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OPENSEQ.org
AlpB and AlpC
Genes: A B A+B
Length: 124 91 208
Sequences: 159 180 147
Seq/Len: 1.28 1.98 0.71
MirrorTree (Pazo et al. 2001) 0.81
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 0.00 0.68
2 0.00 0.00 0.68
5 0.00 0.00 0.68
10 0.00 0.00 0.68
20 0.00 0.00 0.68
100 0.00 0.00 0.69
∞ 0.04 0.03 0.70
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
54_L 41_L 1.44 0.62 0.00
66_Y 25_R 1.44 0.62 0.00
42_V 39_Y 1.40 0.59 0.00
68_G 35_S 1.38 0.57 0.00
41_F 21_I 1.35 0.55 0.00
50_A 41_L 1.35 0.55 0.00
6_S 69_V 1.27 0.48 0.00
32_L 49_A 1.21 0.43 0.00
14_M 4_P 1.21 0.43 0.00
96_I 39_Y 1.17 0.39 0.00
94_G 52_I 1.16 0.39 0.00
44_F 87_V 1.16 0.39 0.00
23_L 11_L 1.15 0.39 0.00
89_T 30_F 1.15 0.38 0.00
96_I 7_T 1.15 0.38 0.00
56_Y 6_S 1.13 0.37 0.00
88_A 65_W 1.13 0.37 0.00
60_S 77_L 1.11 0.35 0.00
86_V 10_V 1.11 0.35 0.00
39_I 42_A 1.10 0.35 0.00
7_A 29_R 1.10 0.34 0.00
26_I 17_C 1.10 0.34 0.00
16_G 24_R 1.09 0.34 0.00
23_L 65_W 1.08 0.33 0.00
43_V 86_R 1.08 0.33 0.00
21_M 84_L 1.08 0.33 0.00
16_G 23_Y 1.07 0.32 0.00
36_G 36_L 1.07 0.32 0.00
96_I 42_A 1.07 0.32 0.00
16_G 74_L 1.07 0.32 0.00
35_F 46_G 1.06 0.32 0.00
97_G 46_G 1.06 0.32 0.00
62_V 15_A 1.06 0.31 0.00
12_S 36_L 1.05 0.31 0.00
30_A 9_T 1.05 0.30 0.00
2_S 9_T 1.05 0.30 0.00
100_E 17_C 1.04 0.30 0.00
62_V 23_Y 1.04 0.30 0.00
13_A 12_V 1.03 0.29 0.00
65_Y 50_L 1.02 0.29 0.00
13_A 35_S 1.02 0.29 0.00
57_L 68_G 1.02 0.28 0.00
8_A 41_L 1.01 0.28 0.00
96_I 21_I 1.00 0.28 0.00
67_A 31_R 1.00 0.27 0.00
37_G 82_G 1.00 0.27 0.00
64_G 82_G 1.00 0.27 0.00
47_D 24_R 1.00 0.27 0.00
104_G 80_A 0.99 0.27 0.00
89_T 39_Y 0.98 0.26 0.00
43_V 36_L 0.98 0.26 0.00
86_V 26_A 0.98 0.26 0.00
22_Y 5_L 0.98 0.26 0.00
117_R 71_L 0.97 0.25 0.00
75_G 67_L 0.97 0.25 0.00
113_G 80_A 0.97 0.25 0.00
59_V 63_S 0.96 0.25 0.00
86_V 33_G 0.96 0.25 0.00
22_Y 62_L 0.96 0.25 0.00
47_D 84_L 0.96 0.25 0.00
15_A 36_L 0.96 0.24 0.00
50_A 24_R 0.96 0.24 0.00
26_I 85_A 0.96 0.24 0.00
88_A 29_R 0.95 0.24 0.00
85_F 17_C 0.95 0.24 0.00
120_G 49_A 0.95 0.24 0.00
23_L 5_L 0.95 0.24 0.00
36_G 53_V 0.94 0.23 0.00
14_M 75_V 0.94 0.23 0.00
61_W 63_S 0.93 0.23 0.00
88_A 27_G 0.92 0.22 0.00
38_A 88_L 0.92 0.22 0.00
9_S 19_R 0.92 0.22 0.00
40_F 40_L 0.92 0.22 0.00
33_G 83_N 0.92 0.22 0.00
81_G 73_L 0.91 0.22 0.00
5_S 48_Q 0.91 0.22 0.00
106_E 29_R 0.91 0.21 0.00
95_G 90_L 0.91 0.21 0.00
70_E 63_S 0.91 0.21 0.00
27_D 53_V 0.90 0.21 0.00
25_G 24_R 0.90 0.21 0.00
27_D 81_R 0.90 0.21 0.00
17_V 53_V 0.89 0.21 0.00
98_M 8_L 0.89 0.20 0.00
22_Y 31_R 0.89 0.20 0.00
24_P 73_L 0.89 0.20 0.00
32_L 45_T 0.89 0.20 0.00
41_F 70_L 0.89 0.20 0.00
36_G 39_Y 0.89 0.20 0.00
36_G 37_C 0.89 0.20 0.00
22_Y 71_L 0.89 0.20 0.00
82_M 39_Y 0.88 0.20 0.00
86_V 27_G 0.88 0.20 0.00
101_W 2_V 0.88 0.20 0.00
23_L 42_A 0.88 0.20 0.00
12_S 84_L 0.88 0.20 0.00
93_T 46_G 0.88 0.20 0.00
28_G 25_R 0.87 0.20 0.00
97_G 37_C 0.87 0.20 0.00
21_M 20_L 0.87 0.19 0.00
4_P 46_G 0.87 0.19 0.00
49_N 35_S 0.86 0.19 0.00
92_V 51_G 0.86 0.19 0.00
107_L 36_L 0.86 0.19 0.00
99_L 13_C 0.86 0.19 0.00
45_A 13_C 0.85 0.18 0.00
47_D 25_R 0.85 0.18 0.00
24_P 45_T 0.85 0.18 0.00
62_V 46_G 0.85 0.18 0.00
61_W 78_L 0.85 0.18 0.00
29_N 9_T 0.85 0.18 0.00
88_A 88_L 0.84 0.18 0.00
55_G 35_S 0.84 0.18 0.00
94_G 40_L 0.84 0.18 0.00
6_S 14_S 0.84 0.18 0.00
69_I 53_V 0.84 0.18 0.00
40_F 17_C 0.84 0.18 0.00
57_L 9_T 0.83 0.18 0.00
40_F 66_M 0.83 0.18 0.00
35_F 28_A 0.83 0.17 0.00
60_S 39_Y 0.83 0.17 0.00
8_A 64_P 0.83 0.17 0.00
16_G 50_L 0.83 0.17 0.00
107_L 25_R 0.83 0.17 0.00
8_A 8_L 0.82 0.17 0.00
98_M 30_F 0.82 0.17 0.00
6_S 72_V 0.82 0.17 0.00
36_G 87_V 0.82 0.17 0.00
52_T 62_L 0.82 0.17 0.00
75_G 70_L 0.82 0.17 0.00
97_G 54_A 0.82 0.17 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
3608 0.71 AlpB and AlpC Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3601 0.04 AlpB and AlpC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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