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OPENSEQ.org
HasB-HasR
Genes: A B A+B
Length: 104 865 848
Sequences: 1364 4558 169
Seq/Len: 13.12 5.27 0.2
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 0.03 0.04
2 0.00 0.03 0.07
5 0.00 0.05 0.12
10 0.01 0.06 0.15
20 0.01 0.07 0.17
100 0.02 0.11 0.27
∞ 0.10 0.18 0.48
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
4_A 437_A 1.46 0.30 0.00
65_E 386_F 1.43 0.28 0.00
89_V 333_W 1.36 0.25 0.00
79_P 780_L 1.33 0.24 0.00
57_A 819_Y 1.32 0.23 0.00
91_L 437_A 1.28 0.22 0.00
65_E 198_I 1.26 0.21 0.00
65_E 100_D 1.26 0.21 0.00
70_V 836_N 1.26 0.21 0.00
46_G 687_G 1.22 0.19 0.00
62_L 166_G 1.22 0.19 0.00
94_P 177_I 1.22 0.19 0.00
90_E 260_G 1.21 0.19 0.00
43_D 624_V 1.20 0.18 0.00
55_S 776_F 1.19 0.18 0.00
21_K 102_L 1.19 0.18 0.00
36_G 103_T 1.17 0.18 0.00
46_G 165_R 1.17 0.17 0.00
29_R 386_F 1.16 0.17 0.00
46_G 833_N 1.15 0.17 0.00
67_Q 769_V 1.15 0.17 0.00
78_T 788_F 1.15 0.17 0.00
9_W 679_N 1.14 0.16 0.00
68_A 337_A 1.14 0.16 0.00
46_G 224_G 1.11 0.16 0.00
56_S 271_G 1.11 0.15 0.00
68_A 409_T 1.10 0.15 0.00
46_G 179_G 1.10 0.15 0.00
38_V 659_I 1.08 0.15 0.00
5_G 213_T 1.07 0.14 0.00
39_R 503_L 1.07 0.14 0.00
53_L 569_V 1.06 0.14 0.00
52_T 818_S 1.05 0.14 0.00
38_V 701_A 1.05 0.14 0.00
81_A 862_E 1.05 0.14 0.00
49_L 505_G 1.03 0.13 0.00
5_G 844_G 1.03 0.13 0.00
91_L 98_A 1.02 0.13 0.00
60_P 341_L 1.01 0.12 0.00
57_A 854_G 1.00 0.12 0.00
8_N 111_N 1.00 0.12 0.00
35_V 769_V 1.00 0.12 0.00
8_N 836_N 1.00 0.12 0.00
23_Y 343_L 1.00 0.12 0.00
82_D 827_L 1.00 0.12 0.00
38_V 447_L 1.00 0.12 0.00
94_P 211_G 1.00 0.12 0.00
67_Q 461_F 1.00 0.12 0.00
23_Y 814_D 0.99 0.12 0.00
9_W 647_F 0.99 0.12 0.00
33_Q 247_L 0.99 0.12 0.00
57_A 769_V 0.99 0.12 0.00
77_P 124_S 0.99 0.12 0.00
40_F 647_F 0.99 0.12 0.00
53_L 653_N 0.99 0.12 0.00
44_R 148_G 0.99 0.12 0.00
40_F 584_Y 0.99 0.12 0.00
68_A 784_V 0.98 0.12 0.00
48_V 278_S 0.98 0.12 0.00
42_L 688_L 0.98 0.12 0.00
36_G 684_R 0.98 0.12 0.00
5_G 395_V 0.97 0.12 0.00
35_V 117_Y 0.97 0.12 0.00
12_R 619_S 0.97 0.12 0.00
91_L 844_G 0.96 0.12 0.00
95_I 708_M 0.96 0.11 0.00
63_D 494_T 0.96 0.11 0.00
68_A 507_L 0.96 0.11 0.00
33_Q 151_S 0.96 0.11 0.00
73_A 839_Y 0.96 0.11 0.00
77_P 196_M 0.96 0.11 0.00
95_I 622_W 0.96 0.11 0.00
71_K 817_A 0.96 0.11 0.00
56_S 126_I 0.96 0.11 0.00
38_V 766_R 0.95 0.11 0.00
53_L 814_D 0.95 0.11 0.00
39_R 834_L 0.95 0.11 0.00
61_S 624_V 0.95 0.11 0.00
80_P 163_N 0.95 0.11 0.00
78_T 274_L 0.95 0.11 0.00
49_L 494_T 0.95 0.11 0.00
52_T 825_L 0.95 0.11 0.00
53_L 858_Q 0.95 0.11 0.00
48_V 172_R 0.95 0.11 0.00
53_L 699_F 0.95 0.11 0.00
11_S 340_R 0.95 0.11 0.00
94_P 224_G 0.94 0.11 0.00
79_P 831_V 0.94 0.11 0.00
95_I 842_S 0.94 0.11 0.00
28_L 102_L 0.94 0.11 0.00
39_R 270_T 0.94 0.11 0.00
80_P 780_L 0.94 0.11 0.00
12_R 513_R 0.94 0.11 0.00
11_S 634_W 0.94 0.11 0.00
21_K 241_K 0.94 0.11 0.00
29_R 819_Y 0.94 0.11 0.00
82_D 684_R 0.93 0.11 0.00
70_V 98_A 0.93 0.11 0.00
98_S 685_F 0.93 0.11 0.00
15_G 236_F 0.93 0.11 0.00
97_F 224_G 0.93 0.11 0.00
12_R 438_Q 0.93 0.11 0.00
67_Q 278_S 0.93 0.11 0.00
15_G 719_A 0.93 0.11 0.00
40_F 815_L 0.93 0.11 0.00
42_L 624_V 0.93 0.11 0.00
29_R 614_L 0.93 0.11 0.00
11_S 106_G 0.93 0.11 0.00
38_V 126_I 0.93 0.10 0.00
15_G 676_Y 0.93 0.10 0.00
95_I 150_Y 0.93 0.10 0.00
45_Q 228_F 0.92 0.10 0.00
40_F 582_T 0.92 0.10 0.00
9_W 200_S 0.92 0.10 0.00
95_I 247_L 0.92 0.10 0.00
38_V 129_E 0.92 0.10 0.00
38_V 430_T 0.92 0.10 0.00
93_L 276_A 0.91 0.10 0.00
72_R 701_A 0.91 0.10 0.00
15_G 576_E 0.91 0.10 0.00
57_A 865_F 0.91 0.10 0.00
93_L 262_G 0.91 0.10 0.00
96_D 208_I 0.91 0.10 0.00
43_D 852_G 0.91 0.10 0.00
50_A 217_G 0.90 0.10 0.00
53_L 331_V 0.90 0.10 0.00
98_S 490_F 0.90 0.10 0.00
89_V 837_R 0.90 0.10 0.00
51_V 393_E 0.90 0.10 0.00
8_N 636_E 0.89 0.10 0.00
52_T 131_M 0.89 0.10 0.00
57_A 149_A 0.89 0.10 0.00
47_H 277_A 0.89 0.10 0.00
51_V 576_E 0.89 0.10 0.00
6_E 776_F 0.89 0.10 0.00
68_A 384_A 0.89 0.10 0.00
65_E 286_W 0.89 0.10 0.00
71_K 514_L 0.89 0.10 0.00
46_G 166_G 0.89 0.10 0.00
43_D 829_G 0.89 0.10 0.00
68_A 578_L 0.89 0.10 0.00
72_R 859_G 0.88 0.10 0.00
16_R 265_A 0.88 0.10 0.00
43_D 502_T 0.88 0.10 0.00
47_H 836_N 0.88 0.10 0.00
65_E 781_D 0.88 0.10 0.00
67_Q 706_T 0.88 0.10 0.00
5_G 642_A 0.88 0.10 0.00
94_P 146_T 0.88 0.10 0.00
38_V 559_D 0.88 0.10 0.00
21_K 256_T 0.88 0.09 0.00
74_S 836_N 0.88 0.09 0.00
29_R 565_P 0.87 0.09 0.00
20_F 217_G 0.87 0.09 0.00
26_D 131_M 0.87 0.09 0.00
77_P 227_T 0.87 0.09 0.00
8_N 621_A 0.87 0.09 0.00
46_G 208_I 0.86 0.09 0.00
68_A 698_V 0.86 0.09 0.00
69_L 206_V 0.86 0.09 0.00
31_K 192_R 0.86 0.09 0.00
63_D 166_G 0.86 0.09 0.00
9_W 835_T 0.86 0.09 0.00
30_L 811_T 0.86 0.09 0.00
28_L 380_M 0.86 0.09 0.00
57_A 166_G 0.86 0.09 0.00
97_F 178_D 0.86 0.09 0.00
58_G 835_T 0.85 0.09 0.00
28_L 250_S 0.85 0.09 0.00
83_A 205_G 0.85 0.09 0.00
75_P 839_Y 0.85 0.09 0.00
32_R 267_G 0.85 0.09 0.00
21_K 253_D 0.85 0.09 0.00
80_P 839_Y 0.85 0.09 0.00
27_A 495_Y 0.85 0.09 0.00
52_T 162_V 0.85 0.09 0.00
46_G 763_P 0.85 0.09 0.00
97_F 588_W 0.85 0.09 0.00
51_V 825_L 0.85 0.09 0.00
37_Q 836_N 0.84 0.09 0.00
15_G 462_Y 0.84 0.09 0.00
23_Y 763_P 0.84 0.09 0.00
36_G 615_Q 0.84 0.09 0.00
56_S 765_D 0.84 0.09 0.00
32_R 241_K 0.84 0.09 0.00
53_L 380_M 0.84 0.09 0.00
100_R 237_L 0.84 0.09 0.00
28_L 386_F 0.84 0.09 0.00
48_V 767_G 0.84 0.09 0.00
95_I 705_Y 0.84 0.09 0.00
54_V 769_V 0.84 0.09 0.00
22_R 484_R 0.84 0.09 0.00
35_V 376_Y 0.84 0.09 0.00
36_G 758_S 0.84 0.09 0.00
34_G 166_G 0.84 0.09 0.00
50_A 198_I 0.84 0.09 0.00
68_A 501_L 0.84 0.09 0.00
35_V 857_V 0.83 0.09 0.00
71_K 162_V 0.83 0.09 0.00
72_R 202_L 0.83 0.09 0.00
69_L 102_L 0.83 0.09 0.00
12_R 812_L 0.83 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)
ID Seq/Len Name Options I_Prob Status
13542 0.2 HasB-HasR Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5128 0.35 HasB160-HasR Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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