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OPENSEQ.org
4FHR-2
Genes: A B A+B
Length: 182 160 342
Sequences: 796 995 505
Seq/Len: 4.37 6.22 1.48
MirrorTree (Pazo et al. 2001) 0.85
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 0.00 0.00 0.03
2 0.00 0.00 0.06
5 0.00 0.00 0.23
10 0.00 0.00 0.93
20 0.00 0.00 1.48
100 0.00 0.01 1.72
∞ 0.02 0.04 2.06
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
102_I 18_T 2.10 0.99 0.95
158_V 70_K 1.94 0.97 0.91
36_V 93_M 1.66 0.92 0.79
179_L 40_E 1.62 0.91 0.77
118_L 32_A 1.56 0.89 0.73
52_V 141_L 1.49 0.85 0.67
125_F 144_V 1.45 0.83 0.64
110_E 140_V 1.43 0.82 0.62
141_F 93_M 1.41 0.81 0.60
137_T 27_D 1.39 0.79 0.58
82_M 19_I 1.37 0.78 0.56
16_E 47_L 1.36 0.77 0.55
139_P 54_E 1.36 0.77 0.55
158_V 32_A 1.33 0.75 0.53
98_P 144_V 1.31 0.73 0.50
18_F 149_L 1.29 0.72 0.49
99_P 147_R 1.26 0.70 0.46
60_I 4_P 1.25 0.69 0.45
152_L 135_R 1.21 0.65 0.40
79_F 137_I 1.21 0.65 0.40
31_R 115_L 1.18 0.62 0.37
123_S 159_E 1.17 0.61 0.36
105_S 63_E 1.17 0.61 0.36
135_V 32_A 1.17 0.61 0.36
87_M 109_V 1.16 0.60 0.35
100_T 107_K 1.16 0.60 0.35
46_E 32_A 1.15 0.59 0.34
149_E 115_L 1.15 0.59 0.34
152_L 60_V 1.14 0.58 0.33
35_D 23_L 1.13 0.57 0.32
137_T 92_I 1.12 0.56 0.31
86_I 7_L 1.12 0.56 0.31
113_N 91_E 1.11 0.55 0.30
58_I 123_M 1.11 0.55 0.30
76_L 157_S 1.11 0.55 0.30
125_F 73_S 1.10 0.54 0.29
80_Y 15_H 1.09 0.53 0.28
130_P 56_T 1.09 0.53 0.28
58_I 19_I 1.07 0.51 0.27
40_I 158_D 1.07 0.51 0.27
160_W 72_I 1.07 0.51 0.26
71_I 60_V 1.06 0.50 0.25
88_G 17_Q 1.06 0.49 0.25
88_G 126_F 1.06 0.49 0.25
8_L 92_I 1.05 0.49 0.25
146_P 45_E 1.05 0.49 0.25
124_D 32_A 1.05 0.49 0.24
60_I 91_E 1.04 0.48 0.24
138_N 142_R 1.03 0.47 0.23
49_I 125_V 1.02 0.46 0.23
144_I 45_E 1.02 0.46 0.22
139_P 128_D 1.02 0.45 0.22
158_V 121_R 1.01 0.45 0.22
114_M 127_E 1.01 0.45 0.21
103_E 14_E 1.01 0.45 0.21
79_F 78_R 0.99 0.42 0.20
149_E 51_A 0.99 0.42 0.20
131_S 26_L 0.98 0.42 0.19
4_S 151_L 0.98 0.42 0.19
171_W 53_L 0.98 0.42 0.19
31_R 25_Y 0.98 0.42 0.19
36_V 91_E 0.98 0.42 0.19
61_F 83_V 0.97 0.41 0.18
138_N 104_I 0.97 0.41 0.18
175_L 125_V 0.97 0.40 0.18
155_T 23_L 0.97 0.40 0.18
75_R 103_K 0.96 0.40 0.18
151_V 45_E 0.96 0.40 0.18
9_R 6_Q 0.96 0.40 0.18
110_E 41_E 0.96 0.40 0.18
171_W 2_M 0.96 0.40 0.18
181_E 116_A 0.96 0.40 0.17
75_R 32_A 0.96 0.39 0.17
108_R 32_A 0.95 0.39 0.17
30_L 97_D 0.95 0.39 0.17
89_G 123_M 0.95 0.39 0.17
12_Q 155_G 0.95 0.39 0.17
65_V 90_A 0.95 0.38 0.17
4_S 57_S 0.94 0.37 0.16
69_S 22_V 0.94 0.37 0.16
75_R 82_K 0.94 0.37 0.16
114_M 130_L 0.93 0.37 0.16
89_G 156_A 0.93 0.37 0.15
25_Y 129_I 0.93 0.37 0.15
18_F 86_I 0.93 0.37 0.15
173_F 29_P 0.93 0.36 0.15
105_S 79_T 0.93 0.36 0.15
177_E 143_E 0.93 0.36 0.15
117_L 12_Q 0.93 0.36 0.15
91_G 116_A 0.93 0.36 0.15
101_E 71_K 0.92 0.36 0.15
20_R 138_Q 0.92 0.36 0.15
22_L 89_A 0.92 0.36 0.15
107_M 93_M 0.92 0.36 0.15
33_F 68_L 0.92 0.36 0.15
16_E 23_L 0.92 0.36 0.15
41_D 83_V 0.92 0.36 0.15
57_F 32_A 0.92 0.35 0.15
45_Y 84_G 0.92 0.35 0.15
152_L 107_K 0.92 0.35 0.15
158_V 86_I 0.91 0.35 0.15
91_G 160_L 0.91 0.35 0.15
30_L 104_I 0.91 0.35 0.15
167_I 98_R 0.91 0.35 0.14
169_V 107_K 0.91 0.35 0.14
72_F 144_V 0.91 0.34 0.14
21_A 11_L 0.90 0.34 0.14
180_L 56_T 0.90 0.34 0.14
142_V 61_V 0.90 0.34 0.14
51_S 38_L 0.90 0.34 0.14
100_T 122_R 0.90 0.34 0.14
129_I 148_D 0.90 0.34 0.14
106_I 32_A 0.90 0.34 0.14
41_D 47_L 0.90 0.34 0.13
109_K 28_P 0.89 0.33 0.13
106_I 59_E 0.89 0.33 0.13
79_F 128_D 0.89 0.33 0.13
18_F 85_G 0.89 0.33 0.13
178_P 135_R 0.89 0.33 0.13
24_T 90_A 0.89 0.33 0.13
159_S 121_R 0.89 0.33 0.13
108_R 91_E 0.88 0.33 0.13
118_L 52_L 0.88 0.32 0.12
41_D 114_E 0.88 0.32 0.12
156_A 45_E 0.88 0.32 0.12
6_E 33_Q 0.88 0.32 0.12
179_L 24_S 0.87 0.32 0.12
148_N 46_V 0.87 0.32 0.12
29_R 157_S 0.87 0.31 0.12
31_R 9_N 0.87 0.31 0.12
47_E 73_S 0.87 0.31 0.12
19_G 54_E 0.87 0.31 0.12
66_F 51_A 0.87 0.31 0.12
12_Q 27_D 0.87 0.31 0.12
137_T 42_L 0.87 0.31 0.12
129_I 140_V 0.86 0.31 0.12
134_N 23_L 0.86 0.31 0.12
86_I 22_V 0.86 0.31 0.12
71_I 91_E 0.86 0.30 0.12
100_T 7_L 0.86 0.30 0.12
30_L 58_P 0.86 0.30 0.12
56_S 100_T 0.86 0.30 0.11
11_F 35_L 0.86 0.30 0.11
14_I 39_P 0.86 0.30 0.11
77_D 70_K 0.86 0.30 0.11
167_I 120_R 0.86 0.30 0.11
46_E 43_Q 0.86 0.30 0.11
179_L 119_I 0.86 0.30 0.11
63_G 91_E 0.86 0.30 0.11
62_T 139_L 0.85 0.30 0.11
16_E 28_P 0.85 0.30 0.11
29_R 47_L 0.85 0.29 0.11
71_I 159_E 0.85 0.29 0.11
89_G 14_E 0.85 0.29 0.11
150_I 134_D 0.84 0.29 0.11
81_T 105_M 0.84 0.29 0.10
145_V 125_V 0.84 0.29 0.10
56_S 34_I 0.84 0.29 0.10
152_L 1_H 0.84 0.28 0.10
148_N 108_L 0.84 0.28 0.10
85_I 128_D 0.84 0.28 0.10
43_L 35_L 0.83 0.28 0.10
40_I 28_P 0.83 0.28 0.10
70_A 110_Q 0.83 0.28 0.10
88_G 152_A 0.83 0.28 0.10
69_S 87_D 0.82 0.27 0.10
64_D 46_V 0.82 0.27 0.10
6_E 141_L 0.82 0.27 0.10
106_I 21_V 0.82 0.27 0.10
53_M 136_S 0.82 0.27 0.10
60_I 38_L 0.82 0.27 0.10
171_W 125_V 0.82 0.27 0.10
130_P 90_A 0.82 0.27 0.10
78_L 122_R 0.82 0.27 0.10
59_V 64_I 0.82 0.27 0.10
35_D 93_M 0.82 0.27 0.10
98_P 158_D 0.82 0.27 0.10
96_N 19_I 0.82 0.27 0.09
22_L 77_S 0.81 0.26 0.09
35_D 54_E 0.81 0.26 0.09
148_N 110_Q 0.81 0.26 0.09
141_F 135_R 0.81 0.26 0.09
169_V 120_R 0.81 0.26 0.09
90_P 48_K 0.81 0.26 0.09
40_I 46_V 0.81 0.26 0.09
98_P 32_A 0.81 0.26 0.09
84_D 49_R 0.81 0.26 0.09
16_E 109_V 0.80 0.26 0.09
139_P 140_V 0.80 0.26 0.09
9_R 65_E 0.80 0.26 0.09
81_T 54_E 0.80 0.26 0.09
132_I 38_L 0.80 0.25 0.09
104_T 24_S 0.80 0.25 0.09
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
13628 1.48 4FHR-2 Δgene:(1, 20) A:(1E-20, 4) B:(1E-20, 8) msa: HHblits (2015_06) 0.95 Done
13627 4FHR-2 Δgene:(1, 20) A:(1E-20, 4) B:(1E-20, 8) msa: HHblits (2015_06) Running
13313 1.49 4FHR-2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.94 Done - Shared
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