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OPENSEQ.org
1efp_AB
Genes: A B A+B
Length: 307 246 549
Sequences: 2900 2559 2404
Seq/Len: 9.45 10.4 4.38
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 0.00 0.00 4.29
2 0.00 0.00 4.32
5 0.00 0.00 4.33
10 0.01 0.01 4.35
20 0.01 0.01 4.35
100 0.02 0.02 4.35
∞ 0.06 0.05 4.39
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 3.78 1.00 1.00
104_L 137_A 2.87 1.00 1.00
136_K 220_E 2.79 1.00 1.00
100_R 137_A 2.64 1.00 1.00
306_K 240_D 2.24 1.00 0.99
123_E 225_R 1.81 1.00 0.97
138_K 220_E 1.73 0.99 0.97
106_D 103_K 1.70 0.99 0.96
134_V 223_S 1.58 0.99 0.94
109_V 130_A 1.57 0.99 0.94
103_A 134_M 1.54 0.98 0.93
302_E 240_D 1.53 0.98 0.93
100_R 143_Q 1.52 0.98 0.93
179_D 168_Q 1.34 0.95 0.86
306_K 244_G 1.29 0.94 0.83
178_A 169_T 1.27 0.93 0.82
69_A 143_Q 1.23 0.92 0.79
173_L 140_G 1.18 0.89 0.75
173_L 142_A 1.14 0.87 0.72
108_M 219_L 1.13 0.87 0.71
291_G 235_K 1.02 0.77 0.59
108_M 97_E 0.99 0.74 0.56
177_V 171_A 0.99 0.74 0.56
103_A 138_I 0.97 0.73 0.53
131_A 19_V 0.95 0.70 0.51
131_A 224_V 0.94 0.69 0.50
274_V 246_L 0.93 0.68 0.49
173_L 173_S 0.90 0.65 0.45
291_G 198_A 0.89 0.63 0.44
136_K 222_V 0.89 0.63 0.43
104_L 140_G 0.86 0.58 0.39
96_N 143_Q 0.84 0.56 0.37
111_S 128_M 0.82 0.54 0.35
74_A 140_G 0.82 0.54 0.34
99_P 129_N 0.82 0.53 0.34
139_D 218_R 0.82 0.53 0.34
111_S 130_A 0.81 0.53 0.34
273_I 230_R 0.81 0.52 0.34
135_V 219_L 0.81 0.52 0.33
177_V 169_T 0.81 0.52 0.33
175_S 173_S 0.81 0.52 0.33
292_L 236_V 0.81 0.52 0.33
180_E 169_T 0.80 0.51 0.32
299_V 239_V 0.77 0.46 0.28
106_D 138_I 0.75 0.44 0.26
96_N 145_T 0.73 0.41 0.24
294_G 242_L 0.72 0.40 0.23
73_A 137_A 0.70 0.38 0.21
294_G 116_L 0.70 0.37 0.21
125_P 127_D 0.70 0.37 0.21
226_R 44_E 0.69 0.36 0.20
280_E 235_K 0.69 0.36 0.20
292_L 239_V 0.69 0.36 0.20
108_M 95_D 0.69 0.36 0.20
243_T 14_N 0.69 0.35 0.20
229_V 127_D 0.68 0.35 0.19
99_P 36_N 0.68 0.35 0.19
121_T 222_V 0.68 0.34 0.19
132_I 225_R 0.67 0.33 0.18
109_V 128_M 0.66 0.32 0.17
116_I 68_A 0.65 0.32 0.17
271_K 202_P 0.65 0.31 0.16
194_R 211_Y 0.64 0.30 0.16
201_G 58_I 0.64 0.30 0.16
149_A 224_V 0.64 0.30 0.15
243_T 180_A 0.64 0.30 0.15
278_K 233_G 0.64 0.29 0.15
121_T 57_E 0.63 0.29 0.15
175_S 156_K 0.63 0.29 0.15
42_A 3_V 0.63 0.29 0.15
236_N 196_M 0.63 0.29 0.15
280_E 168_Q 0.63 0.28 0.15
134_V 225_R 0.63 0.28 0.15
113_V 101_V 0.62 0.28 0.14
174_S 170_I 0.62 0.28 0.14
106_D 99_L 0.62 0.28 0.14
300_V 105_L 0.62 0.28 0.14
177_V 158_K 0.62 0.28 0.14
298_S 238_S 0.62 0.28 0.14
264_L 77_A 0.62 0.28 0.14
43_A 150_V 0.61 0.27 0.14
92_T 164_D 0.61 0.27 0.14
285_F 198_A 0.61 0.26 0.13
99_P 144_A 0.61 0.26 0.13
131_A 17_A 0.60 0.26 0.13
180_E 167_L 0.60 0.26 0.13
94_A 42_A 0.60 0.26 0.13
101_V 220_E 0.60 0.26 0.13
128_A 182_L 0.60 0.25 0.13
70_E 19_V 0.60 0.25 0.13
281_E 233_G 0.60 0.25 0.13
307_L 111_A 0.59 0.25 0.12
118_D 178_V 0.59 0.25 0.12
110_L 219_L 0.59 0.24 0.12
233_Y 6_P 0.59 0.24 0.12
2_V 153_E 0.58 0.24 0.12
95_K 146_F 0.58 0.24 0.12
69_A 170_I 0.58 0.24 0.12
236_N 135_L 0.58 0.23 0.11
145_T 130_A 0.58 0.23 0.11
124_R 127_D 0.57 0.23 0.11
298_S 239_V 0.57 0.23 0.11
7_E 166_G 0.57 0.23 0.11
230_D 188_R 0.57 0.22 0.11
55_K 52_K 0.57 0.22 0.11
26_K 156_K 0.57 0.22 0.10
147_R 36_N 0.56 0.22 0.10
67_R 189_Y 0.56 0.22 0.10
195_V 131_T 0.56 0.22 0.10
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
9327 4.38 1efp_A_B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
2066 4.38 1efp_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
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