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OPENSEQ.org
cI_F_G
Genes: A B A+B
Length: 184 100 279
Sequences: 2037 1241 1650
Seq/Len: 11.07 12.41 5.91
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 5.18
2 0.00 0.00 5.33
5 0.00 0.00 5.42
10 0.00 0.00 5.54
20 0.00 0.00 5.68
100 0.01 0.01 5.80
∞ 0.02 0.02 5.81
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 4.67 1.00 1.00
17_L 17_L 3.01 1.00 1.00
6_Y 6_H 2.67 1.00 1.00
16_T 14_L 2.55 1.00 1.00
132_T 56_T 2.46 1.00 1.00
42_V 10_L 2.37 1.00 1.00
144_A 67_S 2.07 1.00 0.99
39_I 44_L 1.92 1.00 0.98
29_L 33_I 1.87 1.00 0.98
159_G 81_L 1.87 1.00 0.98
19_V 33_I 1.74 1.00 0.97
9_G 10_L 1.66 1.00 0.96
20_I 21_G 1.60 0.99 0.95
104_L 9_I 1.53 0.99 0.94
55_E 40_N 1.50 0.99 0.93
147_L 75_I 1.42 0.98 0.91
16_T 17_L 1.38 0.98 0.89
129_V 60_V 1.34 0.97 0.87
35_S 37_I 1.25 0.96 0.82
46_L 48_V 1.25 0.95 0.82
20_I 17_L 1.21 0.94 0.80
42_V 7_G 1.21 0.94 0.79
154_V 29_L 1.19 0.94 0.78
40_S 11_A 1.18 0.93 0.77
101_A 9_I 1.13 0.92 0.73
19_V 34_G 1.13 0.91 0.73
43_F 44_L 1.12 0.91 0.72
73_M 32_L 1.12 0.91 0.72
9_G 65_A 1.12 0.91 0.72
18_R 33_I 1.07 0.89 0.68
93_W 8_L 1.07 0.88 0.68
111_I 2_I 1.06 0.88 0.67
71_V 45_A 1.04 0.86 0.64
4_A 98_M 1.03 0.85 0.63
63_I 99_R 0.97 0.80 0.56
93_W 93_D 0.96 0.79 0.54
138_V 23_V 0.95 0.79 0.54
124_I 26_R 0.95 0.78 0.53
130_G 73_A 0.95 0.78 0.53
67_F 78_A 0.94 0.78 0.53
43_F 40_N 0.94 0.77 0.52
145_S 85_R 0.94 0.77 0.52
39_I 40_N 0.94 0.77 0.52
141_V 43_A 0.94 0.77 0.52
24_N 17_L 0.93 0.77 0.52
2_E 2_I 0.92 0.76 0.50
155_A 60_V 0.92 0.76 0.50
156_F 21_G 0.92 0.75 0.49
51_A 62_Y 0.91 0.75 0.49
139_L 82_Q 0.90 0.73 0.47
67_F 35_L 0.90 0.73 0.47
74_L 75_I 0.89 0.72 0.46
17_L 3_P 0.89 0.72 0.46
16_T 37_I 0.89 0.71 0.45
157_H 82_Q 0.88 0.71 0.45
62_A 76_G 0.88 0.71 0.45
129_V 56_T 0.88 0.70 0.44
47_G 51_S 0.88 0.70 0.44
77_G 28_L 0.88 0.70 0.44
58_V 23_V 0.87 0.70 0.44
25_P 73_A 0.87 0.69 0.43
39_I 10_L 0.87 0.69 0.43
105_V 98_M 0.86 0.69 0.43
71_V 14_L 0.86 0.69 0.42
55_E 66_I 0.86 0.69 0.42
143_L 95_V 0.86 0.68 0.42
161_E 86_R 0.86 0.68 0.42
32_L 33_I 0.86 0.68 0.42
40_S 20_T 0.86 0.68 0.42
48_A 47_V 0.86 0.68 0.41
64_M 33_I 0.85 0.67 0.41
104_L 2_I 0.85 0.67 0.41
81_I 46_F 0.85 0.67 0.41
140_A 63_I 0.85 0.66 0.40
12_A 38_M 0.84 0.66 0.40
151_G 71_A 0.84 0.65 0.40
150_A 67_S 0.84 0.65 0.39
3_F 1_M 0.84 0.65 0.39
128_A 56_T 0.83 0.64 0.38
28_A 33_I 0.83 0.64 0.38
26_V 60_V 0.83 0.64 0.38
157_H 81_L 0.82 0.63 0.37
48_A 48_V 0.82 0.63 0.37
153_V 81_L 0.82 0.63 0.37
40_S 81_L 0.82 0.63 0.37
12_A 10_L 0.82 0.62 0.36
130_G 69_A 0.81 0.62 0.36
15_A 37_I 0.81 0.61 0.36
94_I 11_A 0.81 0.61 0.35
75_N 50_G 0.80 0.60 0.35
133_L 64_L 0.80 0.60 0.34
157_H 32_L 0.80 0.60 0.34
158_V 47_V 0.79 0.59 0.34
28_A 31_M 0.79 0.58 0.33
162_E 8_L 0.79 0.58 0.33
162_E 27_N 0.79 0.58 0.33
126_A 68_L 0.79 0.58 0.33
137_Y 32_L 0.79 0.58 0.33
17_L 74_S 0.78 0.57 0.33
153_V 28_L 0.78 0.57 0.32
129_V 29_L 0.77 0.56 0.31
12_A 71_A 0.77 0.56 0.31
180_T 99_R 0.77 0.56 0.31
140_A 64_L 0.77 0.56 0.31
46_L 51_S 0.77 0.56 0.31
114_V 73_A 0.77 0.56 0.31
50_F 84_H 0.77 0.55 0.31
127_K 90_L 0.77 0.55 0.30
64_M 25_R 0.77 0.55 0.30
158_V 82_Q 0.76 0.54 0.30
143_L 34_G 0.76 0.54 0.30
73_M 66_I 0.76 0.54 0.29
62_A 21_G 0.76 0.54 0.29
7_I 31_M 0.75 0.53 0.29
55_E 62_Y 0.75 0.53 0.29
80_E 68_L 0.75 0.53 0.28
32_L 19_L 0.75 0.52 0.28
63_I 24_I 0.75 0.52 0.28
160_R 40_N 0.75 0.52 0.28
25_P 22_L 0.75 0.52 0.28
83_Q 98_M 0.74 0.52 0.28
51_A 47_V 0.74 0.52 0.28
149_L 73_A 0.74 0.52 0.28
43_F 18_G 0.74 0.52 0.28
71_V 94_S 0.74 0.51 0.28
36_L 22_L 0.74 0.51 0.28
134_F 50_G 0.74 0.51 0.28
20_I 34_G 0.74 0.51 0.27
137_Y 57_D 0.74 0.51 0.27
146_M 63_I 0.74 0.51 0.27
43_F 63_I 0.73 0.50 0.27
47_G 52_Y 0.73 0.50 0.27
140_A 16_V 0.73 0.50 0.27
66_L 90_L 0.73 0.50 0.27
97_A 53_W 0.73 0.50 0.27
17_L 99_R 0.73 0.50 0.27
54_L 64_L 0.73 0.49 0.26
77_G 80_L 0.73 0.49 0.26
53_A 40_N 0.72 0.48 0.25
43_F 37_I 0.72 0.48 0.25
85_R 23_V 0.72 0.48 0.25
28_A 97_E 0.72 0.48 0.25
172_K 89_N 0.72 0.48 0.25
143_L 38_M 0.72 0.48 0.25
62_A 87_R 0.72 0.48 0.25
43_F 62_Y 0.72 0.48 0.25
11_I 80_L 0.72 0.47 0.25
39_I 66_I 0.72 0.47 0.25
86_Q 2_I 0.71 0.47 0.25
72_M 59_Q 0.71 0.47 0.24
127_K 73_A 0.71 0.47 0.24
146_M 11_A 0.71 0.47 0.24
41_G 10_L 0.71 0.47 0.24
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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