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OPENSEQ.org
2a1t_1_R_S
Genes: A B A+B
Length: 333 255 566
Sequences: 3086 2620 2378
Seq/Len: 9.27 10.27 4.2
MirrorTree (Pazo et al. 2001) 0.91
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 4.01
2 0.01 0.01 4.02
5 0.01 0.01 4.05
10 0.01 0.01 4.04
20 0.02 0.01 4.04
100 0.03 0.03 4.07
∞ 0.09 0.08 4.12
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
198_E 174_R 4.31 1.00 1.00
126_K 140_G 3.25 1.00 1.00
158_K 223_S 3.20 1.00 1.00
122_R 140_G 2.89 1.00 1.00
329_I 243_E 2.30 1.00 0.99
128_E 106_R 2.06 1.00 0.99
297_V 245_L 1.89 1.00 0.98
131_P 133_Q 1.75 0.99 0.97
145_V 228_E 1.73 0.99 0.96
125_A 137_M 1.71 0.99 0.96
156_T 226_S 1.70 0.99 0.96
122_R 146_Q 1.67 0.99 0.96
202_Q 171_E 1.66 0.99 0.96
196_I 143_D 1.48 0.97 0.91
201_D 172_T 1.47 0.97 0.91
329_I 246_V 1.46 0.97 0.91
196_I 145_P 1.38 0.96 0.88
89_P 146_Q 1.36 0.95 0.87
313_Y 245_L 1.26 0.93 0.81
200_L 172_T 1.23 0.91 0.79
333_K 250_K 1.20 0.90 0.77
200_L 174_R 1.19 0.89 0.76
125_A 141_F 1.11 0.84 0.69
130_A 100_G 1.11 0.84 0.68
315_I 242_T 1.10 0.83 0.68
160_D 223_S 1.09 0.83 0.67
315_I 239_V 1.09 0.83 0.67
153_A 22_V 1.04 0.79 0.61
94_P 143_D 1.04 0.78 0.61
153_A 227_V 1.02 0.77 0.59
126_K 143_D 1.02 0.76 0.58
118_N 146_Q 0.97 0.71 0.53
197_S 173_L 0.95 0.69 0.50
158_K 225_I 0.95 0.69 0.50
295_T 252_I 0.94 0.67 0.48
121_P 132_N 0.94 0.67 0.48
133_S 133_Q 0.93 0.67 0.48
333_K 247_A 0.91 0.65 0.46
133_S 131_C 0.88 0.60 0.41
128_E 141_F 0.87 0.59 0.40
203_K 172_T 0.86 0.58 0.39
121_P 39_N 0.84 0.55 0.37
143_T 225_I 0.83 0.54 0.35
317_A 119_L 0.82 0.53 0.34
326_M 246_V 0.81 0.52 0.33
234_L 20_I 0.80 0.50 0.32
196_I 176_K 0.80 0.50 0.32
217_V 214_L 0.80 0.49 0.31
118_N 148_T 0.80 0.49 0.31
294_K 252_I 0.78 0.47 0.29
149_Y 28_G 0.78 0.47 0.29
130_A 222_L 0.78 0.47 0.29
224_G 61_V 0.77 0.45 0.28
200_L 161_K 0.74 0.42 0.25
314_G 201_A 0.74 0.41 0.25
218_V 134_T 0.74 0.41 0.24
299_I 64_V 0.73 0.40 0.24
121_P 147_G 0.73 0.40 0.23
198_E 176_K 0.72 0.39 0.23
131_P 131_C 0.71 0.38 0.22
252_V 130_D 0.70 0.36 0.21
256_F 9_A 0.70 0.36 0.21
167_S 27_T 0.70 0.36 0.20
193_P 145_P 0.69 0.35 0.20
302_D 202_K 0.69 0.34 0.19
154_L 228_E 0.68 0.34 0.19
37_T 50_V 0.68 0.34 0.19
174_D 254_R 0.67 0.33 0.18
169_R 39_N 0.67 0.33 0.18
195_E 143_D 0.67 0.32 0.18
248_S 198_I 0.66 0.32 0.17
249_R 47_E 0.66 0.31 0.17
156_T 225_I 0.66 0.31 0.17
266_T 17_A 0.66 0.31 0.17
266_T 183_A 0.66 0.31 0.17
116_G 45_A 0.66 0.31 0.17
89_P 173_L 0.65 0.31 0.17
130_A 221_K 0.65 0.31 0.17
93_T 140_G 0.65 0.30 0.17
156_T 228_E 0.65 0.30 0.16
155_C 227_V 0.64 0.29 0.16
294_K 205_K 0.64 0.29 0.16
117_K 149_F 0.64 0.29 0.15
301_K 202_K 0.64 0.29 0.15
147_T 130_D 0.64 0.29 0.15
115_F 173_L 0.64 0.29 0.15
287_L 80_A 0.63 0.28 0.15
323_V 108_L 0.63 0.28 0.14
203_K 163_E 0.62 0.27 0.14
40_T 91_V 0.62 0.27 0.14
218_V 121_L 0.62 0.27 0.14
184_S 144_W 0.62 0.27 0.14
296_I 233_R 0.62 0.27 0.14
121_P 133_Q 0.62 0.27 0.14
218_V 247_A 0.61 0.26 0.14
168_V 9_A 0.61 0.26 0.13
303_P 121_L 0.61 0.26 0.13
161_E 223_S 0.61 0.26 0.13
333_K 246_V 0.61 0.26 0.13
271_A 167_D 0.61 0.26 0.13
323_V 76_R 0.61 0.26 0.13
128_E 102_L 0.60 0.25 0.13
297_V 163_E 0.60 0.25 0.13
171_T 227_V 0.60 0.25 0.13
146_R 130_D 0.60 0.25 0.12
112_A 31_T 0.60 0.25 0.12
97_L 143_D 0.60 0.25 0.12
253_D 191_R 0.60 0.24 0.12
251_A 89_V 0.60 0.24 0.12
303_P 171_E 0.60 0.24 0.12
253_D 41_F 0.60 0.24 0.12
112_A 130_D 0.59 0.24 0.12
295_T 246_V 0.59 0.24 0.12
330_L 250_K 0.59 0.24 0.12
297_V 248_K 0.59 0.24 0.12
89_P 140_G 0.59 0.24 0.12
233_L 74_T 0.59 0.24 0.12
322_V 160_L 0.59 0.23 0.12
82_D 250_K 0.58 0.23 0.12
210_P 167_D 0.58 0.23 0.11
265_Q 127_I 0.58 0.23 0.11
150_A 29_V 0.58 0.23 0.11
263_V 185_L 0.58 0.23 0.11
266_T 188_N 0.58 0.23 0.11
73_I 104_V 0.58 0.23 0.11
284_I 67_G 0.58 0.23 0.11
263_V 234_T 0.58 0.23 0.11
96_I 252_I 0.58 0.23 0.11
330_L 153_V 0.58 0.23 0.11
150_A 186_R 0.57 0.22 0.11
167_S 133_Q 0.57 0.22 0.11
168_V 161_K 0.57 0.22 0.10
87_L 192_Y 0.57 0.22 0.10
123_V 223_S 0.57 0.21 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)
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