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OPENSEQ.org
test
Genes: A B A+B
Length: 307 252 555
Sequences: 3060 2737 2522
Seq/Len: 9.97 10.86 4.54
MirrorTree (Pazo et al. 2001) 0.91
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 0.01 0.01 4.46
2 0.01 0.01 4.48
5 0.01 0.01 4.50
10 0.02 0.02 4.51
20 0.02 0.02 4.51
100 0.04 0.04 4.52
∞ 0.09 0.08 4.55
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
175_S 171_A 3.69 1.00 1.00
306_K 240_D 3.54 1.00 1.00
104_L 137_A 2.94 1.00 1.00
136_K 220_E 2.82 1.00 1.00
100_R 137_A 2.65 1.00 1.00
123_E 225_R 1.71 0.99 0.96
106_D 103_K 1.68 0.99 0.96
138_K 220_E 1.61 0.99 0.95
109_V 130_A 1.59 0.99 0.94
274_V 242_L 1.58 0.99 0.94
100_R 143_Q 1.54 0.98 0.93
103_A 134_M 1.52 0.98 0.93
134_V 223_S 1.45 0.98 0.91
179_D 168_Q 1.36 0.96 0.87
302_E 239_V 1.29 0.94 0.84
178_A 169_T 1.25 0.93 0.81
69_A 143_Q 1.22 0.92 0.79
173_L 140_G 1.18 0.90 0.76
173_L 142_A 1.18 0.90 0.75
306_K 243_V 1.16 0.89 0.74
108_M 219_L 1.12 0.86 0.70
290_Y 242_L 1.07 0.83 0.65
177_V 171_A 1.05 0.82 0.64
108_M 97_E 1.01 0.78 0.59
291_G 235_K 0.99 0.76 0.57
103_A 138_I 0.98 0.74 0.55
131_A 224_V 0.98 0.74 0.55
173_L 173_S 0.95 0.71 0.51
292_L 239_V 0.95 0.71 0.51
104_L 140_G 0.93 0.69 0.48
303_L 243_V 0.92 0.67 0.47
74_A 140_G 0.88 0.63 0.42
131_A 19_V 0.86 0.60 0.40
99_P 129_N 0.86 0.60 0.39
175_S 173_S 0.85 0.59 0.39
291_G 198_A 0.85 0.59 0.38
136_K 222_V 0.85 0.58 0.38
96_N 143_Q 0.84 0.57 0.37
111_S 130_A 0.82 0.55 0.35
303_L 239_V 0.80 0.52 0.33
111_S 128_M 0.79 0.50 0.31
96_N 145_T 0.76 0.46 0.27
180_E 169_T 0.75 0.46 0.27
139_D 218_R 0.75 0.45 0.27
299_V 239_V 0.75 0.44 0.26
177_V 169_T 0.74 0.44 0.26
174_S 170_I 0.74 0.44 0.26
99_P 36_N 0.74 0.44 0.26
294_G 116_L 0.74 0.44 0.26
273_I 230_R 0.74 0.43 0.25
106_D 138_I 0.73 0.42 0.24
132_I 225_R 0.72 0.41 0.24
302_E 240_D 0.72 0.41 0.24
229_V 127_D 0.72 0.41 0.24
135_V 219_L 0.72 0.41 0.23
272_V 249_A 0.72 0.41 0.23
292_L 236_V 0.71 0.40 0.23
226_R 44_E 0.70 0.39 0.22
108_M 95_D 0.69 0.37 0.21
243_T 180_A 0.68 0.36 0.20
125_P 127_D 0.67 0.35 0.19
134_V 225_R 0.67 0.34 0.19
116_I 68_A 0.67 0.34 0.18
274_V 246_L 0.66 0.34 0.18
106_D 218_R 0.66 0.33 0.18
278_K 233_G 0.66 0.33 0.18
113_V 101_V 0.66 0.33 0.18
94_A 42_A 0.66 0.33 0.18
233_Y 6_P 0.65 0.32 0.17
243_T 14_N 0.65 0.32 0.17
109_V 128_M 0.65 0.32 0.17
177_V 158_K 0.64 0.31 0.16
106_D 99_L 0.64 0.30 0.16
7_E 227_P 0.63 0.30 0.15
99_P 144_A 0.63 0.29 0.15
271_K 249_A 0.62 0.29 0.15
149_A 224_V 0.62 0.28 0.14
73_A 137_A 0.62 0.28 0.14
289_D 231_K 0.62 0.28 0.14
264_L 77_A 0.62 0.28 0.14
217_K 243_V 0.61 0.28 0.14
7_E 166_G 0.61 0.28 0.14
110_L 219_L 0.61 0.28 0.14
280_E 168_Q 0.61 0.27 0.14
201_G 58_I 0.61 0.27 0.14
300_V 105_L 0.61 0.27 0.14
194_R 211_Y 0.60 0.27 0.13
175_S 156_K 0.60 0.27 0.13
121_T 222_V 0.60 0.26 0.13
236_N 196_M 0.60 0.26 0.13
147_R 36_N 0.60 0.26 0.13
305_G 244_G 0.60 0.26 0.13
127_Y 126_N 0.59 0.26 0.12
128_A 182_L 0.59 0.26 0.12
281_E 233_G 0.59 0.25 0.12
56_V 106_A 0.59 0.25 0.12
285_F 198_A 0.59 0.25 0.12
195_V 118_I 0.59 0.25 0.12
213_E 216_A 0.58 0.25 0.12
69_A 137_A 0.58 0.24 0.12
102_A 19_V 0.58 0.24 0.12
124_R 127_D 0.58 0.24 0.12
283_P 243_V 0.58 0.24 0.11
280_E 235_K 0.58 0.24 0.11
279_D 199_K 0.58 0.24 0.11
62_A 209_A 0.58 0.24 0.11
225_S 195_I 0.58 0.24 0.11
174_S 172_V 0.57 0.23 0.11
195_V 131_T 0.57 0.23 0.11
4_L 235_K 0.57 0.23 0.11
69_A 170_I 0.57 0.23 0.11
271_K 202_P 0.57 0.23 0.11
101_V 220_E 0.57 0.23 0.11
216_D 61_V 0.57 0.23 0.11
76_I 111_A 0.57 0.23 0.11
176_W 170_I 0.57 0.23 0.11
216_D 244_G 0.57 0.23 0.11
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
7247 4.26 1EFP_A_B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
3656 4.54 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
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