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OPENSEQ.org
SMC NTH ScpB
Genes: A B A+B
Length: 161 197 319
Sequences: 4686 2312 125
Seq/Len: 29.11 11.74 0.39
MirrorTree (Pazo et al. 2001) 0.71
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 0.01
2 0.01 0.02 0.10
5 0.02 0.02 0.16
10 0.02 0.02 0.20
20 0.02 0.02 0.35
100 0.05 0.02 0.84
∞ 0.14 0.02 3.25
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
104_V 12_V 2.05 0.82 0.14
52_S 44_M 1.57 0.54 0.04
83_T 90_L 1.56 0.53 0.04
97_E 60_L 1.44 0.45 0.03
40_I 100_I 1.40 0.41 0.02
22_F 91_S 1.29 0.34 0.02
140_I 29_L 1.24 0.31 0.01
143_Q 16_L 1.23 0.30 0.01
156_D 15_L 1.20 0.28 0.01
44_I 143_G 1.18 0.27 0.01
27_T 72_K 1.16 0.27 0.01
98_V 136_V 1.16 0.26 0.01
80_V 159_G 1.16 0.26 0.01
29_V 66_T 1.15 0.26 0.01
20_V 20_G 1.14 0.25 0.01
43_A 37_E 1.12 0.24 0.01
84_L 44_M 1.11 0.24 0.01
112_F 28_Q 1.10 0.23 0.01
149_I 40_L 1.10 0.23 0.01
25_G 70_S 1.10 0.23 0.01
51_Q 107_I 1.09 0.23 0.01
146_V 159_G 1.09 0.23 0.01
84_L 107_I 1.09 0.23 0.01
154_A 12_V 1.08 0.22 0.01
104_V 27_K 1.07 0.22 0.01
70_D 57_G 1.06 0.21 0.01
67_A 135_E 1.06 0.21 0.01
2_F 32_V 1.05 0.21 0.01
48_L 154_F 1.05 0.21 0.01
161_F 165_E 1.05 0.20 0.01
117_Q 63_Y 1.03 0.20 0.01
78_A 69_L 1.03 0.20 0.01
104_V 133_L 1.03 0.20 0.01
28_A 165_E 1.02 0.19 0.01
82_L 99_A 1.02 0.19 0.01
5_R 29_L 1.02 0.19 0.01
78_A 116_R 1.02 0.19 0.01
156_D 18_A 1.01 0.19 0.01
47_V 107_I 1.01 0.19 0.01
46_W 96_E 1.01 0.19 0.01
148_E 139_A 1.01 0.19 0.01
157_R 17_Y 1.00 0.18 0.01
132_G 105_Q 1.00 0.18 0.01
8_V 149_G 1.00 0.18 0.01
47_V 52_R 1.00 0.18 0.01
53_A 128_V 1.00 0.18 0.01
64_I 138_R 0.99 0.18 0.01
156_D 111_E 0.99 0.18 0.01
46_W 112_I 0.99 0.18 0.01
127_L 34_E 0.99 0.18 0.01
20_V 23_G 0.98 0.18 0.01
20_V 88_K 0.98 0.18 0.01
98_V 132_L 0.98 0.17 0.01
32_P 47_V 0.98 0.17 0.01
131_S 145_A 0.98 0.17 0.01
84_L 143_G 0.97 0.17 0.01
122_K 108_T 0.97 0.17 0.01
142_S 158_F 0.97 0.17 0.01
5_R 21_D 0.96 0.17 0.01
101_T 42_T 0.96 0.17 0.01
142_S 71_T 0.96 0.17 0.01
28_A 67_Y 0.96 0.17 0.01
145_K 122_R 0.95 0.17 0.01
112_F 8_W 0.95 0.16 0.01
64_I 109_R 0.95 0.16 0.01
127_L 27_K 0.95 0.16 0.01
55_S 19_A 0.94 0.16 0.01
119_C 57_G 0.94 0.16 0.01
6_L 110_A 0.94 0.16 0.01
120_R 109_R 0.94 0.16 0.01
28_A 49_D 0.94 0.16 0.01
47_V 166_L 0.94 0.16 0.01
25_G 131_A 0.94 0.16 0.01
140_I 168_P 0.93 0.16 0.01
51_Q 157_Q 0.93 0.16 0.01
116_N 71_T 0.93 0.15 0.01
94_D 67_Y 0.93 0.15 0.01
83_T 111_E 0.93 0.15 0.01
67_A 104_K 0.93 0.15 0.01
29_V 42_T 0.93 0.15 0.01
81_T 66_T 0.93 0.15 0.01
46_W 109_R 0.92 0.15 0.01
127_L 136_V 0.92 0.15 0.01
104_V 157_Q 0.91 0.15 0.00
27_T 115_I 0.91 0.15 0.00
6_L 32_V 0.91 0.15 0.00
48_L 78_Y 0.91 0.15 0.00
4_K 21_D 0.91 0.15 0.00
153_K 112_I 0.91 0.15 0.00
85_D 83_I 0.91 0.15 0.00
88_D 144_R 0.91 0.15 0.00
113_L 48_A 0.91 0.15 0.00
47_V 53_G 0.90 0.15 0.00
98_V 92_Q 0.90 0.14 0.00
116_N 31_T 0.90 0.14 0.00
158_R 16_L 0.90 0.14 0.00
28_A 62_E 0.89 0.14 0.00
76_N 79_L 0.89 0.14 0.00
100_V 25_T 0.89 0.14 0.00
83_T 42_T 0.89 0.14 0.00
32_P 14_A 0.89 0.14 0.00
8_V 72_K 0.89 0.14 0.00
151_S 104_K 0.89 0.14 0.00
48_L 80_K 0.89 0.14 0.00
161_F 138_R 0.89 0.14 0.00
160_I 144_R 0.89 0.14 0.00
15_A 121_E 0.89 0.14 0.00
64_I 121_E 0.89 0.14 0.00
29_V 170_P 0.89 0.14 0.00
153_K 140_D 0.89 0.14 0.00
28_A 70_S 0.89 0.14 0.00
150_L 135_E 0.89 0.14 0.00
20_V 37_E 0.88 0.14 0.00
22_F 75_F 0.88 0.14 0.00
107_S 164_D 0.88 0.14 0.00
50_E 116_R 0.88 0.14 0.00
5_R 170_P 0.87 0.14 0.00
116_N 79_L 0.87 0.14 0.00
100_V 107_I 0.87 0.13 0.00
117_Q 76_A 0.87 0.13 0.00
75_L 121_E 0.87 0.13 0.00
154_A 71_T 0.86 0.13 0.00
142_S 100_I 0.86 0.13 0.00
69_S 111_E 0.86 0.13 0.00
27_T 95_L 0.86 0.13 0.00
100_V 18_A 0.86 0.13 0.00
144_G 72_K 0.86 0.13 0.00
104_V 52_R 0.85 0.13 0.00
25_G 51_Y 0.85 0.13 0.00
151_S 92_Q 0.85 0.13 0.00
158_R 59_E 0.85 0.13 0.00
88_D 75_F 0.85 0.13 0.00
4_K 20_G 0.85 0.13 0.00
48_L 17_Y 0.84 0.13 0.00
142_S 96_E 0.84 0.13 0.00
99_S 162_T 0.84 0.12 0.00
80_V 152_P 0.84 0.12 0.00
78_A 70_S 0.84 0.12 0.00
58_G 89_G 0.84 0.12 0.00
141_I 137_G 0.84 0.12 0.00
29_V 34_E 0.84 0.12 0.00
76_N 175_E 0.84 0.12 0.00
63_D 75_F 0.83 0.12 0.00
100_V 53_G 0.83 0.12 0.00
86_N 159_G 0.83 0.12 0.00
129_M 33_L 0.83 0.12 0.00
70_D 25_T 0.83 0.12 0.00
8_V 52_R 0.83 0.12 0.00
22_F 148_Y 0.83 0.12 0.00
42_D 18_A 0.83 0.12 0.00
144_G 16_L 0.83 0.12 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
5411 3.55 SMC NTH ScpB redo w unlim Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.11 Done - Shared
5406 0.39 SMC NTH ScpB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.14 Done - Shared
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