May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
WzC_WzB
Genes: A B A+B
Length: 720 147 834
Sequences: 2459 5421 900
Seq/Len: 3.42 36.88 1.08
MirrorTree (Pazo et al. 2001) 0.63
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 0.02 0.42
2 0.00 0.02 0.44
5 0.01 0.02 0.45
10 0.01 0.02 0.46
20 0.01 0.03 0.48
100 0.04 0.04 0.57
∞ 0.13 0.13 1.04
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
641_I 125_A 1.13 0.48 0.00
541_T 54_A 1.01 0.37 0.00
247_N 77_D 1.00 0.36 0.00
133_N 131_L 0.94 0.31 0.00
453_I 24_Q 0.92 0.29 0.00
700_R 19_A 0.91 0.28 0.00
232_L 139_A 0.90 0.28 0.00
531_M 38_G 0.90 0.28 0.00
282_R 90_L 0.90 0.28 0.00
529_L 41_V 0.87 0.25 0.00
371_E 54_A 0.86 0.25 0.00
428_I 60_L 0.86 0.25 0.00
350_A 45_A 0.86 0.25 0.00
272_L 23_L 0.86 0.25 0.00
250_A 66_R 0.86 0.24 0.00
442_G 24_Q 0.85 0.24 0.00
674_K 127_V 0.84 0.24 0.00
603_K 101_V 0.84 0.23 0.00
584_E 32_V 0.84 0.23 0.00
561_I 117_Y 0.83 0.23 0.00
419_V 141_A 0.82 0.22 0.00
634_K 85_R 0.82 0.22 0.00
238_D 80_L 0.82 0.22 0.00
351_L 41_V 0.82 0.22 0.00
36_G 45_A 0.81 0.21 0.00
559_L 21_R 0.81 0.21 0.00
94_I 113_I 0.80 0.20 0.00
319_Q 20_E 0.79 0.20 0.00
470_I 143_N 0.79 0.20 0.00
544_C 85_R 0.79 0.20 0.00
281_S 133_R 0.78 0.19 0.00
688_I 68_I 0.78 0.19 0.00
441_V 24_Q 0.78 0.19 0.00
128_L 76_Y 0.77 0.19 0.00
652_A 22_L 0.77 0.19 0.00
672_T 60_L 0.77 0.19 0.00
639_V 37_L 0.76 0.18 0.00
261_K 134_S 0.76 0.18 0.00
641_I 22_L 0.76 0.18 0.00
326_K 101_V 0.76 0.18 0.00
34_V 80_L 0.76 0.18 0.00
104_V 131_L 0.76 0.18 0.00
595_A 53_A 0.76 0.18 0.00
580_N 131_L 0.76 0.18 0.00
652_A 131_L 0.76 0.18 0.00
629_V 42_G 0.75 0.18 0.00
44_C 26_Y 0.75 0.18 0.00
557_R 65_A 0.75 0.18 0.00
233_T 8_V 0.74 0.17 0.00
209_G 79_I 0.74 0.17 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)
ID Seq/Len Name Options I_Prob Status
13816 0.52 Full Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13106 1.08 WzC_WzB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
Page generated in 0.2559 seconds.