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OPENSEQ.org
SMC NTH ScpB redo w unlim
Genes: A B A+B
Length: 161 197 327
Sequences: 4686 2312 1162
Seq/Len: 29.11 11.74 3.55
MirrorTree (Pazo et al. 2001) 0.35
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
76_N 23_G 1.16 0.84 0.11
142_S 107_I 1.05 0.75 0.08
157_R 158_F 0.99 0.69 0.06
48_L 28_Q 0.94 0.62 0.05
124_I 6_V 0.91 0.59 0.05
100_V 164_D 0.91 0.59 0.05
26_V 107_I 0.90 0.58 0.05
151_S 121_E 0.90 0.57 0.05
146_V 159_G 0.89 0.57 0.04
153_K 47_V 0.88 0.55 0.04
116_N 92_Q 0.86 0.53 0.04
70_D 62_E 0.85 0.51 0.04
143_Q 16_L 0.84 0.51 0.04
96_H 99_A 0.83 0.49 0.04
64_I 172_N 0.83 0.48 0.04
35_S 20_G 0.82 0.48 0.04
116_N 125_H 0.81 0.46 0.03
48_L 174_E 0.81 0.46 0.03
119_C 95_L 0.81 0.45 0.03
118_P 75_F 0.79 0.43 0.03
44_I 49_D 0.79 0.43 0.03
160_I 15_L 0.79 0.43 0.03
8_V 140_D 0.78 0.43 0.03
156_D 101_V 0.78 0.42 0.03
53_A 58_I 0.78 0.42 0.03
64_I 32_V 0.77 0.41 0.03
144_G 57_G 0.77 0.41 0.03
114_I 27_K 0.77 0.41 0.03
138_F 23_G 0.76 0.40 0.03
153_K 65_D 0.76 0.40 0.03
160_I 6_V 0.75 0.39 0.03
5_R 124_L 0.75 0.39 0.03
20_V 76_A 0.74 0.37 0.03
118_P 47_V 0.74 0.37 0.03
138_F 113_E 0.73 0.36 0.03
6_L 174_E 0.73 0.36 0.03
40_I 91_S 0.73 0.36 0.03
88_D 20_G 0.73 0.36 0.03
27_T 17_Y 0.73 0.36 0.02
100_V 40_L 0.72 0.35 0.02
118_P 58_I 0.72 0.35 0.02
161_F 19_A 0.71 0.34 0.02
94_D 11_I 0.71 0.33 0.02
128_F 174_E 0.71 0.33 0.02
20_V 48_A 0.70 0.33 0.02
48_L 18_A 0.70 0.33 0.02
76_N 159_G 0.70 0.32 0.02
100_V 41_N 0.69 0.32 0.02
112_F 59_E 0.69 0.32 0.02
119_C 111_E 0.69 0.31 0.02
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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