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OPENSEQ.org
SMC H ScpB redo w unlim
Genes: A B A+B
Length: 190 197 361
Sequences: 483 2312 87
Seq/Len: 2.54 11.74 0.24
MirrorTree (Pazo et al. 2001) 0.57
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 0.01 0.02 0.00
2 0.01 0.02 0.01
5 0.01 0.02 0.01
10 0.01 0.02 0.01
20 0.01 0.02 0.02
100 0.02 0.02 0.05
∞ 0.02 0.02 0.22
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
54_E 57_G 1.71 0.49 0.00
182_G 132_L 1.58 0.41 0.00
70_T 97_V 1.46 0.34 0.00
12_L 160_L 1.46 0.34 0.00
61_L 99_A 1.35 0.28 0.00
101_D 12_V 1.33 0.27 0.00
88_F 51_Y 1.32 0.27 0.00
95_P 16_L 1.32 0.26 0.00
116_S 165_E 1.31 0.26 0.00
61_L 150_T 1.30 0.26 0.00
47_I 109_R 1.28 0.24 0.00
99_I 60_L 1.24 0.23 0.00
12_L 150_T 1.24 0.23 0.00
119_L 112_I 1.23 0.22 0.00
103_Q 25_T 1.22 0.22 0.00
52_K 60_L 1.20 0.21 0.00
57_I 133_L 1.19 0.20 0.00
63_A 107_I 1.19 0.20 0.00
132_Y 158_F 1.19 0.20 0.00
68_V 58_I 1.19 0.20 0.00
167_T 162_T 1.18 0.20 0.00
99_I 26_K 1.18 0.20 0.00
133_R 100_I 1.17 0.20 0.00
13_E 24_L 1.17 0.20 0.00
157_K 65_D 1.16 0.19 0.00
73_E 144_R 1.15 0.19 0.00
155_L 165_E 1.15 0.19 0.00
165_I 152_P 1.14 0.19 0.00
76_A 126_S 1.14 0.18 0.00
181_G 132_L 1.14 0.18 0.00
25_G 111_E 1.13 0.18 0.00
181_G 90_L 1.13 0.18 0.00
61_L 145_A 1.11 0.17 0.00
37_G 104_K 1.11 0.17 0.00
149_L 99_A 1.11 0.17 0.00
144_L 69_L 1.11 0.17 0.00
102_R 28_Q 1.10 0.17 0.00
22_F 145_A 1.10 0.17 0.00
170_G 98_L 1.10 0.17 0.00
170_G 106_P 1.10 0.17 0.00
170_G 127_L 1.10 0.17 0.00
170_G 154_F 1.10 0.17 0.00
182_G 90_L 1.10 0.17 0.00
51_Q 101_V 1.09 0.17 0.00
12_L 109_R 1.09 0.17 0.00
72_D 124_L 1.08 0.16 0.00
65_A 145_A 1.08 0.16 0.00
49_T 30_L 1.08 0.16 0.00
61_L 166_L 1.07 0.16 0.00
61_L 96_E 1.07 0.16 0.00
147_E 24_L 1.07 0.16 0.00
124_E 91_S 1.07 0.16 0.00
97_S 51_Y 1.07 0.16 0.00
65_A 29_L 1.07 0.16 0.00
65_A 113_E 1.05 0.15 0.00
29_V 23_G 1.05 0.15 0.00
58_E 93_A 1.05 0.15 0.00
51_Q 28_Q 1.05 0.15 0.00
54_E 93_A 1.05 0.15 0.00
145_I 76_A 1.04 0.15 0.00
53_Y 90_L 1.04 0.15 0.00
125_L 137_G 1.03 0.15 0.00
68_V 44_M 1.02 0.14 0.00
135_V 115_I 1.02 0.14 0.00
61_L 167_P 1.01 0.14 0.00
61_L 95_L 1.01 0.14 0.00
119_L 44_M 1.01 0.14 0.00
61_L 105_Q 1.01 0.14 0.00
172_V 27_K 1.01 0.14 0.00
101_D 113_E 1.00 0.14 0.00
136_I 107_I 1.00 0.14 0.00
67_H 72_K 1.00 0.14 0.00
50_E 115_I 1.00 0.14 0.00
61_L 109_R 1.00 0.14 0.00
169_E 52_R 0.99 0.14 0.00
57_I 44_M 0.99 0.13 0.00
49_T 58_I 0.98 0.13 0.00
131_A 19_A 0.98 0.13 0.00
170_G 116_R 0.97 0.13 0.00
143_V 28_Q 0.97 0.13 0.00
117_S 101_V 0.97 0.13 0.00
13_E 170_P 0.97 0.13 0.00
87_S 31_T 0.97 0.13 0.00
183_A 82_L 0.97 0.13 0.00
83_L 132_L 0.97 0.13 0.00
38_G 20_G 0.96 0.13 0.00
49_T 160_L 0.96 0.13 0.00
142_T 28_Q 0.96 0.12 0.00
157_K 140_D 0.96 0.12 0.00
147_E 119_K 0.96 0.12 0.00
6_R 172_N 0.96 0.12 0.00
122_A 139_A 0.96 0.12 0.00
39_I 9_K 0.96 0.12 0.00
21_G 118_V 0.95 0.12 0.00
53_Y 60_L 0.95 0.12 0.00
122_A 132_L 0.95 0.12 0.00
112_A 66_T 0.95 0.12 0.00
122_A 146_I 0.95 0.12 0.00
139_L 166_L 0.94 0.12 0.00
10_D 75_F 0.94 0.12 0.00
42_A 47_V 0.94 0.12 0.00
47_I 145_A 0.94 0.12 0.00
84_K 33_L 0.94 0.12 0.00
7_S 158_F 0.94 0.12 0.00
71_D 25_T 0.93 0.12 0.00
55_T 16_L 0.93 0.12 0.00
41_G 132_L 0.93 0.12 0.00
73_E 150_T 0.93 0.12 0.00
65_A 47_V 0.93 0.12 0.00
152_A 25_T 0.93 0.12 0.00
151_G 45_A 0.93 0.12 0.00
75_S 121_E 0.93 0.12 0.00
54_E 167_P 0.93 0.12 0.00
144_L 110_A 0.93 0.12 0.00
82_Y 14_A 0.93 0.12 0.00
165_I 133_L 0.92 0.12 0.00
93_F 144_R 0.92 0.12 0.00
47_I 124_L 0.92 0.12 0.00
26_V 71_T 0.92 0.11 0.00
181_G 69_L 0.92 0.11 0.00
177_G 129_A 0.91 0.11 0.00
38_G 69_L 0.91 0.11 0.00
8_K 118_V 0.91 0.11 0.00
92_T 120_S 0.91 0.11 0.00
164_R 97_V 0.91 0.11 0.00
48_S 77_P 0.91 0.11 0.00
92_T 158_F 0.91 0.11 0.00
168_L 152_P 0.91 0.11 0.00
12_L 147_L 0.90 0.11 0.00
88_F 119_K 0.90 0.11 0.00
91_A 57_G 0.90 0.11 0.00
177_G 158_F 0.90 0.11 0.00
127_T 24_L 0.90 0.11 0.00
78_K 32_V 0.90 0.11 0.00
64_S 88_K 0.89 0.11 0.00
53_Y 29_L 0.89 0.11 0.00
82_Y 50_E 0.89 0.11 0.00
43_V 110_A 0.89 0.11 0.00
22_F 22_E 0.89 0.11 0.00
148_D 144_R 0.88 0.11 0.00
175_P 24_L 0.88 0.10 0.00
61_L 159_G 0.88 0.10 0.00
142_T 113_E 0.88 0.10 0.00
4_Q 139_A 0.88 0.10 0.00
11_M 118_V 0.88 0.10 0.00
180_T 152_P 0.88 0.10 0.00
86_N 12_V 0.88 0.10 0.00
64_S 47_V 0.88 0.10 0.00
25_G 148_Y 0.88 0.10 0.00
12_L 96_E 0.88 0.10 0.00
116_S 44_M 0.87 0.10 0.00
5_A 160_L 0.87 0.10 0.00
45_E 72_K 0.87 0.10 0.00
6_R 162_T 0.87 0.10 0.00
65_A 170_P 0.87 0.10 0.00
26_V 15_L 0.87 0.10 0.00
57_I 27_K 0.87 0.10 0.00
77_R 91_S 0.87 0.10 0.00
43_V 94_S 0.87 0.10 0.00
159_L 28_Q 0.87 0.10 0.00
176_G 120_S 0.86 0.10 0.00
17_G 25_T 0.86 0.10 0.00
18_D 140_D 0.86 0.10 0.00
167_T 121_E 0.86 0.10 0.00
21_G 13_E 0.85 0.10 0.00
143_V 99_A 0.85 0.10 0.00
87_S 79_L 0.85 0.10 0.00
81_Q 40_L 0.85 0.10 0.00
141_G 170_P 0.85 0.10 0.00
45_E 24_L 0.85 0.10 0.00
51_Q 53_G 0.85 0.10 0.00
140_L 96_E 0.85 0.10 0.00
44_L 150_T 0.85 0.10 0.00
164_R 108_T 0.85 0.10 0.00
48_S 62_E 0.85 0.10 0.00
140_L 138_R 0.85 0.10 0.00
70_T 40_L 0.85 0.10 0.00
132_Y 68_M 0.84 0.10 0.00
107_R 145_A 0.84 0.10 0.00
170_G 102_S 0.84 0.10 0.00
142_T 75_F 0.84 0.10 0.00
122_A 15_L 0.84 0.10 0.00
16_Q 94_S 0.84 0.10 0.00
89_G 69_L 0.84 0.10 0.00
97_S 121_E 0.84 0.10 0.00
96_L 14_A 0.84 0.10 0.00
8_K 104_K 0.84 0.10 0.00
144_L 163_L 0.83 0.10 0.00
164_R 164_D 0.83 0.09 0.00
59_I 67_Y 0.83 0.09 0.00
116_S 31_T 0.83 0.09 0.00
9_K 73_K 0.83 0.09 0.00
55_T 24_L 0.83 0.09 0.00
93_F 26_K 0.83 0.09 0.00
155_L 33_L 0.83 0.09 0.00
36_L 92_Q 0.83 0.09 0.00
45_E 50_E 0.83 0.09 0.00
135_V 12_V 0.83 0.09 0.00
139_L 96_E 0.83 0.09 0.00
34_E 40_L 0.83 0.09 0.00
148_D 12_V 0.83 0.09 0.00
136_I 174_E 0.82 0.09 0.00
126_V 133_L 0.82 0.09 0.00
59_I 97_V 0.82 0.09 0.00
126_V 50_E 0.82 0.09 0.00
54_E 155_L 0.82 0.09 0.00
60_A 159_G 0.82 0.09 0.00
92_T 20_G 0.82 0.09 0.00
127_T 112_I 0.82 0.09 0.00
21_G 138_R 0.82 0.09 0.00
53_Y 15_L 0.82 0.09 0.00
118_F 23_G 0.82 0.09 0.00
103_Q 152_P 0.82 0.09 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)
ID Seq/Len Name Options I_Prob Status
5413 0.24 SMC H ScpB redo w unlim Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5408 0.02 SMC H ScpB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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