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OPENSEQ.org
a
Genes: A B A+B
Length: 184 100 262
Sequences: 2185 2614 1768
Seq/Len: 11.88 26.14 6.75
MirrorTree (Pazo et al. 2001) 0.82
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 0.02 0.07 5.43
2 0.02 0.07 5.64
5 0.02 0.07 5.82
10 0.02 0.07 6.04
20 0.02 0.07 6.23
100 0.03 0.08 6.31
∞ 0.05 0.08 6.31
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
13_I 13_I 4.96 1.00 1.00
6_Y 6_H 3.05 1.00 1.00
17_L 17_L 2.73 1.00 1.00
16_T 14_L 2.49 1.00 1.00
42_V 10_L 2.25 1.00 0.99
19_V 33_I 2.13 1.00 0.99
39_I 44_L 2.06 1.00 0.99
16_T 17_L 1.99 1.00 0.99
144_A 67_S 1.95 1.00 0.99
29_L 33_I 1.72 1.00 0.97
159_G 81_L 1.69 1.00 0.96
20_I 21_G 1.59 1.00 0.95
147_L 75_I 1.50 0.99 0.93
55_E 40_N 1.45 0.99 0.92
129_V 60_V 1.37 0.98 0.89
19_V 34_G 1.33 0.98 0.87
73_M 32_L 1.33 0.98 0.87
46_L 48_V 1.32 0.98 0.87
28_A 31_M 1.31 0.98 0.86
9_G 10_L 1.30 0.98 0.86
57_I 19_L 1.29 0.97 0.85
130_G 73_A 1.25 0.96 0.82
43_F 44_L 1.22 0.96 0.81
35_S 37_I 1.19 0.95 0.79
158_V 82_Q 1.18 0.95 0.78
2_E 6_H 1.18 0.95 0.78
4_A 98_M 1.16 0.94 0.76
139_L 82_Q 1.10 0.92 0.70
150_A 67_S 1.09 0.91 0.69
43_F 40_N 1.07 0.90 0.68
153_V 24_I 1.06 0.90 0.67
48_A 47_V 1.06 0.90 0.67
40_S 81_L 1.04 0.89 0.65
18_R 33_I 1.03 0.88 0.63
155_A 60_V 1.02 0.87 0.62
28_A 97_E 1.00 0.86 0.60
77_G 28_L 0.99 0.85 0.59
157_H 81_L 0.99 0.85 0.59
2_E 3_P 0.98 0.84 0.57
140_A 64_L 0.98 0.84 0.57
145_S 66_I 0.97 0.83 0.56
42_V 7_G 0.97 0.83 0.56
71_V 14_L 0.96 0.83 0.55
129_V 56_T 0.96 0.82 0.55
154_V 99_R 0.95 0.82 0.55
49_Y 60_V 0.95 0.81 0.54
40_S 11_A 0.94 0.81 0.54
75_N 50_G 0.94 0.81 0.53
60_A 76_G 0.94 0.81 0.53
43_F 62_Y 0.92 0.79 0.50
24_N 17_L 0.91 0.78 0.49
81_I 46_F 0.91 0.78 0.49
46_L 38_M 0.91 0.77 0.49
48_A 48_V 0.91 0.77 0.48
36_L 22_L 0.90 0.77 0.48
132_T 56_T 0.89 0.76 0.47
39_I 10_L 0.89 0.76 0.47
39_I 40_N 0.88 0.75 0.46
142_E 86_R 0.88 0.74 0.45
24_N 68_L 0.87 0.73 0.44
143_L 95_V 0.87 0.73 0.44
81_I 34_G 0.87 0.73 0.44
151_G 71_A 0.87 0.73 0.44
28_A 82_Q 0.86 0.72 0.43
154_V 18_G 0.86 0.72 0.42
40_S 48_V 0.86 0.72 0.42
66_L 90_L 0.86 0.72 0.42
73_M 41_A 0.85 0.71 0.42
46_L 52_Y 0.85 0.71 0.42
65_V 23_V 0.85 0.70 0.41
67_F 78_A 0.84 0.70 0.40
123_P 11_A 0.84 0.69 0.40
157_H 82_Q 0.84 0.69 0.40
130_G 67_S 0.83 0.69 0.39
32_L 19_L 0.83 0.69 0.39
41_G 10_L 0.83 0.68 0.39
136_P 57_D 0.83 0.68 0.39
128_A 26_R 0.83 0.68 0.39
33_I 95_V 0.83 0.68 0.39
9_G 65_A 0.83 0.68 0.38
64_M 33_I 0.82 0.67 0.38
147_L 24_I 0.82 0.67 0.38
25_P 73_A 0.82 0.66 0.37
20_I 24_I 0.82 0.66 0.37
5_F 7_G 0.81 0.66 0.37
145_S 20_T 0.81 0.66 0.37
52_G 93_D 0.81 0.66 0.37
111_I 65_A 0.81 0.66 0.36
22_H 13_I 0.81 0.65 0.36
121_G 9_I 0.81 0.65 0.36
137_Y 32_L 0.81 0.65 0.36
140_A 63_I 0.81 0.65 0.36
55_E 66_I 0.81 0.65 0.36
39_I 14_L 0.81 0.65 0.36
145_S 57_D 0.81 0.65 0.36
51_A 47_V 0.80 0.65 0.35
17_L 3_P 0.80 0.64 0.35
129_V 30_F 0.80 0.64 0.35
71_V 19_L 0.80 0.64 0.35
20_I 17_L 0.79 0.63 0.34
11_I 86_R 0.79 0.63 0.34
64_M 25_R 0.79 0.63 0.34
50_F 84_H 0.79 0.62 0.34
124_I 26_R 0.79 0.62 0.34
140_A 45_A 0.79 0.62 0.34
142_E 9_I 0.79 0.62 0.34
146_M 38_M 0.79 0.62 0.33
145_S 85_R 0.78 0.62 0.33
154_V 29_L 0.77 0.60 0.32
71_V 94_S 0.77 0.60 0.32
162_E 17_L 0.77 0.59 0.31
58_V 70_A 0.77 0.59 0.31
54_L 64_L 0.77 0.59 0.31
36_L 40_N 0.76 0.59 0.31
47_G 17_L 0.76 0.58 0.30
73_M 66_I 0.76 0.58 0.30
74_L 75_I 0.75 0.57 0.29
4_A 38_M 0.75 0.56 0.29
29_L 49_A 0.75 0.56 0.29
71_V 45_A 0.75 0.56 0.29
7_I 89_N 0.75 0.56 0.29
147_L 32_L 0.75 0.56 0.29
102_I 9_I 0.75 0.56 0.29
154_V 80_L 0.75 0.56 0.28
79_S 38_M 0.74 0.55 0.28
46_L 7_G 0.74 0.55 0.28
55_E 18_G 0.74 0.55 0.28
133_L 56_T 0.73 0.54 0.27
132_T 57_D 0.73 0.54 0.27
43_F 18_G 0.73 0.54 0.27
23_T 42_S 0.73 0.53 0.27
144_A 66_I 0.73 0.53 0.27
128_A 56_T 0.73 0.53 0.27
149_L 73_A 0.73 0.53 0.27
58_V 92_I 0.73 0.53 0.26
57_I 20_T 0.72 0.53 0.26
52_G 91_N 0.72 0.53 0.26
112_L 13_I 0.72 0.52 0.26
81_I 80_L 0.72 0.52 0.26
1_M 29_L 0.72 0.51 0.25
127_K 90_L 0.72 0.51 0.25
156_F 57_D 0.72 0.51 0.25
14_L 13_I 0.71 0.51 0.25
114_V 60_V 0.71 0.51 0.25
20_I 20_T 0.71 0.51 0.25
156_F 81_L 0.71 0.51 0.25
3_F 26_R 0.71 0.51 0.25
159_G 45_A 0.71 0.51 0.25
55_E 84_H 0.71 0.51 0.25
92_V 44_L 0.71 0.50 0.24
68_V 80_L 0.71 0.50 0.24
151_G 93_D 0.70 0.50 0.24
104_L 45_A 0.70 0.49 0.24
15_A 37_I 0.70 0.49 0.24
146_M 11_A 0.70 0.49 0.24
152_L 96_S 0.70 0.49 0.23
56_I 82_Q 0.70 0.48 0.23
69_F 85_R 0.70 0.48 0.23
19_V 46_F 0.69 0.48 0.23
8_C 46_F 0.69 0.48 0.23
77_G 80_L 0.69 0.47 0.23
10_L 9_I 0.69 0.47 0.22
131_I 11_A 0.69 0.47 0.22
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
14274 6.75 a Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
2308 5.91 cI_F_G Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
0001 3.75 NUOJ NUOK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 1.00 Done - Shared
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