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OPENSEQ.org
ORM1_ORM2
Genes: A B A+B
Length: 136 135 269
Sequences: 234 224 191
Seq/Len: 1.72 1.66 0.71
MirrorTree (Pazo et al. 2001) 1.00
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 0.03 0.04 0.70
2 0.03 0.04 0.70
5 0.03 0.04 0.70
10 0.03 0.04 0.70
20 0.03 0.04 0.70
100 0.04 0.04 0.70
∞ 0.04 0.04 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
21_I 21_V 4.18 1.00 1.00
115_W 114_S 4.01 1.00 1.00
17_V 17_I 3.98 1.00 1.00
121_T 120_V 3.86 1.00 1.00
25_L 25_L 3.84 1.00 1.00
30_F 30_F 3.83 1.00 1.00
97_A 96_V 3.77 1.00 1.00
122_F 121_L 3.71 1.00 1.00
126_V 125_V 3.66 1.00 1.00
27_Y 27_Y 3.64 1.00 1.00
118_F 117_A 3.59 1.00 1.00
48_I 47_I 3.57 1.00 1.00
117_C 116_L 3.55 1.00 1.00
14_I 14_L 3.54 1.00 1.00
52_V 51_I 3.53 1.00 1.00
44_M 43_M 3.46 1.00 1.00
101_V 100_I 3.45 1.00 1.00
22_L 22_L 3.45 1.00 1.00
26_F 26_F 3.41 1.00 1.00
34_T 33_T 3.34 1.00 1.00
114_S 113_L 3.29 1.00 1.00
92_I 91_L 3.27 1.00 1.00
5_T 5_T 3.26 1.00 1.00
49_G 48_G 3.26 1.00 1.00
87_S 86_T 3.26 1.00 1.00
45_T 44_T 3.23 1.00 1.00
63_D 62_D 3.20 1.00 1.00
93_S 92_I 3.19 1.00 1.00
80_D 79_D 3.14 1.00 0.99
19_I 19_V 3.09 1.00 0.99
37_W 36_W 3.08 1.00 0.99
29_L 29_L 3.06 1.00 0.99
125_V 124_V 3.05 1.00 0.99
18_V 18_V 2.99 1.00 0.99
78_I 77_I 2.95 1.00 0.99
109_D 108_D 2.92 1.00 0.99
38_S 37_T 2.92 1.00 0.99
20_I 20_I 2.88 0.99 0.99
132_T 131_T 2.87 0.99 0.99
107_H 106_R 2.86 0.99 0.99
123_G 122_I 2.79 0.99 0.99
119_L 118_V 2.77 0.99 0.99
51_Y 50_Y 2.77 0.99 0.99
50_S 49_F 2.75 0.99 0.99
41_L 40_L 2.75 0.99 0.98
96_I 95_I 2.72 0.99 0.98
10_R 10_R 2.71 0.99 0.98
33_V 32_S 2.70 0.99 0.98
4_A 4_A 2.68 0.99 0.98
56_L 55_L 2.67 0.99 0.98
134_R 133_R 2.67 0.99 0.98
9_Q 9_Q 2.63 0.99 0.98
23_L 23_L 2.60 0.99 0.98
60_T 59_T 2.59 0.99 0.98
131_V 130_I 2.58 0.99 0.98
120_T 119_T 2.57 0.99 0.97
57_I 56_V 2.56 0.99 0.97
94_V 93_V 2.51 0.98 0.97
110_L 109_M 2.49 0.98 0.97
66_G 65_G 2.49 0.98 0.97
36_E 35_K 2.38 0.97 0.96
111_K 110_T 2.37 0.97 0.95
8_D 8_D 2.35 0.97 0.95
84_Y 83_Y 2.31 0.97 0.95
82_T 81_T 2.30 0.97 0.94
112_L 111_L 2.29 0.97 0.94
15_I 15_I 2.27 0.96 0.94
32_G 31_G 2.27 0.96 0.94
69_Y 68_Y 2.25 0.96 0.94
71_N 70_N 2.24 0.96 0.93
88_R 87_R 2.17 0.95 0.92
135_L 134_L 2.11 0.94 0.90
64_F 63_F 2.08 0.94 0.89
53_M 52_M 2.08 0.94 0.89
42_T 41_T 2.05 0.93 0.88
47_V 46_I 2.04 0.93 0.88
91_L 90_L 2.01 0.92 0.87
65_N 64_N 1.99 0.91 0.86
35_T 34_P 1.97 0.91 0.85
100_L 99_L 1.96 0.91 0.84
68_A 67_A 1.94 0.90 0.84
28_N 28_S 1.92 0.89 0.82
106_A 105_Y 1.91 0.89 0.82
2_M 2_M 1.90 0.89 0.81
74_M 73_M 1.85 0.87 0.79
108_Y 107_N 1.83 0.86 0.77
129_L 128_L 1.81 0.85 0.76
7_V 7_V 1.80 0.85 0.76
85_T 84_T 1.78 0.84 0.74
133_H 132_H 1.77 0.83 0.73
86_P 85_P 1.73 0.81 0.70
102_S 101_S 1.71 0.81 0.69
90_F 89_F 1.71 0.81 0.69
99_F 98_F 1.71 0.80 0.69
58_K 57_K 1.70 0.80 0.68
67_G 66_G 1.69 0.79 0.67
24_K 24_R 1.67 0.78 0.65
54_F 53_F 1.56 0.72 0.56
81_E 80_E 1.55 0.71 0.55
62_F 61_F 1.55 0.70 0.54
105_Y 104_Y 1.54 0.70 0.54
72_L 71_L 1.53 0.69 0.53
12_A 12_A 1.53 0.69 0.53
113_F 112_F 1.51 0.68 0.51
40_T 39_T 1.46 0.64 0.46
79_D 78_N 1.45 0.63 0.44
73_T 72_T 1.43 0.61 0.42
43_N 42_N 1.42 0.61 0.42
103_T 102_N 1.39 0.58 0.39
104_H 103_Q 1.35 0.55 0.35
83_L 82_L 1.35 0.55 0.35
127_P 126_P 1.35 0.55 0.35
130_P 129_G 1.34 0.54 0.34
136_R 135_R 1.31 0.52 0.32
11_G 11_G 1.31 0.52 0.31
98_L 97_L 1.30 0.50 0.30
70_D 69_D 1.29 0.50 0.29
39_W 38_W 1.16 0.39 0.19
3_N 3_N 1.12 0.36 0.16
6_W 6_W 1.11 0.35 0.15
16_H 16_H 1.00 0.27 0.10
13_W 13_W 1.00 0.27 0.10
46_Y 45_Y 0.95 0.24 0.08
1_N 1_N 0.94 0.23 0.08
89_K 88_K 0.76 0.14 0.03
95_P 94_P 0.73 0.13 0.03
132_T 125_V 0.67 0.11 0.02
126_V 131_T 0.67 0.11 0.02
116_N 115_N 0.67 0.11 0.02
46_Y 16_H 0.64 0.10 0.01
16_H 45_Y 0.64 0.10 0.01
133_H 135_R 0.56 0.08 0.01
136_R 132_H 0.56 0.08 0.01
75_W 74_W 0.54 0.07 0.01
47_V 118_V 0.51 0.07 0.01
81_E 107_N 0.51 0.07 0.01
119_L 46_I 0.50 0.06 0.01
134_R 135_R 0.49 0.06 0.01
108_Y 80_E 0.49 0.06 0.01
136_R 133_R 0.49 0.06 0.01
42_T 27_Y 0.48 0.06 0.01
27_Y 41_T 0.48 0.06 0.01
31_P 104_Y 0.47 0.06 0.01
79_D 88_K 0.46 0.06 0.01
89_K 78_N 0.46 0.06 0.01
24_K 28_S 0.45 0.06 0.00
28_N 24_R 0.45 0.05 0.00
82_T 89_F 0.43 0.05 0.00
90_F 81_T 0.43 0.05 0.00
109_D 43_M 0.42 0.05 0.00
44_M 108_D 0.42 0.05 0.00
123_G 46_I 0.41 0.05 0.00
70_D 12_A 0.40 0.05 0.00
47_V 122_I 0.40 0.05 0.00
12_A 69_D 0.40 0.05 0.00
6_W 3_N 0.40 0.05 0.00
3_N 6_W 0.40 0.05 0.00
102_S 45_Y 0.39 0.04 0.00
125_V 89_F 0.39 0.04 0.00
90_F 124_V 0.39 0.04 0.00
46_Y 101_S 0.39 0.04 0.00
113_F 122_I 0.39 0.04 0.00
65_N 63_F 0.39 0.04 0.00
64_F 64_N 0.39 0.04 0.00
123_G 112_F 0.39 0.04 0.00
56_L 96_V 0.39 0.04 0.00
97_A 55_L 0.38 0.04 0.00
8_D 78_N 0.38 0.04 0.00
67_G 65_G 0.38 0.04 0.00
66_G 66_G 0.38 0.04 0.00
40_T 105_Y 0.38 0.04 0.00
81_E 82_L 0.38 0.04 0.00
83_L 80_E 0.38 0.04 0.00
106_A 39_T 0.38 0.04 0.00
130_P 88_K 0.38 0.04 0.00
96_I 83_Y 0.37 0.04 0.00
84_Y 95_I 0.37 0.04 0.00
89_K 129_G 0.37 0.04 0.00
99_F 94_P 0.36 0.04 0.00
95_P 98_F 0.36 0.04 0.00
122_F 126_P 0.36 0.04 0.00
127_P 121_L 0.36 0.04 0.00
79_D 8_D 0.35 0.04 0.00
57_I 51_I 0.35 0.04 0.00
113_F 126_P 0.35 0.04 0.00
127_P 112_F 0.35 0.04 0.00
24_K 37_T 0.35 0.04 0.00
16_H 134_L 0.35 0.04 0.00
135_L 16_H 0.35 0.04 0.00
42_T 46_I 0.34 0.04 0.00
47_V 41_T 0.34 0.04 0.00
62_F 3_N 0.34 0.04 0.00
3_N 61_F 0.34 0.04 0.00
93_S 96_V 0.34 0.04 0.00
109_D 110_T 0.34 0.04 0.00
1_N 3_N 0.34 0.04 0.00
130_P 115_N 0.34 0.04 0.00
3_N 1_N 0.34 0.04 0.00
80_D 72_T 0.34 0.04 0.00
62_F 53_F 0.34 0.04 0.00
73_T 79_D 0.34 0.04 0.00
15_I 16_H 0.34 0.04 0.00
54_F 61_F 0.34 0.04 0.00
58_K 72_T 0.34 0.04 0.00
90_F 23_L 0.34 0.04 0.00
16_H 15_I 0.34 0.04 0.00
23_L 89_F 0.34 0.04 0.00
70_D 53_F 0.34 0.04 0.00
73_T 57_K 0.34 0.04 0.00
38_S 24_R 0.34 0.04 0.00
54_F 69_D 0.34 0.04 0.00
52_V 56_V 0.34 0.04 0.00
45_T 27_Y 0.34 0.04 0.00
116_N 129_G 0.34 0.04 0.00
27_Y 44_T 0.34 0.04 0.00
99_F 116_L 0.33 0.04 0.00
31_P 129_G 0.33 0.04 0.00
96_I 117_A 0.33 0.04 0.00
111_K 108_D 0.33 0.04 0.00
118_F 95_I 0.33 0.04 0.00
117_C 98_F 0.33 0.04 0.00
34_T 79_D 0.33 0.04 0.00
7_V 16_H 0.33 0.04 0.00
80_D 33_T 0.33 0.04 0.00
16_H 7_V 0.33 0.04 0.00
97_A 92_I 0.33 0.04 0.00
76_E 75_E 0.33 0.04 0.00
95_P 3_N 0.33 0.04 0.00
3_N 94_P 0.32 0.04 0.00
89_K 82_L 0.32 0.04 0.00
83_L 88_K 0.32 0.04 0.00
48_I 124_V 0.32 0.04 0.00
125_V 47_I 0.32 0.04 0.00
125_V 117_A 0.32 0.04 0.00
118_F 124_V 0.32 0.04 0.00
117_C 50_Y 0.32 0.04 0.00
51_Y 116_L 0.32 0.04 0.00
116_N 39_T 0.32 0.04 0.00
40_T 115_N 0.32 0.04 0.00
104_H 107_N 0.31 0.04 0.00
121_T 121_L 0.31 0.04 0.00
130_P 78_N 0.31 0.04 0.00
67_G 7_V 0.31 0.04 0.00
7_V 66_G 0.31 0.04 0.00
108_Y 103_Q 0.31 0.04 0.00
134_R 17_I 0.31 0.04 0.00
43_N 39_T 0.31 0.04 0.00
123_G 121_L 0.31 0.04 0.00
96_I 91_L 0.31 0.03 0.00
40_T 42_N 0.31 0.03 0.00
92_I 95_I 0.31 0.03 0.00
129_L 90_L 0.31 0.03 0.00
91_L 128_L 0.30 0.03 0.00
116_N 88_K 0.30 0.03 0.00
89_K 115_N 0.30 0.03 0.00
106_A 107_N 0.30 0.03 0.00
122_F 122_I 0.30 0.03 0.00
17_V 133_R 0.30 0.03 0.00
53_M 66_G 0.30 0.03 0.00
67_G 52_M 0.30 0.03 0.00
75_W 53_F 0.30 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 = 0.014), 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).
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