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OPENSEQ.org
H3-H4
Genes: A B A+B
Length: 103 136 230
Sequences: 2181 580 527
Seq/Len: 21.17 4.26 2.29
MirrorTree (Pazo et al. 2001) 0.76
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 0.24 0.02 2.20
2 0.26 0.03 2.20
5 0.26 0.03 2.20
10 0.27 0.04 2.20
20 0.28 0.05 2.20
100 0.29 0.06 2.21
∞ 0.31 0.08 2.21
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
45_K 78_D 4.67 1.00 1.00
87_V 125_I 4.57 1.00 1.00
59_L 97_C 4.52 1.00 1.00
53_E 91_M 4.46 1.00 1.00
21_K 54_R 4.45 1.00 1.00
27_I 60_E 4.44 1.00 1.00
70_A 108_T 4.34 1.00 1.00
44_V 77_Q 4.32 1.00 1.00
52_Y 90_V 4.28 1.00 1.00
24_R 57_K 4.07 1.00 1.00
50_L 88_S 4.03 1.00 1.00
84_A 122_P 4.01 1.00 1.00
43_G 76_A 3.97 1.00 1.00
25_D 58_S 3.93 1.00 1.00
42_G 75_I 3.93 1.00 1.00
6_K 39_P 3.92 1.00 1.00
7_G 40_H 3.90 1.00 1.00
62_F 100_Y 3.86 1.00 1.00
49_G 87_S 3.77 1.00 1.00
85_M 123_K 3.77 1.00 1.00
9_K 42_Y 3.77 1.00 1.00
30_I 63_I 3.74 1.00 1.00
10_G 43_R 3.73 1.00 1.00
75_E 113_I 3.70 1.00 1.00
31_T 64_R 3.65 1.00 1.00
93_R 131_I 3.62 1.00 1.00
5_G 38_K 3.61 1.00 1.00
82_V 120_I 3.57 1.00 1.00
88_V 126_Q 3.57 1.00 1.00
17_K 50_R 3.57 1.00 1.00
65_N 103_G 3.56 1.00 1.00
14_G 47_V 3.55 1.00 1.00
38_L 71_L 3.51 1.00 1.00
64_E 102_V 3.43 1.00 1.00
33_P 66_L 3.41 1.00 1.00
36_R 69_Q 3.38 1.00 1.00
63_L 101_L 3.31 1.00 1.00
22_V 55_Y 3.25 1.00 1.00
78_K 116_K 3.21 1.00 1.00
13_K 46_T 3.17 1.00 1.00
32_K 65_K 3.15 1.00 1.00
40_R 73_R 3.13 1.00 1.00
61_V 99_A 3.08 1.00 1.00
83_T 121_M 3.08 1.00 1.00
4_R 37_K 3.00 1.00 1.00
66_V 104_L 2.99 1.00 1.00
67_I 105_F 2.96 1.00 1.00
73_Y 111_C 2.92 1.00 1.00
48_S 86_Q 2.81 1.00 1.00
71_V 109_N 2.77 1.00 1.00
74_T 112_A 2.73 1.00 1.00
90_A 128_A 2.72 1.00 1.00
47_I 85_F 2.68 1.00 1.00
91_L 129_R 2.67 1.00 1.00
26_N 59_T 2.66 1.00 1.00
39_A 72_V 2.64 1.00 1.00
58_V 96_A 2.56 1.00 1.00
96_R 134_E 2.56 1.00 1.00
55_T 93_L 2.53 1.00 1.00
28_Q 61_L 2.45 1.00 0.99
68_R 106_E 2.45 1.00 0.99
20_R 53_R 2.33 1.00 0.99
80_K 118_V 2.25 1.00 0.99
41_R 74_E 2.22 1.00 0.99
72_T 110_L 2.22 1.00 0.99
77_A 115_A 2.20 1.00 0.99
15_G 48_A 2.16 1.00 0.99
46_R 84_R 2.16 1.00 0.99
34_A 67_P 2.15 1.00 0.98
54_E 92_A 2.12 1.00 0.98
8_G 41_R 2.08 0.99 0.98
57_G 95_E 2.01 0.99 0.98
11_L 44_P 1.95 0.99 0.97
69_D 107_D 1.94 0.99 0.97
95_G 133_G 1.94 0.99 0.97
3_G 36_V 1.91 0.99 0.97
92_K 130_R 1.87 0.99 0.96
51_I 89_A 1.82 0.98 0.95
94_Q 132_R 1.72 0.97 0.94
16_A 49_L 1.70 0.97 0.93
12_G 45_G 1.68 0.97 0.93
18_R 51_E 1.63 0.96 0.91
37_R 70_R 1.52 0.94 0.87
29_G 62_L 1.46 0.92 0.84
19_H 52_I 1.37 0.88 0.79
97_T 135_R 1.36 0.87 0.78
89_Y 127_L 1.24 0.80 0.69
23_L 56_Q 1.22 0.78 0.67
56_R 94_Q 1.14 0.71 0.57
79_R 117_R 0.89 0.44 0.29
76_H 114_H 0.80 0.34 0.20
81_T 119_T 0.76 0.30 0.17
82_V 108_T 0.74 0.28 0.15
70_A 120_I 0.73 0.27 0.15
86_D 124_D 0.62 0.18 0.08
82_V 109_N 0.54 0.13 0.05
71_V 120_I 0.53 0.13 0.05
74_T 109_N 0.52 0.12 0.04
17_K 47_V 0.51 0.12 0.04
35_I 68_F 0.51 0.12 0.04
71_V 112_A 0.51 0.12 0.04
60_K 98_E 0.46 0.10 0.03
47_I 76_A 0.42 0.08 0.02
43_G 85_F 0.42 0.08 0.02
14_G 50_R 0.40 0.07 0.02
36_R 85_F 0.36 0.06 0.01
30_I 64_R 0.36 0.06 0.01
43_G 83_L 0.34 0.06 0.01
47_I 69_Q 0.33 0.06 0.01
35_I 94_Q 0.33 0.05 0.01
31_T 63_I 0.32 0.05 0.01
66_V 107_D 0.32 0.05 0.01
56_R 68_F 0.32 0.05 0.01
33_P 65_K 0.31 0.05 0.01
97_T 134_E 0.30 0.05 0.01
12_G 41_R 0.30 0.05 0.01
69_D 104_L 0.29 0.05 0.01
32_K 66_L 0.28 0.04 0.01
12_G 44_P 0.28 0.04 0.01
71_V 113_I 0.28 0.04 0.01
7_G 35_G 0.28 0.04 0.01
33_P 69_Q 0.27 0.04 0.01
36_R 66_L 0.27 0.04 0.01
11_L 45_G 0.27 0.04 0.01
7_G 39_P 0.27 0.04 0.01
15_G 45_G 0.27 0.04 0.01
13_K 47_V 0.27 0.04 0.01
8_G 45_G 0.27 0.04 0.01
75_E 109_N 0.27 0.04 0.01
91_L 133_G 0.26 0.04 0.01
12_G 48_A 0.26 0.04 0.01
4_R 36_V 0.26 0.04 0.01
54_E 110_L 0.26 0.04 0.01
48_S 88_S 0.26 0.04 0.01
90_A 107_D 0.25 0.04 0.01
82_V 112_A 0.25 0.04 0.01
62_F 35_G 0.25 0.04 0.01
72_T 92_A 0.25 0.04 0.01
13_K 14_G 0.24 0.04 0.01
6_K 40_H 0.24 0.04 0.01
37_R 119_T 0.24 0.04 0.01
47_I 103_G 0.24 0.04 0.01
79_R 119_T 0.24 0.04 0.01
7_G 38_K 0.24 0.04 0.01
43_G 82_D 0.24 0.04 0.01
69_D 128_A 0.23 0.04 0.01
86_D 127_L 0.23 0.04 0.00
50_L 86_Q 0.23 0.04 0.00
24_R 16_A 0.23 0.04 0.00
65_N 85_F 0.23 0.04 0.00
67_I 81_T 0.23 0.04 0.00
65_N 122_P 0.23 0.04 0.00
27_I 58_S 0.23 0.04 0.00
30_I 3_R 0.23 0.04 0.00
37_R 84_R 0.23 0.04 0.00
90_A 132_R 0.23 0.04 0.00
83_T 131_I 0.23 0.03 0.00
5_G 40_H 0.22 0.03 0.00
44_V 81_T 0.22 0.03 0.00
19_H 51_E 0.22 0.03 0.00
69_D 103_G 0.22 0.03 0.00
81_T 70_R 0.22 0.03 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)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.113), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
ID Seq/Len Name Options I_Prob Status
4281 2.29 H3-H4 Δgene:(0, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
4279 0.16 H3-H4 Δgene:(0, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) Killed - Shared
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