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OPENSEQ.org
GerAA-SpoVAEB
Genes: A B A+B
Length: 482 116 581
Sequences: 1718 1031 145
Seq/Len: 3.56 8.89 0.25
MirrorTree (Pazo et al. 2001) 0.33
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 0.18
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
316_I 9_C 1.86 0.59 0.00
212_L 29_A 1.38 0.30 0.00
175_A 16_V 1.37 0.30 0.00
428_Y 54_F 1.37 0.29 0.00
473_N 47_I 1.20 0.21 0.00
176_I 42_L 1.19 0.21 0.00
356_I 32_M 1.19 0.21 0.00
58_I 111_I 1.19 0.21 0.00
280_R 48_Y 1.17 0.20 0.00
289_I 16_V 1.15 0.19 0.00
282_L 46_G 1.14 0.19 0.00
174_A 46_G 1.12 0.18 0.00
221_F 64_V 1.12 0.18 0.00
292_F 41_I 1.11 0.18 0.00
383_S 38_I 1.11 0.18 0.00
103_F 76_H 1.08 0.17 0.00
223_Q 49_D 1.07 0.16 0.00
253_L 69_S 1.05 0.16 0.00
104_I 8_V 1.04 0.15 0.00
280_R 62_P 1.04 0.15 0.00
402_R 93_L 1.03 0.15 0.00
198_I 41_I 1.03 0.15 0.00
465_K 61_V 1.03 0.15 0.00
336_V 33_T 1.02 0.15 0.00
200_L 111_I 1.02 0.15 0.00
280_R 91_F 1.02 0.15 0.00
150_I 35_F 1.00 0.14 0.00
436_S 29_A 1.00 0.14 0.00
373_L 78_A 1.00 0.14 0.00
101_A 33_T 1.00 0.14 0.00
103_F 84_I 0.99 0.14 0.00
196_K 19_L 0.99 0.14 0.00
333_L 55_A 0.99 0.14 0.00
340_L 77_Q 0.98 0.14 0.00
435_T 51_F 0.98 0.14 0.00
339_E 72_H 0.98 0.14 0.00
174_A 4_L 0.98 0.13 0.00
359_V 87_G 0.97 0.13 0.00
340_L 93_L 0.97 0.13 0.00
383_S 9_C 0.96 0.13 0.00
318_A 94_T 0.96 0.13 0.00
328_I 38_I 0.95 0.13 0.00
176_I 2_D 0.95 0.13 0.00
384_V 87_G 0.95 0.12 0.00
92_I 109_A 0.95 0.12 0.00
279_I 29_A 0.94 0.12 0.00
359_V 68_H 0.94 0.12 0.00
49_T 86_I 0.94 0.12 0.00
108_D 19_L 0.94 0.12 0.00
186_S 47_I 0.94 0.12 0.00
250_P 55_A 0.94 0.12 0.00
286_S 8_V 0.94 0.12 0.00
90_K 86_I 0.93 0.12 0.00
95_I 100_A 0.93 0.12 0.00
147_L 95_S 0.93 0.12 0.00
431_L 44_G 0.93 0.12 0.00
238_F 105_A 0.93 0.12 0.00
359_V 71_L 0.93 0.12 0.00
287_I 52_I 0.93 0.12 0.00
154_T 90_I 0.92 0.12 0.00
380_I 16_V 0.92 0.12 0.00
291_L 19_L 0.92 0.12 0.00
48_M 3_Y 0.92 0.12 0.00
207_G 95_S 0.92 0.12 0.00
358_L 95_S 0.92 0.12 0.00
290_T 67_G 0.92 0.12 0.00
408_S 69_S 0.92 0.12 0.00
43_L 20_L 0.92 0.12 0.00
122_S 16_V 0.92 0.12 0.00
461_P 19_L 0.92 0.12 0.00
336_V 12_A 0.92 0.12 0.00
196_K 41_I 0.92 0.12 0.00
19_P 75_M 0.91 0.12 0.00
445_N 33_T 0.91 0.12 0.00
408_S 3_Y 0.91 0.12 0.00
228_E 35_F 0.91 0.11 0.00
206_S 45_F 0.91 0.11 0.00
279_I 41_I 0.91 0.11 0.00
437_F 32_M 0.91 0.11 0.00
97_N 103_L 0.90 0.11 0.00
84_P 32_M 0.90 0.11 0.00
436_S 100_A 0.89 0.11 0.00
259_L 44_G 0.89 0.11 0.00
359_V 93_L 0.89 0.11 0.00
458_I 45_F 0.89 0.11 0.00
453_T 33_T 0.89 0.11 0.00
434_Q 105_A 0.88 0.11 0.00
87_T 96_A 0.88 0.11 0.00
417_L 38_I 0.88 0.11 0.00
223_Q 91_F 0.88 0.11 0.00
206_S 61_V 0.88 0.11 0.00
103_F 103_L 0.88 0.11 0.00
300_L 15_I 0.87 0.11 0.00
120_T 111_I 0.87 0.11 0.00
321_E 95_S 0.87 0.11 0.00
461_P 95_S 0.87 0.11 0.00
58_I 37_V 0.87 0.10 0.00
366_Q 37_V 0.87 0.10 0.00
110_A 4_L 0.87 0.10 0.00
333_L 78_A 0.87 0.10 0.00
130_K 93_L 0.87 0.10 0.00
346_L 78_A 0.87 0.10 0.00
424_M 4_L 0.87 0.10 0.00
34_L 63_I 0.86 0.10 0.00
384_V 108_V 0.86 0.10 0.00
429_T 75_M 0.85 0.10 0.00
179_I 9_C 0.85 0.10 0.00
421_I 91_F 0.85 0.10 0.00
32_K 45_F 0.85 0.10 0.00
146_N 56_G 0.84 0.10 0.00
250_P 9_C 0.84 0.10 0.00
116_G 109_A 0.84 0.10 0.00
58_I 76_H 0.84 0.10 0.00
250_P 13_I 0.84 0.10 0.00
335_E 77_Q 0.84 0.10 0.00
192_K 76_H 0.84 0.10 0.00
72_Q 33_T 0.84 0.10 0.00
200_L 107_I 0.84 0.10 0.00
38_L 8_V 0.83 0.10 0.00
476_K 41_I 0.83 0.10 0.00
369_V 61_V 0.83 0.10 0.00
431_L 105_A 0.83 0.10 0.00
284_F 60_T 0.82 0.09 0.00
403_V 46_G 0.82 0.09 0.00
260_G 1_M 0.82 0.09 0.00
393_P 55_A 0.82 0.09 0.00
59_K 105_A 0.82 0.09 0.00
301_V 86_I 0.81 0.09 0.00
366_Q 115_K 0.81 0.09 0.00
128_T 87_G 0.81 0.09 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 (0.76 > 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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