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OPENSEQ.org
HasB160-HasR
Genes: A B A+B
Length: 104 865 855
Sequences: 1009 25672 298
Seq/Len: 9.7 29.68 0.35
MirrorTree (Pazo et al. 2001) 0.13
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 0.06 0.12 0.01
2 0.07 0.15 0.02
5 0.08 0.19 0.06
10 0.08 0.22 0.16
20 0.09 0.26 0.31
100 0.11 0.31 0.65
∞ 0.15 0.33 0.72
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
95_I 58_S 1.40 0.39 0.00
95_I 577_W 1.39 0.38 0.00
92_T 162_V 1.33 0.35 0.00
63_D 58_S 1.21 0.27 0.00
17_L 574_G 1.19 0.26 0.00
42_L 228_F 1.18 0.26 0.00
19_R 323_R 1.15 0.24 0.00
61_S 580_L 1.12 0.23 0.00
30_L 214_G 1.12 0.22 0.00
38_V 54_N 1.11 0.22 0.00
70_V 850_T 1.11 0.22 0.00
95_I 75_R 1.10 0.21 0.00
93_L 77_Q 1.08 0.20 0.00
18_N 782_A 1.07 0.20 0.00
62_L 765_D 1.06 0.20 0.00
56_S 859_G 1.05 0.19 0.00
48_V 573_P 1.05 0.19 0.00
95_I 615_Q 1.05 0.19 0.00
56_S 138_H 1.05 0.19 0.00
60_P 58_S 1.04 0.19 0.00
85_V 63_L 1.04 0.19 0.00
17_L 228_F 1.03 0.18 0.00
69_L 139_A 1.02 0.18 0.00
32_R 75_R 1.02 0.18 0.00
51_V 104_V 1.01 0.18 0.00
70_V 52_A 1.01 0.18 0.00
17_L 104_V 1.01 0.17 0.00
18_N 82_I 1.00 0.17 0.00
82_D 73_A 1.00 0.17 0.00
71_K 82_I 0.99 0.17 0.00
51_V 95_G 0.99 0.17 0.00
95_I 715_C 0.98 0.16 0.00
38_V 373_R 0.97 0.16 0.00
15_G 493_L 0.97 0.16 0.00
43_D 381_A 0.97 0.16 0.00
38_V 809_K 0.96 0.16 0.00
42_L 275_L 0.96 0.16 0.00
95_I 283_G 0.95 0.15 0.00
74_S 447_L 0.94 0.15 0.00
89_V 859_G 0.94 0.15 0.00
45_Q 442_T 0.94 0.15 0.00
100_R 573_P 0.94 0.15 0.00
42_L 213_T 0.94 0.15 0.00
91_L 433_R 0.94 0.15 0.00
18_N 64_R 0.94 0.15 0.00
16_R 580_L 0.94 0.15 0.00
83_A 66_L 0.94 0.15 0.00
83_A 509_Y 0.93 0.15 0.00
35_V 125_V 0.93 0.15 0.00
47_H 69_G 0.92 0.14 0.00
35_V 766_R 0.92 0.14 0.00
100_R 92_G 0.91 0.14 0.00
32_R 861_V 0.91 0.14 0.00
48_V 786_V 0.91 0.14 0.00
48_V 646_Y 0.90 0.14 0.00
95_I 143_L 0.90 0.13 0.00
16_R 102_L 0.89 0.13 0.00
80_P 641_V 0.89 0.13 0.00
78_T 650_K 0.89 0.13 0.00
39_R 206_V 0.89 0.13 0.00
95_I 801_Y 0.88 0.13 0.00
95_I 814_D 0.88 0.13 0.00
78_T 53_L 0.88 0.13 0.00
60_P 135_P 0.88 0.13 0.00
76_L 394_D 0.88 0.13 0.00
17_L 75_R 0.86 0.12 0.00
62_L 70_N 0.86 0.12 0.00
46_G 80_G 0.86 0.12 0.00
55_S 702_D 0.86 0.12 0.00
38_V 832_E 0.85 0.12 0.00
82_D 453_F 0.85 0.12 0.00
11_S 488_S 0.84 0.12 0.00
49_L 65_R 0.84 0.12 0.00
37_Q 503_L 0.84 0.12 0.00
22_R 424_N 0.84 0.12 0.00
42_L 167_I 0.84 0.12 0.00
95_I 49_Q 0.84 0.12 0.00
32_R 860_G 0.84 0.12 0.00
75_P 99_L 0.83 0.12 0.00
51_V 696_A 0.83 0.12 0.00
33_Q 445_F 0.83 0.12 0.00
32_R 259_I 0.83 0.11 0.00
91_L 578_L 0.83 0.11 0.00
12_R 75_R 0.83 0.11 0.00
12_R 789_A 0.82 0.11 0.00
76_L 386_F 0.82 0.11 0.00
28_L 206_V 0.82 0.11 0.00
95_I 82_I 0.82 0.11 0.00
97_F 49_Q 0.81 0.11 0.00
80_P 483_N 0.81 0.11 0.00
67_Q 53_L 0.81 0.11 0.00
20_F 861_V 0.81 0.11 0.00
22_R 864_R 0.81 0.11 0.00
21_K 755_Q 0.81 0.11 0.00
81_A 61_Q 0.81 0.11 0.00
95_I 641_V 0.81 0.11 0.00
95_I 718_K 0.81 0.11 0.00
76_L 453_F 0.81 0.11 0.00
67_Q 126_I 0.80 0.11 0.00
55_S 99_L 0.80 0.11 0.00
31_K 65_R 0.80 0.11 0.00
85_V 199_D 0.80 0.11 0.00
80_P 327_R 0.80 0.11 0.00
90_E 226_A 0.80 0.11 0.00
78_T 269_E 0.80 0.11 0.00
30_L 653_N 0.80 0.11 0.00
64_R 626_F 0.80 0.10 0.00
51_V 58_S 0.80 0.10 0.00
43_D 817_A 0.80 0.10 0.00
22_R 754_T 0.80 0.10 0.00
45_Q 854_G 0.79 0.10 0.00
75_P 54_N 0.79 0.10 0.00
15_G 837_R 0.79 0.10 0.00
81_A 770_T 0.79 0.10 0.00
42_L 48_M 0.79 0.10 0.00
56_S 177_I 0.79 0.10 0.00
99_L 782_A 0.79 0.10 0.00
91_L 265_A 0.79 0.10 0.00
95_I 53_L 0.78 0.10 0.00
28_L 170_Y 0.78 0.10 0.00
29_R 44_K 0.78 0.10 0.00
69_L 481_A 0.78 0.10 0.00
93_L 638_D 0.78 0.10 0.00
35_V 433_R 0.78 0.10 0.00
19_R 634_W 0.78 0.10 0.00
85_V 448_A 0.77 0.10 0.00
44_R 661_R 0.77 0.10 0.00
69_L 75_R 0.77 0.10 0.00
45_Q 53_L 0.77 0.10 0.00
85_V 754_T 0.77 0.10 0.00
39_R 226_A 0.76 0.10 0.00
50_A 175_M 0.76 0.10 0.00
42_L 859_G 0.76 0.10 0.00
69_L 764_G 0.76 0.10 0.00
11_S 580_L 0.76 0.10 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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