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OPENSEQ.org
SMC CTH ScpB
Genes: A B A+B
Length: 155 197 320
Sequences: 2381 2312 1044
Seq/Len: 15.36 11.74 3.26
MirrorTree (Pazo et al. 2001) 0.80
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 0.11
5 0.01 0.02 0.16
10 0.01 0.02 0.20
20 0.02 0.02 0.33
100 0.03 0.02 0.71
∞ 0.05 0.02 2.97
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
80_V 23_G 1.34 0.92 0.43
15_Q 40_L 1.27 0.89 0.37
43_I 17_Y 1.12 0.79 0.25
88_V 139_A 1.09 0.77 0.23
114_I 20_G 1.05 0.72 0.20
106_K 24_L 1.03 0.71 0.19
88_V 129_A 1.03 0.70 0.19
116_I 131_A 1.02 0.69 0.18
139_V 12_V 1.00 0.68 0.17
129_L 107_I 1.00 0.67 0.17
42_E 148_Y 0.99 0.66 0.17
111_T 60_L 0.97 0.64 0.16
64_A 18_A 0.97 0.64 0.15
91_A 30_L 0.97 0.64 0.15
119_R 135_E 0.97 0.63 0.15
49_G 99_A 0.96 0.62 0.15
88_V 156_E 0.95 0.62 0.15
111_T 138_R 0.93 0.59 0.14
123_M 96_E 0.93 0.59 0.14
45_A 114_E 0.93 0.59 0.13
116_I 60_L 0.93 0.59 0.13
116_I 108_T 0.92 0.58 0.13
89_E 125_H 0.92 0.58 0.13
102_Q 12_V 0.92 0.57 0.13
55_L 76_A 0.92 0.57 0.13
128_V 128_V 0.92 0.57 0.13
88_V 64_A 0.92 0.57 0.13
118_H 96_E 0.91 0.57 0.13
69_A 122_R 0.90 0.55 0.12
73_S 53_G 0.88 0.53 0.11
119_R 20_G 0.88 0.53 0.11
83_C 142_P 0.88 0.52 0.11
116_I 120_S 0.88 0.52 0.11
140_S 138_R 0.87 0.52 0.11
20_L 57_G 0.87 0.52 0.11
100_F 139_A 0.87 0.51 0.11
75_L 121_E 0.87 0.51 0.11
101_A 114_E 0.87 0.51 0.11
13_F 124_L 0.87 0.51 0.10
95_A 163_L 0.87 0.51 0.10
67_A 103_Y 0.86 0.50 0.10
57_L 109_R 0.86 0.50 0.10
142_V 18_A 0.85 0.49 0.10
41_V 134_C 0.85 0.48 0.10
151_K 21_D 0.85 0.48 0.10
146_K 65_D 0.84 0.48 0.10
111_T 165_E 0.84 0.47 0.10
88_V 57_G 0.84 0.47 0.09
19_S 60_L 0.83 0.47 0.09
143_I 93_A 0.83 0.47 0.09
97_V 158_F 0.83 0.46 0.09
16_V 62_E 0.83 0.46 0.09
42_E 94_S 0.82 0.45 0.09
95_A 133_L 0.82 0.45 0.09
42_E 80_K 0.82 0.45 0.09
14_D 28_Q 0.82 0.45 0.09
119_R 89_G 0.82 0.45 0.09
39_S 170_P 0.81 0.44 0.09
57_L 126_S 0.81 0.43 0.08
78_R 83_I 0.81 0.43 0.08
116_I 57_G 0.81 0.43 0.08
122_T 118_V 0.80 0.42 0.08
128_V 17_Y 0.80 0.42 0.08
144_S 122_R 0.80 0.42 0.08
75_L 89_G 0.79 0.41 0.08
41_V 168_P 0.79 0.41 0.08
63_R 143_G 0.79 0.41 0.08
45_A 52_R 0.78 0.41 0.07
106_K 44_M 0.78 0.41 0.07
114_I 12_V 0.78 0.40 0.07
119_R 121_E 0.78 0.40 0.07
19_S 44_M 0.77 0.39 0.07
25_R 79_L 0.77 0.39 0.07
98_F 58_I 0.77 0.39 0.07
97_V 144_R 0.77 0.39 0.07
94_E 67_Y 0.77 0.39 0.07
91_A 70_S 0.77 0.39 0.07
37_L 10_A 0.77 0.39 0.07
20_L 16_L 0.77 0.39 0.07
117_T 88_K 0.77 0.38 0.07
103_Y 133_L 0.77 0.38 0.07
11_S 77_P 0.76 0.38 0.07
63_R 135_E 0.76 0.38 0.07
133_T 113_E 0.76 0.38 0.07
152_E 38_P 0.76 0.38 0.07
24_G 16_L 0.76 0.38 0.07
16_V 121_E 0.76 0.37 0.07
78_R 121_E 0.75 0.37 0.07
149_E 42_T 0.75 0.36 0.07
104_L 90_L 0.75 0.36 0.06
83_C 145_A 0.74 0.36 0.06
9_I 21_D 0.74 0.36 0.06
6_F 140_D 0.74 0.36 0.06
36_L 110_A 0.74 0.35 0.06
5_T 11_I 0.74 0.35 0.06
24_G 151_T 0.74 0.35 0.06
74_I 104_K 0.74 0.35 0.06
63_R 92_Q 0.74 0.35 0.06
74_I 87_S 0.74 0.35 0.06
127_D 161_K 0.74 0.35 0.06
122_T 103_Y 0.73 0.34 0.06
16_V 125_H 0.73 0.34 0.06
69_A 7_N 0.73 0.34 0.06
140_S 150_T 0.72 0.33 0.06
126_A 136_V 0.72 0.33 0.06
117_T 84_E 0.72 0.33 0.06
75_L 122_R 0.72 0.33 0.06
71_L 121_E 0.72 0.33 0.06
71_L 70_S 0.72 0.33 0.06
20_L 121_E 0.72 0.33 0.06
139_V 45_A 0.72 0.33 0.06
12_H 141_G 0.72 0.33 0.06
66_T 88_K 0.72 0.33 0.06
142_V 173_A 0.72 0.33 0.06
33_P 49_D 0.72 0.33 0.06
19_S 131_A 0.71 0.32 0.06
9_I 169_L 0.71 0.32 0.06
84_V 110_A 0.71 0.32 0.06
90_A 96_E 0.71 0.32 0.06
95_A 149_G 0.71 0.32 0.06
73_S 21_D 0.71 0.32 0.05
143_I 75_F 0.71 0.31 0.05
99_R 109_R 0.70 0.31 0.05
116_I 87_S 0.70 0.31 0.05
129_L 160_L 0.70 0.31 0.05
63_R 141_G 0.70 0.31 0.05
152_E 42_T 0.70 0.31 0.05
43_I 67_Y 0.70 0.31 0.05
80_V 129_A 0.70 0.31 0.05
118_H 91_S 0.70 0.31 0.05
11_S 12_V 0.70 0.31 0.05
41_V 133_L 0.70 0.31 0.05
55_L 30_L 0.70 0.30 0.05
113_F 114_E 0.70 0.30 0.05
76_K 165_E 0.70 0.30 0.05
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)
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