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OPENSEQ.org
HipAB validation
Genes: A B A+B
Length: 78 433 476
Sequences: 35041 1898 483
Seq/Len: 449.24 4.38 1.01
MirrorTree (Pazo et al. 2001) 0.66
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.09 0.01 0.95
2 0.10 0.02 0.98
5 0.12 0.03 1.07
10 0.15 0.04 1.12
20 0.17 0.05 1.27
100 0.23 0.07 1.80
∞ 0.26 0.12 2.65
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
38_T 222_F 1.40 0.69 0.01
56_I 162_K 1.30 0.62 0.00
50_I 39_Q 1.26 0.58 0.00
28_A 103_I 1.23 0.55 0.00
36_K 146_L 1.22 0.54 0.00
56_I 362_A 1.08 0.41 0.00
62_I 271_S 1.07 0.40 0.00
14_I 87_N 1.05 0.39 0.00
10_L 256_N 1.04 0.38 0.00
56_I 157_L 1.04 0.38 0.00
22_A 369_L 1.03 0.37 0.00
27_V 12_H 1.01 0.35 0.00
20_S 123_E 1.01 0.35 0.00
31_L 177_V 0.99 0.33 0.00
47_D 365_D 0.98 0.33 0.00
15_K 197_K 0.98 0.32 0.00
10_L 380_R 0.97 0.32 0.00
14_I 15_D 0.97 0.31 0.00
62_I 104_A 0.96 0.31 0.00
8_Q 95_I 0.95 0.30 0.00
47_D 332_V 0.95 0.30 0.00
61_G 125_V 0.94 0.29 0.00
61_G 213_R 0.93 0.29 0.00
24_T 191_I 0.92 0.28 0.00
50_I 37_D 0.92 0.28 0.00
40_I 46_S 0.91 0.27 0.00
14_I 80_S 0.91 0.27 0.00
56_I 108_K 0.90 0.26 0.00
35_T 170_T 0.90 0.26 0.00
6_N 108_K 0.89 0.26 0.00
56_I 12_H 0.89 0.26 0.00
19_K 340_Q 0.89 0.26 0.00
50_I 35_T 0.89 0.26 0.00
15_K 125_V 0.89 0.26 0.00
60_L 207_D 0.88 0.25 0.00
9_S 298_F 0.88 0.25 0.00
10_L 378_L 0.87 0.24 0.00
38_T 167_A 0.87 0.24 0.00
60_L 45_L 0.86 0.24 0.00
24_T 110_A 0.86 0.24 0.00
29_A 157_L 0.86 0.24 0.00
44_K 369_L 0.86 0.23 0.00
64_I 245_L 0.86 0.23 0.00
38_T 173_S 0.86 0.23 0.00
29_A 246_G 0.85 0.23 0.00
23_L 80_S 0.85 0.23 0.00
32_C 121_K 0.85 0.23 0.00
24_T 73_G 0.85 0.23 0.00
56_I 378_L 0.85 0.23 0.00
42_V 302_T 0.84 0.22 0.00
26_D 103_I 0.83 0.22 0.00
39_L 208_I 0.83 0.22 0.00
11_G 77_L 0.83 0.22 0.00
60_L 313_S 0.83 0.21 0.00
38_T 146_L 0.83 0.21 0.00
39_L 369_L 0.82 0.21 0.00
25_Q 50_P 0.82 0.21 0.00
50_I 313_S 0.82 0.21 0.00
46_E 302_T 0.81 0.21 0.00
50_I 71_N 0.81 0.21 0.00
44_K 84_S 0.81 0.20 0.00
30_M 10_E 0.81 0.20 0.00
60_L 47_P 0.80 0.20 0.00
31_L 412_T 0.80 0.20 0.00
30_M 75_D 0.80 0.20 0.00
35_T 32_V 0.80 0.20 0.00
37_K 162_K 0.80 0.20 0.00
32_C 35_T 0.79 0.19 0.00
57_L 106_V 0.79 0.19 0.00
28_A 378_L 0.79 0.19 0.00
15_K 206_V 0.79 0.19 0.00
18_R 50_P 0.79 0.19 0.00
32_C 236_R 0.79 0.19 0.00
19_K 421_Y 0.79 0.19 0.00
14_I 126_I 0.78 0.19 0.00
25_Q 46_S 0.78 0.19 0.00
34_V 24_D 0.78 0.19 0.00
17_R 55_G 0.78 0.19 0.00
10_L 83_V 0.78 0.18 0.00
51_S 32_V 0.77 0.18 0.00
15_K 158_F 0.77 0.18 0.00
45_G 21_L 0.77 0.18 0.00
24_T 97_L 0.77 0.18 0.00
16_E 346_I 0.77 0.18 0.00
35_T 251_K 0.77 0.18 0.00
7_Q 183_H 0.77 0.18 0.00
22_A 336_E 0.77 0.18 0.00
17_R 377_N 0.76 0.18 0.00
33_G 49_I 0.76 0.18 0.00
32_C 43_F 0.76 0.18 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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