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OPENSEQ.org
pred_2HQS_l_u_ApdbAfas_2HQS_r_u_ApdbAfastable_PRtxt
Genes: A B A+B
Length: 108 397 500
Sequences: 11328 976 843
Seq/Len: 104.89 2.46 1.69
MirrorTree (Pazo et al. 2001) 0.77
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 0.02 0.08 1.59
2 0.02 0.08 1.62
5 0.03 0.08 1.64
10 0.05 0.08 1.65
20 0.07 0.08 1.67
100 0.13 0.08 1.71
∞ 0.21 0.08 1.81
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
49_T 306_Q 1.44 0.85 0.15
54_I 219_G 1.37 0.82 0.13
85_K 233_A 1.32 0.78 0.11
87_K 173_Q 1.30 0.77 0.10
18_D 244_V 1.29 0.76 0.10
69_Q 211_V 1.15 0.63 0.07
12_K 143_V 1.11 0.59 0.06
50_P 390_F 1.10 0.58 0.06
15_I 168_V 1.09 0.57 0.05
99_S 296_Q 1.09 0.56 0.05
58_E 235_S 1.08 0.56 0.05
21_Q 69_I 1.08 0.56 0.05
63_A 381_L 1.07 0.55 0.05
66_M 259_S 1.06 0.54 0.05
98_Y 259_S 1.05 0.53 0.05
73_V 369_N 1.04 0.52 0.05
6_V 54_G 1.04 0.51 0.04
75_A 223_F 1.02 0.50 0.04
27_A 335_G 1.01 0.49 0.04
78_I 83_G 1.01 0.48 0.04
58_E 241_N 1.00 0.47 0.04
26_H 372_S 1.00 0.47 0.04
18_D 259_S 0.99 0.47 0.04
74_S 285_V 0.99 0.46 0.04
6_V 143_V 0.98 0.46 0.04
64_V 262_T 0.98 0.45 0.04
83_Y 85_Y 0.98 0.45 0.04
44_A 28_G 0.96 0.43 0.03
39_T 16_Q 0.95 0.42 0.03
93_H 34_D 0.94 0.41 0.03
26_H 276_T 0.94 0.41 0.03
103_R 234_L 0.94 0.41 0.03
6_V 154_E 0.94 0.41 0.03
10_L 274_A 0.94 0.41 0.03
59_R 194_G 0.94 0.41 0.03
63_A 167_V 0.94 0.41 0.03
11_D 143_V 0.94 0.41 0.03
37_K 228_S 0.93 0.40 0.03
38_V 2_S 0.93 0.40 0.03
9_D 127_E 0.91 0.38 0.03
15_I 261_N 0.91 0.38 0.03
65_K 40_K 0.91 0.38 0.03
65_K 208_V 0.89 0.36 0.03
99_S 31_V 0.89 0.36 0.03
29_F 82_D 0.89 0.35 0.03
40_V 360_S 0.88 0.35 0.03
17_S 273_L 0.88 0.35 0.03
11_D 127_E 0.88 0.35 0.03
80_I 67_L 0.87 0.34 0.02
94_D 186_L 0.86 0.34 0.02
17_S 139_R 0.86 0.33 0.02
80_I 308_A 0.86 0.33 0.02
67_Y 223_F 0.86 0.33 0.02
24_D 10_I 0.86 0.33 0.02
76_D 6_S 0.86 0.33 0.02
41_E 327_I 0.85 0.32 0.02
6_V 361_S 0.85 0.32 0.02
40_V 364_G 0.85 0.32 0.02
9_D 124_E 0.85 0.32 0.02
41_E 352_A 0.85 0.32 0.02
40_V 14_P 0.84 0.32 0.02
7_Y 74_V 0.84 0.31 0.02
58_E 239_S 0.84 0.31 0.02
76_D 252_R 0.84 0.31 0.02
85_K 337_V 0.84 0.31 0.02
94_D 140_I 0.84 0.31 0.02
97_A 360_S 0.83 0.30 0.02
54_I 216_R 0.83 0.30 0.02
81_V 210_Q 0.83 0.30 0.02
78_I 60_Q 0.83 0.30 0.02
10_L 150_Q 0.82 0.30 0.02
27_A 341_S 0.82 0.30 0.02
43_H 351_L 0.82 0.30 0.02
50_P 145_Q 0.82 0.30 0.02
15_I 254_V 0.82 0.30 0.02
67_Y 351_L 0.82 0.30 0.02
40_V 271_Q 0.82 0.29 0.02
66_M 186_L 0.82 0.29 0.02
38_V 387_Q 0.82 0.29 0.02
104_A 25_E 0.82 0.29 0.02
76_D 285_V 0.82 0.29 0.02
58_E 297_R 0.81 0.29 0.02
43_H 266_W 0.81 0.28 0.02
81_V 318_V 0.81 0.28 0.02
106_L 156_R 0.81 0.28 0.02
23_L 122_S 0.81 0.28 0.02
49_T 392_A 0.81 0.28 0.02
67_Y 394_S 0.80 0.28 0.02
95_E 144_V 0.80 0.28 0.02
105_V 43_P 0.80 0.28 0.02
63_A 6_S 0.80 0.28 0.02
18_D 100_T 0.80 0.28 0.02
98_Y 88_A 0.80 0.28 0.02
54_I 143_V 0.79 0.27 0.02
17_S 220_A 0.79 0.27 0.02
50_P 370_L 0.79 0.27 0.02
50_P 366_S 0.79 0.27 0.02
58_E 248_S 0.79 0.27 0.02
107_V 7_G 0.78 0.26 0.02
37_K 200_I 0.78 0.26 0.02
5_I 179_W 0.78 0.26 0.02
36_Y 299_T 0.78 0.26 0.02
65_K 100_T 0.78 0.26 0.02
83_Y 211_V 0.77 0.25 0.02
90_V 202_T 0.77 0.25 0.02
75_A 100_T 0.77 0.25 0.02
71_K 107_Y 0.77 0.25 0.02
61_A 298_I 0.77 0.25 0.02
30_L 27_I 0.76 0.24 0.02
106_L 31_V 0.76 0.24 0.02
49_T 318_V 0.76 0.24 0.02
87_K 374_D 0.76 0.24 0.02
98_Y 160_Y 0.76 0.24 0.01
16_R 373_T 0.76 0.24 0.01
4_N 230_L 0.75 0.24 0.01
31_R 392_A 0.75 0.24 0.01
14_D 38_S 0.75 0.24 0.01
64_V 359_Y 0.75 0.24 0.01
41_E 65_S 0.75 0.24 0.01
73_V 319_S 0.75 0.24 0.01
6_V 66_A 0.75 0.23 0.01
95_E 207_A 0.75 0.23 0.01
40_V 253_Q 0.75 0.23 0.01
54_I 72_V 0.74 0.23 0.01
68_L 6_S 0.74 0.23 0.01
14_D 285_V 0.74 0.23 0.01
37_K 60_Q 0.74 0.23 0.01
81_V 103_A 0.74 0.23 0.01
44_A 351_L 0.74 0.23 0.01
99_S 109_V 0.74 0.23 0.01
107_V 175_L 0.74 0.23 0.01
20_A 110_N 0.74 0.23 0.01
44_A 341_S 0.73 0.23 0.01
43_H 232_F 0.73 0.22 0.01
39_T 10_I 0.73 0.22 0.01
51_E 262_T 0.73 0.22 0.01
39_T 202_T 0.72 0.22 0.01
6_V 138_T 0.72 0.22 0.01
97_A 335_G 0.72 0.22 0.01
94_D 357_V 0.72 0.21 0.01
10_L 100_T 0.72 0.21 0.01
94_D 256_D 0.72 0.21 0.01
104_A 44_L 0.72 0.21 0.01
10_L 10_I 0.72 0.21 0.01
59_R 357_V 0.71 0.21 0.01
93_H 331_D 0.71 0.21 0.01
94_D 184_S 0.71 0.21 0.01
83_Y 98_P 0.71 0.21 0.01
13_Y 87_V 0.71 0.21 0.01
94_D 12_V 0.71 0.21 0.01
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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