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OPENSEQ.org
gerAB-spoVAEB
Genes: A B A+B
Length: 365 116 476
Sequences: 1686 1031 234
Seq/Len: 4.62 8.89 0.49
MirrorTree (Pazo et al. 2001) 0.09
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 0.03 0.01 0.00
2 0.05 0.72 0.00
5 0.07 0.74 0.01
10 0.08 0.75 0.01
20 0.12 0.75 0.03
100 0.20 0.76 0.11
∞ 0.25 0.77 0.49
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
351_I 35_F 1.19 0.33 0.00
274_S 44_G 1.14 0.29 0.00
76_E 51_F 1.14 0.29 0.00
198_F 4_L 1.12 0.28 0.00
160_L 19_L 1.05 0.24 0.00
224_G 31_V 1.03 0.23 0.00
273_E 1_M 1.01 0.22 0.00
156_T 61_V 1.01 0.22 0.00
277_L 44_G 1.00 0.21 0.00
56_I 47_I 0.99 0.21 0.00
275_F 54_F 0.99 0.21 0.00
90_I 111_I 0.99 0.21 0.00
133_C 98_I 0.98 0.20 0.00
138_M 109_A 0.97 0.20 0.00
165_G 111_I 0.96 0.20 0.00
164_F 47_I 0.95 0.19 0.00
231_L 38_I 0.95 0.19 0.00
64_L 16_V 0.94 0.18 0.00
149_F 103_L 0.93 0.18 0.00
119_E 44_G 0.92 0.18 0.00
352_L 86_I 0.92 0.17 0.00
229_I 75_M 0.92 0.17 0.00
130_F 16_V 0.92 0.17 0.00
281_I 16_V 0.92 0.17 0.00
203_V 55_A 0.92 0.17 0.00
173_I 29_A 0.91 0.17 0.00
198_F 34_S 0.91 0.17 0.00
191_L 8_V 0.91 0.17 0.00
226_L 55_A 0.91 0.17 0.00
268_F 44_G 0.90 0.16 0.00
348_L 15_I 0.88 0.16 0.00
318_V 82_G 0.87 0.15 0.00
50_L 111_I 0.87 0.15 0.00
201_M 69_S 0.87 0.15 0.00
109_M 45_F 0.86 0.15 0.00
351_I 16_V 0.86 0.15 0.00
11_N 17_G 0.86 0.15 0.00
324_W 109_A 0.85 0.15 0.00
90_I 34_S 0.85 0.15 0.00
274_S 35_F 0.85 0.15 0.00
312_V 61_V 0.85 0.15 0.00
226_L 107_I 0.85 0.14 0.00
161_L 46_G 0.84 0.14 0.00
207_L 42_L 0.84 0.14 0.00
180_L 83_F 0.84 0.14 0.00
23_M 91_F 0.84 0.14 0.00
270_E 91_F 0.83 0.14 0.00
224_G 53_E 0.83 0.14 0.00
216_Y 16_V 0.83 0.14 0.00
314_I 19_L 0.83 0.14 0.00
228_P 34_S 0.83 0.14 0.00
89_I 16_V 0.83 0.14 0.00
262_F 4_L 0.82 0.14 0.00
129_T 69_S 0.82 0.14 0.00
230_I 69_S 0.82 0.14 0.00
326_D 61_V 0.82 0.14 0.00
86_I 41_I 0.82 0.14 0.00
119_E 75_M 0.82 0.13 0.00
67_K 16_V 0.82 0.13 0.00
151_F 102_I 0.82 0.13 0.00
152_Y 72_H 0.81 0.13 0.00
190_S 40_A 0.81 0.13 0.00
128_L 34_S 0.81 0.13 0.00
206_F 24_F 0.81 0.13 0.00
179_V 86_I 0.80 0.13 0.00
102_A 61_V 0.80 0.13 0.00
338_L 41_I 0.79 0.12 0.00
59_I 102_I 0.79 0.12 0.00
39_A 8_V 0.79 0.12 0.00
268_F 56_G 0.79 0.12 0.00
14_Q 48_Y 0.79 0.12 0.00
53_F 102_I 0.79 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.77 > 0.4) of paralogs.
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