OPENSEQ.org
GerAA-SpoVAEB

Genes: A B A+B
Length: 482 116 587
Sequences: 1718 1031 287
Seq/Len: 3.56 8.89 0.49
MirrorTree (Pazo et al. 2001) 0.20
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 0.00 0.01 0.07
2 0.01 0.72 0.15
5 0.01 0.74 0.16
10 0.02 0.75 0.17
20 0.06 0.75 0.19
100 0.13 0.76 0.24
0.20 0.77 0.48
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
84_P 32_M 1.31 0.41 0.00
420_I 55_A 1.19 0.33 0.00
27_L 8_V 1.16 0.31 0.00
473_N 47_I 1.13 0.29 0.00
252_V 51_F 1.12 0.28 0.00
48_M 41_I 1.12 0.28 0.00
84_P 47_I 1.10 0.27 0.00
34_L 69_S 1.09 0.26 0.00
400_S 8_V 1.08 0.26 0.00
73_V 21_L 1.08 0.26 0.00
191_V 61_V 1.04 0.23 0.00
183_A 40_A 1.03 0.23 0.00
288_F 29_A 1.03 0.23 0.00
346_L 78_A 1.02 0.23 0.00
332_L 42_L 1.02 0.22 0.00
132_V 8_V 1.01 0.22 0.00
175_A 16_V 0.99 0.21 0.00
354_Q 55_A 0.99 0.21 0.00
290_T 71_L 0.98 0.20 0.00
253_L 69_S 0.97 0.20 0.00
307_L 47_I 0.97 0.20 0.00
356_I 102_I 0.97 0.20 0.00
50_D 9_C 0.96 0.19 0.00
165_M 44_G 0.96 0.19 0.00
182_K 29_A 0.95 0.19 0.00
97_N 111_I 0.95 0.19 0.00
212_L 29_A 0.94 0.18 0.00
409_M 76_H 0.93 0.18 0.00
277_S 91_F 0.93 0.18 0.00
46_S 103_L 0.92 0.17 0.00
45_F 45_F 0.91 0.17 0.00
431_L 16_V 0.90 0.16 0.00
174_A 46_G 0.89 0.16 0.00
411_S 54_F 0.89 0.16 0.00
316_I 59_A 0.89 0.16 0.00
323_V 20_L 0.88 0.16 0.00
288_F 4_L 0.88 0.16 0.00
154_T 2_D 0.88 0.16 0.00
159_L 17_G 0.87 0.15 0.00
105_N 21_L 0.87 0.15 0.00
27_L 35_F 0.87 0.15 0.00
59_K 103_L 0.86 0.15 0.00
52_N 34_S 0.86 0.15 0.00
140_V 36_V 0.86 0.15 0.00
235_S 51_F 0.85 0.15 0.00
194_R 51_F 0.85 0.15 0.00
280_R 62_P 0.85 0.15 0.00
351_P 36_V 0.85 0.14 0.00
117_K 86_I 0.85 0.14 0.00
140_V 107_I 0.84 0.14 0.00
196_K 19_L 0.84 0.14 0.00
90_K 35_F 0.84 0.14 0.00
176_I 42_L 0.84 0.14 0.00
150_I 35_F 0.84 0.14 0.00
316_I 34_S 0.84 0.14 0.00
192_K 38_I 0.83 0.14 0.00
291_L 19_L 0.83 0.14 0.00
398_G 61_V 0.83 0.14 0.00
329_F 8_V 0.83 0.14 0.00
303_F 61_V 0.83 0.14 0.00
369_V 103_L 0.82 0.14 0.00
194_R 75_M 0.82 0.14 0.00
102_V 103_L 0.81 0.13 0.00
359_V 34_S 0.81 0.13 0.00
196_K 41_I 0.81 0.13 0.00
387_L 29_A 0.81 0.13 0.00
237_L 2_D 0.81 0.13 0.00
198_I 42_L 0.80 0.13 0.00
149_L 35_F 0.80 0.13 0.00
316_I 105_A 0.80 0.13 0.00
432_T 41_I 0.80 0.13 0.00
436_S 29_A 0.79 0.12 0.00
165_M 51_F 0.79 0.12 0.00
296_I 38_I 0.79 0.12 0.00
422_L 12_A 0.78 0.12 0.00
23_E 4_L 0.78 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.

ID Seq/Len Name Options I_Prob Status
8039 0.49 GerAA-SpoVAEB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8038 0.25 GerAA-SpoVAEB Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared

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