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OPENSEQ.org
cI_E_F
Genes: A B A+B
Length: 147 184 299
Sequences: 3696 2037 1643
Seq/Len: 25.14 11.07 5.49
MirrorTree (Pazo et al. 2001) 0.82
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 0.00 0.00 0.21
2 0.00 0.00 0.31
5 0.00 0.00 0.87
10 0.00 0.00 3.83
20 0.00 0.00 4.29
100 0.01 0.01 4.67
∞ 0.01 0.02 4.96
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
94_E 127_K 2.42 1.00 1.00
102_E 145_S 2.39 1.00 1.00
117_L 156_F 1.92 1.00 0.98
109_V 145_S 1.86 1.00 0.98
117_L 145_S 1.82 1.00 0.98
102_E 142_E 1.77 1.00 0.97
103_A 141_V 1.63 0.99 0.95
83_L 29_L 1.40 0.98 0.89
102_E 138_V 1.39 0.98 0.89
98_V 138_V 1.39 0.98 0.89
31_L 141_V 1.34 0.97 0.87
111_L 57_I 1.34 0.97 0.86
13_H 49_Y 1.32 0.97 0.86
65_S 25_P 1.31 0.96 0.85
71_V 70_V 1.31 0.96 0.85
113_G 152_L 1.29 0.96 0.84
25_G 143_L 1.23 0.94 0.80
117_L 142_E 1.22 0.94 0.80
72_A 65_V 1.18 0.92 0.76
122_A 20_I 1.15 0.91 0.74
102_E 134_F 1.14 0.91 0.73
83_L 54_L 1.12 0.90 0.71
123_L 154_V 1.11 0.89 0.71
72_A 16_T 1.09 0.88 0.69
117_L 152_L 1.07 0.87 0.67
66_A 68_V 1.06 0.86 0.65
52_S 87_W 1.06 0.86 0.65
113_G 149_L 1.05 0.86 0.64
61_R 33_I 1.05 0.86 0.64
75_F 69_F 1.04 0.84 0.63
80_V 60_A 1.03 0.84 0.62
49_P 51_A 1.03 0.84 0.61
24_I 116_D 1.02 0.83 0.61
90_T 130_G 1.01 0.82 0.60
77_I 146_M 1.00 0.81 0.58
54_I 36_L 0.99 0.81 0.57
23_A 33_I 0.98 0.80 0.57
102_E 141_V 0.98 0.79 0.56
91_S 131_I 0.97 0.79 0.55
70_L 32_L 0.97 0.79 0.55
68_F 57_I 0.97 0.78 0.54
82_A 57_I 0.96 0.78 0.54
60_A 86_Q 0.96 0.78 0.54
74_F 32_L 0.96 0.77 0.53
68_F 74_L 0.95 0.77 0.53
55_D 12_A 0.95 0.77 0.52
18_I 8_C 0.94 0.75 0.51
96_G 142_E 0.93 0.75 0.50
97_W 129_V 0.92 0.73 0.49
17_A 4_A 0.92 0.73 0.49
36_F 63_I 0.91 0.73 0.48
100_F 73_M 0.91 0.72 0.48
67_K 52_G 0.91 0.72 0.47
55_D 54_L 0.91 0.72 0.47
92_I 155_A 0.91 0.72 0.47
75_F 61_G 0.90 0.71 0.46
80_V 51_A 0.90 0.71 0.46
37_L 73_M 0.90 0.71 0.46
110_L 71_V 0.90 0.70 0.46
49_P 13_I 0.89 0.70 0.45
87_A 141_V 0.89 0.70 0.45
80_V 55_E 0.88 0.69 0.44
120_I 130_G 0.88 0.69 0.44
101_V 28_A 0.88 0.68 0.43
76_V 75_N 0.88 0.68 0.43
86_F 39_I 0.88 0.68 0.43
110_L 148_L 0.87 0.68 0.43
82_A 46_L 0.87 0.67 0.42
14_W 19_V 0.87 0.67 0.42
28_C 13_I 0.86 0.66 0.41
120_I 36_L 0.86 0.66 0.41
124_D 39_I 0.86 0.65 0.41
49_P 32_L 0.85 0.65 0.40
109_V 152_L 0.85 0.65 0.40
94_E 131_I 0.85 0.64 0.39
73_M 70_V 0.84 0.64 0.39
90_T 146_M 0.84 0.63 0.39
122_A 24_N 0.84 0.63 0.39
59_S 77_G 0.84 0.63 0.38
16_F 157_H 0.84 0.63 0.38
73_M 64_M 0.83 0.61 0.37
30_M 54_L 0.82 0.61 0.36
56_S 73_M 0.82 0.60 0.36
61_R 76_L 0.82 0.60 0.35
15_A 67_F 0.82 0.60 0.35
50_F 44_F 0.82 0.60 0.35
122_A 71_V 0.81 0.60 0.35
54_I 73_M 0.81 0.60 0.35
76_V 27_H 0.81 0.59 0.35
16_F 107_I 0.81 0.59 0.35
62_L 65_V 0.81 0.59 0.34
91_S 141_V 0.81 0.58 0.34
14_W 133_L 0.80 0.57 0.33
83_L 57_I 0.80 0.57 0.33
65_S 68_V 0.80 0.57 0.33
109_V 65_V 0.79 0.56 0.32
67_K 62_A 0.79 0.56 0.32
27_C 15_A 0.79 0.56 0.32
91_S 130_G 0.79 0.56 0.32
47_N 93_W 0.79 0.56 0.32
69_Y 160_R 0.79 0.55 0.32
82_A 54_L 0.78 0.55 0.31
82_A 146_M 0.78 0.55 0.31
76_V 72_M 0.78 0.55 0.31
36_F 106_V 0.78 0.55 0.31
37_L 107_I 0.78 0.54 0.31
31_L 129_V 0.78 0.54 0.31
91_S 80_E 0.78 0.54 0.31
80_V 103_M 0.78 0.54 0.31
21_I 46_L 0.78 0.54 0.31
54_I 158_V 0.78 0.54 0.30
19_F 60_A 0.77 0.54 0.30
75_F 50_F 0.77 0.53 0.30
93_R 142_E 0.77 0.53 0.30
61_R 25_P 0.77 0.53 0.30
72_A 172_K 0.77 0.53 0.30
114_L 23_T 0.77 0.53 0.30
71_V 132_T 0.77 0.53 0.29
123_L 32_L 0.77 0.53 0.29
30_M 57_I 0.77 0.53 0.29
86_F 57_I 0.76 0.52 0.29
104_A 34_I 0.76 0.52 0.29
86_F 53_A 0.76 0.52 0.29
87_A 156_F 0.76 0.52 0.29
125_W 141_V 0.76 0.52 0.28
122_A 156_F 0.76 0.51 0.28
68_F 45_S 0.76 0.51 0.28
88_W 52_G 0.76 0.51 0.28
28_C 91_Q 0.75 0.51 0.28
91_S 39_I 0.75 0.51 0.28
108_F 108_V 0.75 0.51 0.28
68_F 143_L 0.75 0.50 0.27
91_S 163_R 0.75 0.50 0.27
17_A 99_L 0.75 0.50 0.27
54_I 55_E 0.75 0.50 0.27
90_T 79_S 0.75 0.50 0.27
67_K 68_V 0.74 0.50 0.27
39_G 16_T 0.74 0.50 0.27
24_I 107_I 0.74 0.50 0.27
84_Y 158_V 0.74 0.49 0.27
34_G 50_F 0.74 0.49 0.27
34_G 154_V 0.74 0.49 0.27
23_A 43_F 0.74 0.49 0.27
64_L 38_A 0.74 0.49 0.27
66_A 67_F 0.74 0.49 0.27
29_L 135_G 0.74 0.49 0.27
92_I 73_M 0.74 0.49 0.27
120_I 152_L 0.74 0.49 0.27
88_W 31_Y 0.74 0.49 0.26
100_F 18_R 0.74 0.49 0.26
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
7433 1.02 3rko_2_E_F Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.59 Done - Shared
2306 5.49 cI_E_F Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
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