 0.93
122_Q 88_Y 1.40 0.99 0.90
211_P 171_G 1.37 0.98 0.89
52_Q 17_D 1.36 0.98 0.88
208_D 167_D 1.32 0.98 0.87
141_G 102_G 1.31 0.98 0.86
208_D 168_G 1.28 0.97 0.84
211_P 170_S 1.25 0.97 0.83
125_T 91_R 1.19 0.95 0.78
210_K 169_S 1.14 0.94 0.74
67_H 33_K 1.12 0.93 0.73
209_F 169_S 1.03 0.88 0.64
132_P 93_D 0.83 0.68 0.38
35_G 1_T 0.77 0.60 0.31
157_G 118_G 0.75 0.57 0.29
227_R 185_E 0.75 0.57 0.29
225_K 184_V 0.75 0.57 0.29
85_D 51_D 0.66 0.42 0.19
128_A 90_Y 0.64 0.40 0.18
127_N 93_D 0.64 0.40 0.18
227_R 186_R 0.63 0.38 0.17
226_F 184_V 0.57 0.30 0.12
228_I 186_R 0.52 0.23 0.09
208_D 169_S 0.43 0.16 0.05
226_F 185_E 0.42 0.15 0.05
192_Q 148_T 0.41 0.14 0.04
189_T 151_E 0.40 0.13 0.04
50_V 156_T 0.35 0.10 0.03
197_A 15_G 0.35 0.10 0.03
227_R 193_Q 0.33 0.09 0.02
45_D 9_D 0.29 0.07 0.02
239_V 195_P 0.28 0.07 0.02
44_K 10_G 0.28 0.07 0.01
161_G 110_Q 0.26 0.06 0.01
130_M 92_E 0.26 0.06 0.01
235_D 199_V 0.26 0.06 0.01
40_A 111_V 0.26 0.06 0.01
146_Q 108_G 0.26 0.06 0.01
150_V 5_A 0.25 0.06 0.01
44_K 146_G 0.25 0.06 0.01
193_T 8_F 0.25 0.06 0.01
43_G 152_C 0.24 0.05 0.01
149_Q 122_R 0.24 0.05 0.01
43_G 10_G 0.24 0.05 0.01
45_D 8_F 0.24 0.05 0.01
49_I 5_A 0.24 0.05 0.01
223_N 180_A 0.23 0.05 0.01
141_G 76_V 0.23 0.05 0.01
46_C 8_F 0.23 0.05 0.01
40_A 14_L 0.23 0.05 0.01
43_G 11_G 0.22 0.05 0.01
110_V 102_G 0.22 0.05 0.01
187_D 9_D 0.22 0.05 0.01
38_S 44_C 0.22 0.05 0.01
147_G 107_E 0.21 0.05 0.01
81_G 47_G 0.21 0.04 0.01
143_D 108_G 0.21 0.04 0.01
49_I 101_A 0.21 0.04 0.01
122_Q 91_R 0.21 0.04 0.01
74_N 38_H 0.21 0.04 0.01
72_T 40_R 0.21 0.04 0.01
78_V 3_I 0.21 0.04 0.01
147_G 104_D 0.21 0.04 0.01
101_K 38_H 0.21 0.04 0.01
220_T 183_G 0.20 0.04 0.01
140_I 14_L 0.20 0.04 0.01
72_T 67_S 0.20 0.04 0.01
125_T 88_Y 0.20 0.04 0.01
149_Q 108_G 0.20 0.04 0.01
225_K 186_R 0.20 0.04 0.01
147_G 110_Q 0.20 0.04 0.01
220_T 182_S 0.20 0.04 0.01
233_E 187_Q 0.20 0.04 0.01
222_E 180_A 0.20 0.04 0.01
122_Q 92_E 0.19 0.04 0.01
190_F 180_A 0.19 0.04 0.01
129_E 91_R 0.19 0.04 0.01
75_I 76_V 0.19 0.04 0.01
226_F 42_F 0.19 0.04 0.01
110_V 41_I 0.19 0.04 0.01
74_N 73_P 0.19 0.04 0.01
221_V 182_S 0.19 0.04 0.01
107_E 40_R 0.18 0.04 0.01
220_T 149_K 0.18 0.04 0.01
41_V 156_T 0.18 0.04 0.01
145_E 108_G 0.18 0.04 0.01
197_A 6_V 0.18 0.04 0.01
126_Q 88_Y 0.18 0.04 0.01
181_K 158_N 0.18 0.04 0.01
223_N 184_V 0.17 0.04 0.01
230_T 192_D 0.17 0.04 0.01
199_T 142_T 0.17 0.04 0.01
232_A 190_L 0.17 0.03 0.01
97_A 79_A 0.16 0.03 0.00
161_G 7_Q 0.16 0.03 0.00
163_K 145_E 0.16 0.03 0.00
75_I 79_A 0.16 0.03 0.00
113_L 63_L 0.16 0.03 0.00
113_L 41_I 0.15 0.03 0.00
125_T 92_E 0.15 0.03 0.00
101_K 73_P 0.15 0.03 0.00
222_E 183_G 0.15 0.03 0.00
126_Q 91_R 0.15 0.03 0.00
37_T 135_I 0.15 0.03 0.00
62_S 27_A 0.15 0.03 0.00
107_E 67_S 0.15 0.03 0.00
223_N 182_S 0.15 0.03 0.00
42_R 122_R 0.15 0.03 0.00
184_K 124_S 0.15 0.03 0.00
183_K 151_E 0.15 0.03 0.00
147_G 106_Q 0.15 0.03 0.00
47_A 101_A 0.15 0.03 0.00
140_I 12_V 0.14 0.03 0.00
233_E 190_L 0.14 0.03 0.00
185_K 146_G 0.14 0.03 0.00
222_E 181_E 0.14 0.03 0.00
240_A 154_Q 0.14 0.03 0.00
226_F 177_A 0.14 0.03 0.00
187_D 144_R 0.14 0.03 0.00
224_P 182_S 0.14 0.03 0.00
240_A 196_K 0.14 0.03 0.00
170_K 2_T 0.14 0.03 0.00
190_F 8_F 0.14 0.03 0.00
58_K 26_I 0.14 0.03 0.00
37_T 131_G 0.14 0.03 0.00
211_P 195_P 0.14 0.03 0.00
136_C 116_M 0.14 0.03 0.00
192_Q 144_R 0.14 0.03 0.00
151_Y 122_R 0.14 0.03 0.00
220_T 185_E 0.14 0.03 0.00
183_K 146_G 0.13 0.03 0.00
155_P 97_G 0.13 0.03 0.00
156_A 116_M 0.13 0.03 0.00
223_N 185_E 0.13 0.03 0.00
190_F 153_L 0.13 0.03 0.00
43_G 149_K 0.13 0.03 0.00
189_T 150_E 0.13 0.03 0.00
237_H 196_K 0.13 0.03 0.00
187_D 147_M 0.13 0.03 0.00
86_S 45_R 0.13 0.03 0.00
41_V 152_C 0.13 0.03 0.00
230_T 193_Q 0.13 0.03 0.00
193_T 6_V 0.13 0.03 0.00
79_M 52_T 0.13 0.03 0.00
63_S 28_N 0.13 0.03 0.00
21_L 19_R 0.13 0.03 0.00
147_G 105_P 0.13 0.03 0.00
194_V 149_K 0.13 0.03 0.00
161_G 112_Y 0.13 0.03 0.00
236_A 197_F 0.13 0.03 0.00
70_K 39_D 0.12 0.03 0.00
34_G 33_K 0.12 0.03 0.00
154_D 117_G 0.12 0.03 0.00
156_A 115_P 0.12 0.03 0.00
155_P 117_G 0.12 0.03 0.00
168_G 129_G 0.12 0.03 0.00
96_E 82_L 0.12 0.03 0.00
127_N 89_R 0.12 0.03 0.00
131_R 95_M 0.12 0.03 0.00
215_E 18_S 0.12 0.03 0.00
116_R 62_Q 0.12 0.03 0.00
28_F 115_P 0.12 0.03 0.00
194_V 176_L 0.12 0.03 0.00
191_E 148_T 0.12 0.03 0.00
210_K 172_G 0.12 0.03 0.00
188_W 146_G 0.12 0.03 0.00
236_A 200_A 0.12 0.03 0.00
108_I 73_P 0.12 0.03 0.00
153_C 87_C 0.12 0.03 0.00
53_K 175_R 0.12 0.03 0.00
129_E 88_Y 0.12 0.03 0.00
190_F 10_G 0.12 0.03 0.00
195_E 200_A 0.12 0.03 0.00
58_K 23_G 0.12 0.03 0.00
45_D 11_G 0.12 0.03 0.00
61_D 26_I 0.12 0.03 0.00
73_E 38_H 0.12 0.03 0.00
144_E 108_G 0.12 0.03 0.00
96_E 65_F 0.12 0.03 0.00
239_V 196_K 0.12 0.03 0.00
72_T 73_P 0.12 0.03 0.00
46_C 10_G 0.12 0.03 0.00
182_V 144_R 0.12 0.03 0.00
148_P 7_Q 0.12 0.03 0.00
42_R 109_G 0.12 0.03 0.00
183_K 143_Y 0.12 0.03 0.00
196_T 142_T 0.12 0.03 0.00
93_A 83_F 0.12 0.03 0.00
107_E 38_H 0.12 0.03 0.00
134_G 91_R 0.12 0.03 0.00
44_K 148_T 0.12 0.03 0.00
142_I 181_E 0.12 0.03 0.00
213_E 172_G 0.12 0.03 0.00
45_D 149_K 0.12 0.03 0.00
114_C 75_L 0.12 0.03 0.00
158_Y 120_M 0.12 0.03 0.00
121_S 114_V 0.12 0.03 0.00
143_D 110_Q 0.11 0.03 0.00
28_F 119_M 0.11 0.03 0.00
73_E 36_P 0.11 0.03 0.00
138_I 126_A 0.11 0.03 0.00
99_N 62_Q 0.11 0.03 0.00
216_V 153_L 0.11 0.03 0.00
107_E 74_P 0.11 0.03 0.00
189_T 9_D 0.11 0.03 0.00
181_K 138_Y 0.11 0.03 0.00
131_R 91_R 0.11 0.03 0.00
196_T 147_M 0.11 0.03 0.00
72_T 39_D 0.11 0.03 0.00
236_A 199_V 0.11 0.03 0.00
129_E 92_E 0.11 0.03 0.00
174_S 2_T 0.11 0.03 0.00
241_L 200_A 0.11 0.03 0.00
165_T 99_I 0.11 0.02 0.00
200_C 138_Y 0.11 0.02 0.00
224_P 183_G 0.11 0.02 0.00
177_F 142_T 0.11 0.02 0.00
47_A 11_G 0.11 0.02 0.00
114_C 120_M 0.11 0.02 0.00
149_Q 104_D 0.11 0.02 0.00
130_M 90_Y 0.11 0.02 0.00
85_D 93_D 0.11 0.02 0.00
96_E 58_A 0.11 0.02 0.00
92_R 62_Q 0.11 0.02 0.00
126_Q 93_D 0.11 0.02 0.00
46_C 12_V 0.11 0.02 0.00
177_F 159_A 0.11 0.02 0.00
50_V 176_L 0.11 0.02 0.00
188_W 155_F 0.11 0.02 0.00
133_L 90_Y 0.11 0.02 0.00
129_E 102_G 0.11 0.02 0.00
151_Y 110_Q 0.11 0.02 0.00
217_G 42_F 0.10 0.02 0.00
166_A 139_V 0.10 0.02 0.00
178_L 127_I 0.10 0.02 0.00
61_D 22_T 0.10 0.02 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 = 0.118), 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).
ID Seq/Len Name Options I_Prob Status
2123 6.83 proteasome ab6 Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done
2122 0 proteasome ab6 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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