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pred_1WDW_l_u_ApdbAfas_1WDW_r_u_ApdbAfastable_PRtxt
Genes: A B A+B
Length: 241 386 563
Sequences: 2583 7048 1786
Seq/Len: 10.72 18.26 3.17
MirrorTree (Pazo et al. 2001) 0.67
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 0.08 0.03 2.60
2 0.08 0.03 2.69
5 0.08 0.03 2.74
10 0.08 0.04 2.82
20 0.08 0.04 2.85
100 0.08 0.06 2.89
∞ 0.09 0.18 3.16
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
94_R 270_Q 2.74 1.00 1.00
45_I 169_L 2.57 1.00 1.00
89_Y 273_V 1.97 1.00 0.98
93_Y 278_L 1.67 0.98 0.95
65_L 286_E 1.39 0.93 0.85
64_K 286_E 1.34 0.92 0.82
66_R 286_E 1.33 0.91 0.82
52_Q 167_E 1.31 0.90 0.81
93_Y 273_V 1.24 0.87 0.75
166_Y 177_E 1.12 0.78 0.64
66_R 285_E 1.06 0.73 0.58
45_I 192_Y 0.88 0.52 0.36
81_T 178_Y 0.75 0.36 0.22
143_N 176_F 0.75 0.36 0.22
30_E 309_A 0.75 0.36 0.22
21_T 54_Y 0.73 0.33 0.20
102_A 362_R 0.72 0.33 0.19
41_F 289_I 0.72 0.32 0.19
124_E 278_L 0.72 0.32 0.19
177_R 325_E 0.71 0.32 0.18
46_A 80_A 0.71 0.31 0.18
7_L 192_Y 0.70 0.30 0.17
109_V 47_A 0.69 0.29 0.16
93_Y 277_M 0.69 0.29 0.16
94_R 208_K 0.69 0.29 0.16
52_Q 170_R 0.69 0.29 0.16
94_R 127_I 0.69 0.29 0.16
49_K 238_P 0.68 0.28 0.16
64_K 318_E 0.67 0.27 0.15
217_V 169_L 0.66 0.26 0.14
166_Y 174_A 0.65 0.26 0.14
197_E 383_K 0.65 0.25 0.14
141_A 176_F 0.65 0.25 0.13
45_I 274_F 0.65 0.25 0.13
140_A 335_S 0.65 0.25 0.13
66_R 195_I 0.65 0.25 0.13
45_I 165_I 0.64 0.24 0.13
133_G 122_G 0.63 0.24 0.12
144_T 259_S 0.63 0.23 0.12
165_L 275_H 0.63 0.23 0.12
28_L 341_I 0.63 0.23 0.12
83_I 321_T 0.62 0.23 0.12
68_A 83_T 0.62 0.23 0.12
21_T 145_K 0.62 0.22 0.11
164_S 102_I 0.62 0.22 0.11
166_Y 176_F 0.61 0.22 0.11
210_V 238_P 0.61 0.22 0.11
194_S 335_S 0.61 0.21 0.11
39_I 286_E 0.61 0.21 0.11
60_K 246_K 0.61 0.21 0.11
154_D 315_Q 0.61 0.21 0.10
117_L 53_L 0.60 0.21 0.10
30_E 369_N 0.60 0.21 0.10
106_A 87_I 0.60 0.21 0.10
166_Y 118_G 0.60 0.21 0.10
60_K 383_K 0.60 0.20 0.10
147_E 61_E 0.60 0.20 0.10
202_L 253_G 0.59 0.20 0.10
148_R 85_N 0.59 0.20 0.10
76_R 93_A 0.59 0.20 0.10
58_A 169_L 0.59 0.20 0.09
149_L 94_K 0.58 0.19 0.09
93_Y 271_V 0.58 0.19 0.09
137_V 202_V 0.58 0.19 0.09
29_D 221_V 0.58 0.19 0.09
162_L 279_S 0.58 0.19 0.09
35_I 237_Y 0.58 0.19 0.09
59_L 322_V 0.57 0.19 0.09
61_N 265_S 0.57 0.19 0.09
115_V 277_M 0.57 0.18 0.09
50_T 132_E 0.57 0.18 0.09
114_V 247_L 0.57 0.18 0.09
67_E 286_E 0.57 0.18 0.08
177_R 223_V 0.56 0.18 0.08
176_L 158_S 0.56 0.18 0.08
142_P 192_Y 0.56 0.17 0.08
52_Q 156_S 0.56 0.17 0.08
106_A 213_E 0.56 0.17 0.08
86_M 170_R 0.56 0.17 0.08
188_A 178_Y 0.55 0.17 0.08
196_R 253_G 0.55 0.17 0.08
54_S 312_K 0.55 0.17 0.08
77_R 362_R 0.55 0.17 0.08
45_I 183_I 0.55 0.17 0.08
37_L 214_A 0.55 0.17 0.08
220_I 370_L 0.55 0.17 0.08
142_P 167_E 0.55 0.17 0.08
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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