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OPENSEQ.org
t0999_4_5
Genes: A B A+B
Length: 232 288 486
Sequences: 1522 5110 295
Seq/Len: 6.56 17.74 0.61
MirrorTree (Pazo et al. 2001) 0.69
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 0.07 0.06 0.34
2 0.08 0.07 0.42
5 0.08 0.08 0.50
10 0.08 0.08 0.55
20 0.08 0.08 0.57
100 0.08 0.09 0.65
∞ 0.09 0.14 1.02
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
148_Y 272_W 1.46 0.59 0.00
49_Q 198_I 1.31 0.47 0.00
203_T 59_S 1.26 0.43 0.00
195_S 145_A 1.23 0.41 0.00
63_Y 158_I 1.19 0.38 0.00
221_A 39_T 1.14 0.34 0.00
195_S 137_V 1.13 0.33 0.00
212_S 254_T 1.11 0.32 0.00
167_L 256_G 1.09 0.30 0.00
144_K 50_I 1.07 0.29 0.00
144_K 88_I 1.06 0.29 0.00
122_A 9_G 1.06 0.28 0.00
128_Q 245_T 1.04 0.27 0.00
63_Y 262_A 1.02 0.26 0.00
20_I 143_A 1.01 0.25 0.00
90_L 275_I 1.00 0.25 0.00
15_A 146_A 1.00 0.24 0.00
30_A 76_T 1.00 0.24 0.00
70_Q 89_I 0.99 0.24 0.00
87_Q 134_A 0.99 0.24 0.00
195_S 8_F 0.98 0.23 0.00
130_K 260_V 0.98 0.23 0.00
63_Y 82_I 0.97 0.23 0.00
9_L 163_R 0.97 0.23 0.00
123_S 272_W 0.96 0.23 0.00
192_G 109_G 0.96 0.22 0.00
67_T 255_V 0.96 0.22 0.00
62_V 251_G 0.96 0.22 0.00
212_S 16_R 0.96 0.22 0.00
94_V 61_T 0.95 0.22 0.00
155_V 154_G 0.95 0.22 0.00
222_T 198_I 0.95 0.21 0.00
210_L 101_V 0.95 0.21 0.00
160_E 44_K 0.94 0.21 0.00
99_L 249_D 0.93 0.21 0.00
99_L 66_L 0.92 0.20 0.00
167_L 175_F 0.92 0.20 0.00
225_R 93_R 0.91 0.20 0.00
70_Q 6_Y 0.91 0.19 0.00
192_G 260_V 0.91 0.19 0.00
17_A 255_V 0.90 0.19 0.00
226_Q 82_I 0.90 0.19 0.00
30_A 197_V 0.90 0.19 0.00
16_D 113_A 0.90 0.19 0.00
50_V 61_T 0.89 0.19 0.00
174_M 49_L 0.89 0.18 0.00
99_L 88_I 0.89 0.18 0.00
231_I 108_R 0.88 0.18 0.00
40_S 136_V 0.88 0.18 0.00
122_A 61_T 0.88 0.18 0.00
197_V 256_G 0.88 0.18 0.00
165_F 114_L 0.88 0.18 0.00
51_A 254_T 0.87 0.18 0.00
199_N 164_S 0.87 0.18 0.00
163_D 109_G 0.87 0.17 0.00
143_N 143_A 0.86 0.17 0.00
138_W 73_D 0.86 0.17 0.00
122_A 172_V 0.86 0.17 0.00
12_P 8_F 0.86 0.17 0.00
206_S 265_G 0.85 0.17 0.00
221_A 88_I 0.85 0.17 0.00
224_I 145_A 0.85 0.17 0.00
154_L 221_H 0.84 0.16 0.00
61_I 254_T 0.84 0.16 0.00
86_Y 246_L 0.84 0.16 0.00
15_A 116_H 0.84 0.16 0.00
209_A 71_L 0.84 0.16 0.00
163_D 15_S 0.84 0.16 0.00
77_E 168_V 0.83 0.16 0.00
221_A 235_A 0.83 0.16 0.00
97_L 249_D 0.83 0.16 0.00
155_V 107_W 0.83 0.16 0.00
221_A 252_W 0.83 0.16 0.00
187_N 260_V 0.83 0.16 0.00
151_V 74_S 0.83 0.16 0.00
84_R 6_Y 0.82 0.15 0.00
168_T 6_Y 0.82 0.15 0.00
198_L 68_I 0.82 0.15 0.00
160_E 157_P 0.82 0.15 0.00
90_L 156_A 0.82 0.15 0.00
203_T 107_W 0.81 0.15 0.00
53_L 129_A 0.81 0.15 0.00
206_S 20_L 0.81 0.15 0.00
187_N 205_Q 0.81 0.15 0.00
214_A 164_S 0.81 0.15 0.00
50_V 55_F 0.81 0.15 0.00
116_G 160_I 0.81 0.15 0.00
154_L 39_T 0.81 0.15 0.00
31_V 268_Q 0.80 0.15 0.00
163_D 260_V 0.80 0.15 0.00
198_L 88_I 0.80 0.15 0.00
169_N 270_Q 0.80 0.15 0.00
134_K 68_I 0.80 0.15 0.00
67_T 235_A 0.80 0.15 0.00
169_N 54_D 0.80 0.14 0.00
89_G 143_A 0.80 0.14 0.00
76_D 7_L 0.79 0.14 0.00
99_L 8_F 0.79 0.14 0.00
58_Q 80_R 0.79 0.14 0.00
89_G 116_H 0.79 0.14 0.00
219_L 230_V 0.78 0.14 0.00
30_A 75_A 0.78 0.14 0.00
172_A 68_I 0.78 0.14 0.00
87_Q 44_K 0.78 0.14 0.00
229_S 60_V 0.77 0.14 0.00
34_R 140_G 0.77 0.14 0.00
125_H 140_G 0.77 0.14 0.00
196_R 140_G 0.77 0.14 0.00
197_V 212_R 0.77 0.14 0.00
195_S 36_R 0.77 0.14 0.00
134_K 93_R 0.77 0.14 0.00
115_K 248_E 0.77 0.13 0.00
124_H 64_L 0.77 0.13 0.00
169_N 82_I 0.77 0.13 0.00
212_S 115_L 0.77 0.13 0.00
49_Q 134_A 0.77 0.13 0.00
220_S 54_D 0.77 0.13 0.00
156_G 256_G 0.77 0.13 0.00
147_Q 72_L 0.77 0.13 0.00
119_S 76_T 0.76 0.13 0.00
99_L 206_P 0.76 0.13 0.00
49_Q 272_W 0.76 0.13 0.00
206_S 234_M 0.76 0.13 0.00
126_D 8_F 0.76 0.13 0.00
31_V 83_G 0.76 0.13 0.00
174_M 235_A 0.76 0.13 0.00
106_H 121_G 0.75 0.13 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)
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