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OPENSEQ.org
1efp_A_B
Genes: A B A+B
Length: 307 246 551
Sequences: 3025 2651 2416
Seq/Len: 9.85 10.78 4.38
MirrorTree (Pazo et al. 2001) 0.90
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 0.01 4.31
2 0.01 0.01 4.33
5 0.01 0.01 4.35
10 0.01 0.01 4.37
20 0.02 0.02 4.37
100 0.03 0.03 4.37
∞ 0.09 0.08 4.41
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 4.29 1.00 1.00
104_L 137_A 3.29 1.00 1.00
100_R 137_A 2.96 1.00 1.00
136_K 220_E 2.72 1.00 1.00
306_K 240_D 2.30 1.00 0.99
106_D 103_K 2.06 1.00 0.99
109_V 130_A 1.77 1.00 0.97
123_E 225_R 1.75 0.99 0.97
100_R 143_Q 1.73 0.99 0.97
179_D 168_Q 1.73 0.99 0.97
103_A 134_M 1.72 0.99 0.96
134_V 223_S 1.64 0.99 0.95
178_A 169_T 1.54 0.98 0.93
173_L 140_G 1.52 0.98 0.93
306_K 243_V 1.36 0.96 0.87
69_A 143_Q 1.32 0.95 0.85
173_L 142_A 1.31 0.94 0.84
177_V 169_T 1.30 0.94 0.84
274_V 242_L 1.21 0.91 0.77
292_L 236_V 1.19 0.90 0.76
103_A 138_I 1.17 0.89 0.75
177_V 171_A 1.16 0.88 0.73
290_Y 242_L 1.11 0.85 0.69
108_M 97_E 1.10 0.85 0.68
292_L 239_V 1.04 0.80 0.62
74_A 140_G 1.03 0.79 0.61
174_S 170_I 1.00 0.75 0.57
96_N 143_Q 0.99 0.75 0.56
131_A 19_V 0.99 0.75 0.56
131_A 224_V 0.98 0.74 0.55
136_K 222_V 0.97 0.73 0.54
104_L 140_G 0.96 0.71 0.52
99_P 129_N 0.95 0.70 0.51
111_S 130_A 0.94 0.69 0.49
111_S 128_M 0.93 0.68 0.49
201_G 58_I 0.88 0.61 0.41
106_D 138_I 0.87 0.60 0.41
177_V 158_K 0.85 0.58 0.39
138_K 220_E 0.85 0.58 0.39
96_N 145_T 0.84 0.57 0.37
294_G 116_L 0.84 0.56 0.36
194_R 211_Y 0.83 0.55 0.35
127_Y 25_G 0.82 0.54 0.35
175_S 173_S 0.81 0.53 0.34
180_E 169_T 0.79 0.49 0.30
121_T 222_V 0.78 0.48 0.30
173_L 173_S 0.78 0.48 0.29
211_I 17_A 0.77 0.46 0.28
99_P 36_N 0.76 0.46 0.28
69_A 170_I 0.76 0.45 0.28
132_I 225_R 0.74 0.43 0.26
109_V 128_M 0.74 0.42 0.25
99_P 144_A 0.73 0.42 0.25
243_T 180_A 0.73 0.42 0.25
291_G 198_A 0.73 0.41 0.24
147_R 36_N 0.72 0.40 0.23
73_A 137_A 0.71 0.39 0.22
93_D 170_I 0.71 0.38 0.22
299_V 157_A 0.69 0.35 0.20
243_T 14_N 0.69 0.35 0.20
94_A 42_A 0.69 0.35 0.20
273_I 230_R 0.68 0.35 0.20
108_M 219_L 0.68 0.35 0.19
264_L 77_A 0.68 0.35 0.19
274_V 160_T 0.68 0.34 0.19
229_V 127_D 0.67 0.34 0.19
271_K 202_P 0.67 0.34 0.18
279_D 199_K 0.67 0.33 0.18
170_D 142_A 0.67 0.33 0.18
145_T 24_S 0.67 0.33 0.18
195_V 118_I 0.66 0.32 0.17
134_V 222_V 0.66 0.32 0.17
303_L 243_V 0.65 0.31 0.17
195_V 131_T 0.65 0.31 0.16
240_V 182_L 0.65 0.30 0.16
146_I 6_P 0.64 0.30 0.16
276_I 222_V 0.64 0.30 0.16
108_M 218_R 0.64 0.30 0.15
125_P 127_D 0.64 0.29 0.15
233_Y 6_P 0.63 0.29 0.15
69_A 137_A 0.63 0.29 0.15
106_D 99_L 0.63 0.29 0.15
180_E 158_K 0.63 0.29 0.15
101_V 220_E 0.63 0.29 0.15
230_D 188_R 0.63 0.29 0.15
226_R 44_E 0.62 0.28 0.15
133_Q 224_V 0.62 0.28 0.14
124_R 127_D 0.62 0.28 0.14
280_E 168_Q 0.62 0.28 0.14
300_V 105_L 0.62 0.28 0.14
278_K 199_K 0.61 0.27 0.14
225_S 195_I 0.61 0.27 0.14
95_K 146_F 0.61 0.27 0.14
113_V 101_V 0.61 0.27 0.14
134_V 225_R 0.61 0.27 0.14
180_E 160_T 0.61 0.27 0.13
151_F 162_E 0.61 0.27 0.13
145_T 130_A 0.60 0.25 0.13
149_A 224_V 0.60 0.25 0.13
64_Y 139_L 0.60 0.25 0.12
276_I 61_V 0.59 0.25 0.12
74_A 101_V 0.59 0.25 0.12
236_N 135_L 0.59 0.25 0.12
135_V 128_M 0.59 0.24 0.12
3_L 2_K 0.59 0.24 0.12
99_P 130_A 0.59 0.24 0.12
38_A 86_V 0.58 0.24 0.12
210_I 71_T 0.58 0.24 0.12
278_K 29_A 0.58 0.24 0.12
280_E 118_I 0.58 0.24 0.12
283_P 243_V 0.58 0.24 0.12
3_L 43_V 0.58 0.23 0.11
53_V 101_V 0.58 0.23 0.11
90_A 28_L 0.58 0.23 0.11
21_A 88_A 0.58 0.23 0.11
242_Q 124_I 0.58 0.23 0.11
286_Q 190_A 0.58 0.23 0.11
82_D 223_S 0.57 0.23 0.11
274_V 245_K 0.57 0.23 0.11
223_G 109_A 0.57 0.23 0.11
279_D 86_V 0.57 0.23 0.11
7_E 166_G 0.57 0.23 0.11
291_G 235_K 0.57 0.23 0.11
280_E 5_V 0.57 0.22 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
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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