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OPENSEQ.org
1
Genes: A B A+B
Length: 357 280 607
Sequences: 10484 26700 6388
Seq/Len: 29.37 95.36 10.52
MirrorTree (Pazo et al. 2001) 0.39
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 0.04 0.55 6.39
2 0.05 0.55 8.72
5 0.05 0.56 9.64
10 0.06 0.56 9.85
20 0.08 0.57 10.03
100 0.15 0.58 10.84
∞ 0.23 0.60 11.73
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
49_R 174_E 3.17 1.00 1.00
100_F 189_R 2.94 1.00 1.00
100_F 176_A 2.35 1.00 1.00
103_K 189_R 2.32 1.00 1.00
89_Y 179_D 1.84 1.00 0.98
85_N 171_D 1.82 1.00 0.98
75_K 177_I 1.41 0.99 0.91
101_A 179_D 1.31 0.99 0.86
104_V 189_R 1.24 0.98 0.82
104_V 185_Q 1.23 0.98 0.81
91_H 194_H 1.17 0.97 0.78
104_V 181_C 1.15 0.97 0.75
54_L 178_L 1.14 0.97 0.75
79_V 178_L 1.13 0.97 0.74
92_M 189_R 1.07 0.95 0.69
100_F 181_C 1.02 0.93 0.63
92_M 190_I 1.00 0.92 0.60
141_R 171_D 1.00 0.92 0.60
104_V 180_G 0.95 0.89 0.54
80_A 178_L 0.89 0.85 0.47
81_M 178_L 0.88 0.84 0.46
83_F 175_A 0.87 0.83 0.44
152_R 179_D 0.85 0.81 0.42
75_K 182_S 0.83 0.79 0.39
85_N 169_P 0.79 0.74 0.34
104_V 182_S 0.72 0.64 0.26
55_E 174_E 0.66 0.54 0.20
73_D 177_I 0.65 0.52 0.19
90_P 172_L 0.63 0.49 0.17
189_T 178_L 0.62 0.47 0.16
75_K 183_P 0.60 0.44 0.15
174_T 251_S 0.58 0.41 0.13
105_A 180_G 0.57 0.39 0.12
78_D 178_L 0.56 0.38 0.12
90_P 194_H 0.54 0.33 0.10
175_R 215_L 0.53 0.33 0.10
152_R 178_L 0.52 0.31 0.09
26_L 204_V 0.50 0.28 0.08
133_P 249_A 0.50 0.28 0.08
76_D 182_S 0.49 0.27 0.08
69_V 178_L 0.49 0.27 0.08
51_V 147_I 0.49 0.27 0.08
87_A 175_A 0.49 0.26 0.07
75_K 180_G 0.47 0.23 0.07
223_L 232_G 0.46 0.23 0.06
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.57 > 0.4) of paralogs.
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