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OPENSEQ.org
pred_1GLA_l_u_ApdbAfas_1GLA_r_u_OpdbOfastable_PRtxt
Genes: A B A+B
Length: 150 497 641
Sequences: 2925 8763 166
Seq/Len: 19.5 17.63 0.26
MirrorTree (Pazo et al. 2001) 0.16
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 0.03 0.01
2 0.01 0.04 0.03
5 0.02 0.06 0.07
10 0.04 0.07 0.15
20 0.05 0.10 0.26
100 0.10 0.15 0.81
∞ 0.18 0.22 1.82
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
93_Q 172_T 1.63 0.46 0.00
93_Q 199_D 1.30 0.27 0.00
75_I 169_W 1.28 0.26 0.00
15_I 421_S 1.27 0.25 0.00
28_V 200_K 1.25 0.24 0.00
6_A 95_I 1.22 0.23 0.00
43_A 108_E 1.20 0.22 0.00
123_S 302_G 1.19 0.22 0.00
43_A 182_T 1.19 0.21 0.00
120_V 358_A 1.17 0.21 0.00
52_I 192_I 1.15 0.20 0.00
83_E 422_D 1.13 0.19 0.00
43_A 92_G 1.13 0.19 0.00
102_I 220_E 1.12 0.19 0.00
121_V 258_M 1.10 0.18 0.00
119_P 428_V 1.09 0.17 0.00
45_V 74_A 1.08 0.17 0.00
6_A 342_V 1.08 0.17 0.00
116_T 171_M 1.07 0.17 0.00
121_V 213_P 1.07 0.17 0.00
104_F 356_P 1.07 0.17 0.00
92_G 387_R 1.06 0.16 0.00
49_I 191_N 1.05 0.16 0.00
93_Q 89_K 1.04 0.15 0.00
21_V 366_T 1.03 0.15 0.00
43_A 472_I 1.03 0.15 0.00
41_M 356_P 1.03 0.15 0.00
18_V 357_Y 1.02 0.15 0.00
118_T 278_V 1.02 0.15 0.00
109_L 375_I 1.01 0.15 0.00
105_D 366_T 1.00 0.14 0.00
106_L 428_V 1.00 0.14 0.00
52_I 26_I 1.00 0.14 0.00
101_V 468_F 0.99 0.14 0.00
50_G 76_G 0.99 0.14 0.00
73_F 428_V 0.99 0.14 0.00
56_N 456_D 0.97 0.14 0.00
75_I 192_I 0.96 0.13 0.00
99_D 122_I 0.96 0.13 0.00
52_I 426_T 0.96 0.13 0.00
93_Q 448_A 0.94 0.12 0.00
80_L 382_I 0.93 0.12 0.00
15_I 269_M 0.92 0.12 0.00
62_E 425_G 0.92 0.12 0.00
12_I 147_E 0.92 0.12 0.00
103_E 74_A 0.92 0.12 0.00
52_I 473_E 0.91 0.12 0.00
58_A 387_R 0.91 0.12 0.00
76_D 369_V 0.91 0.12 0.00
90_E 88_E 0.90 0.12 0.00
95_V 425_G 0.90 0.12 0.00
118_T 485_K 0.90 0.11 0.00
31_G 243_D 0.90 0.11 0.00
44_P 243_D 0.90 0.11 0.00
57_H 243_D 0.90 0.11 0.00
72_H 243_D 0.90 0.11 0.00
74_G 243_D 0.90 0.11 0.00
75_I 61_V 0.89 0.11 0.00
97_V 61_V 0.89 0.11 0.00
64_D 190_F 0.88 0.11 0.00
59_F 182_T 0.88 0.11 0.00
80_L 281_E 0.88 0.11 0.00
4_I 252_L 0.87 0.11 0.00
110_E 412_A 0.87 0.11 0.00
86_K 93_K 0.87 0.11 0.00
31_G 408_G 0.87 0.11 0.00
44_P 408_G 0.87 0.11 0.00
57_H 408_G 0.87 0.11 0.00
72_H 408_G 0.87 0.11 0.00
74_G 408_G 0.87 0.11 0.00
53_F 185_S 0.86 0.10 0.00
89_A 99_I 0.86 0.10 0.00
13_V 85_I 0.86 0.10 0.00
89_A 41_G 0.86 0.10 0.00
24_A 398_G 0.86 0.10 0.00
109_L 34_E 0.86 0.10 0.00
15_I 193_H 0.86 0.10 0.00
59_F 180_D 0.86 0.10 0.00
17_D 357_Y 0.85 0.10 0.00
45_V 411_V 0.85 0.10 0.00
52_I 479_Y 0.85 0.10 0.00
29_G 243_D 0.85 0.10 0.00
121_V 85_I 0.85 0.10 0.00
42_V 83_T 0.85 0.10 0.00
46_D 169_W 0.85 0.10 0.00
73_F 390_L 0.84 0.10 0.00
63_S 428_V 0.84 0.10 0.00
49_I 95_I 0.84 0.10 0.00
42_V 481_Y 0.84 0.10 0.00
43_A 185_S 0.84 0.10 0.00
103_E 311_I 0.84 0.10 0.00
93_Q 373_H 0.84 0.10 0.00
10_G 243_D 0.84 0.10 0.00
89_A 56_S 0.84 0.10 0.00
101_V 440_G 0.83 0.10 0.00
59_F 362_I 0.83 0.10 0.00
89_A 184_A 0.83 0.10 0.00
15_I 423_I 0.82 0.10 0.00
118_T 373_H 0.82 0.10 0.00
25_E 450_G 0.82 0.10 0.00
27_I 298_Y 0.82 0.10 0.00
84_G 193_H 0.82 0.10 0.00
122_I 489_K 0.82 0.10 0.00
6_A 472_I 0.82 0.10 0.00
17_D 212_L 0.82 0.10 0.00
108_L 205_L 0.82 0.10 0.00
29_G 408_G 0.82 0.09 0.00
33_A 72_I 0.82 0.09 0.00
83_E 148_G 0.81 0.09 0.00
118_T 267_C 0.81 0.09 0.00
71_V 165_T 0.81 0.09 0.00
81_K 347_T 0.81 0.09 0.00
13_V 357_Y 0.81 0.09 0.00
64_D 111_E 0.81 0.09 0.00
17_D 204_V 0.81 0.09 0.00
69_L 362_I 0.81 0.09 0.00
76_D 351_A 0.81 0.09 0.00
61_I 304_V 0.81 0.09 0.00
109_L 72_I 0.81 0.09 0.00
24_A 449_V 0.81 0.09 0.00
12_I 76_G 0.81 0.09 0.00
70_F 184_A 0.81 0.09 0.00
41_M 224_Q 0.81 0.09 0.00
45_V 112_H 0.81 0.09 0.00
4_I 390_L 0.80 0.09 0.00
31_G 264_G 0.80 0.09 0.00
44_P 264_G 0.80 0.09 0.00
57_H 264_G 0.80 0.09 0.00
72_H 264_G 0.80 0.09 0.00
74_G 264_G 0.80 0.09 0.00
90_E 237_I 0.80 0.09 0.00
10_G 408_G 0.80 0.09 0.00
93_Q 152_R 0.80 0.09 0.00
21_V 167_L 0.80 0.09 0.00
110_E 19_M 0.80 0.09 0.00
69_L 392_A 0.80 0.09 0.00
55_T 425_G 0.80 0.09 0.00
81_K 375_I 0.80 0.09 0.00
119_P 235_I 0.80 0.09 0.00
126_D 370_N 0.80 0.09 0.00
75_I 188_M 0.80 0.09 0.00
71_V 62_L 0.79 0.09 0.00
17_D 193_H 0.79 0.09 0.00
43_A 124_S 0.79 0.09 0.00
22_V 17_V 0.79 0.09 0.00
52_I 151_E 0.79 0.09 0.00
90_E 404_L 0.79 0.09 0.00
71_V 373_H 0.79 0.09 0.00
14_N 468_F 0.79 0.09 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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