May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_3_20_cI_6_20_tt
Genes: A B A+B
Length: 783 181 906
Sequences: 1254 1141 650
Seq/Len: 1.6 6.3 0.72
MirrorTree (Pazo et al. 2001) 0.59
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.01 0.01 0.48
10 0.01 0.02 0.49
20 0.01 0.02 0.49
100 0.03 0.03 0.51
∞ 0.10 0.08 0.67
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
597_Y 152_M 1.34 0.55 0.00
323_E 53_S 1.33 0.54 0.00
16_G 57_R 1.18 0.41 0.00
618_E 31_G 1.11 0.35 0.00
89_D 156_K 1.07 0.33 0.00
4_V 151_V 1.01 0.28 0.00
290_I 24_L 1.01 0.28 0.00
583_V 27_L 0.99 0.27 0.00
293_A 150_A 0.97 0.26 0.00
42_I 71_S 0.97 0.25 0.00
15_P 103_K 0.95 0.24 0.00
285_V 67_V 0.95 0.24 0.00
270_R 83_R 0.94 0.24 0.00
493_A 56_A 0.94 0.23 0.00
616_N 152_M 0.93 0.23 0.00
188_V 81_A 0.93 0.23 0.00
730_E 122_A 0.93 0.23 0.00
336_A 26_K 0.92 0.22 0.00
389_D 13_E 0.92 0.22 0.00
597_Y 62_R 0.91 0.22 0.00
301_A 135_V 0.91 0.22 0.00
79_L 67_V 0.91 0.21 0.00
671_E 56_A 0.90 0.21 0.00
192_E 71_S 0.90 0.21 0.00
12_E 23_T 0.89 0.20 0.00
201_D 29_A 0.88 0.20 0.00
606_T 58_N 0.88 0.20 0.00
21_D 77_V 0.88 0.20 0.00
449_A 17_E 0.88 0.20 0.00
237_D 63_F 0.87 0.20 0.00
123_D 47_A 0.87 0.20 0.00
44_A 43_L 0.87 0.19 0.00
769_L 118_F 0.87 0.19 0.00
361_A 23_T 0.86 0.19 0.00
358_S 106_I 0.86 0.19 0.00
311_V 156_K 0.86 0.19 0.00
177_D 118_F 0.85 0.19 0.00
615_V 36_L 0.85 0.19 0.00
423_P 97_E 0.84 0.18 0.00
20_M 107_S 0.84 0.18 0.00
228_D 18_G 0.84 0.18 0.00
315_G 150_A 0.84 0.18 0.00
369_L 33_S 0.84 0.18 0.00
743_V 103_K 0.84 0.18 0.00
524_L 94_R 0.83 0.18 0.00
336_A 130_V 0.83 0.17 0.00
82_S 15_E 0.83 0.17 0.00
729_P 17_E 0.82 0.17 0.00
498_E 56_A 0.82 0.17 0.00
706_G 80_V 0.82 0.17 0.00
6_V 77_V 0.82 0.17 0.00
407_P 77_V 0.82 0.17 0.00
367_P 60_L 0.81 0.17 0.00
710_E 148_I 0.81 0.17 0.00
646_E 152_M 0.81 0.17 0.00
7_N 19_I 0.81 0.17 0.00
219_P 31_G 0.81 0.17 0.00
267_A 97_E 0.81 0.17 0.00
530_A 27_L 0.81 0.16 0.00
420_L 92_M 0.80 0.16 0.00
692_F 60_L 0.80 0.16 0.00
638_L 120_N 0.80 0.16 0.00
664_L 97_E 0.80 0.16 0.00
105_A 29_A 0.80 0.16 0.00
179_E 144_P 0.80 0.16 0.00
226_I 85_S 0.80 0.16 0.00
475_E 131_V 0.80 0.16 0.00
166_K 24_L 0.79 0.15 0.00
182_I 95_V 0.78 0.15 0.00
177_D 24_L 0.78 0.15 0.00
323_E 78_M 0.78 0.15 0.00
492_K 103_K 0.78 0.15 0.00
15_P 67_V 0.78 0.15 0.00
30_V 71_S 0.78 0.15 0.00
272_G 135_V 0.78 0.15 0.00
171_S 48_I 0.78 0.15 0.00
40_S 153_Q 0.77 0.15 0.00
102_E 80_V 0.77 0.15 0.00
183_H 26_K 0.77 0.15 0.00
21_D 21_F 0.77 0.15 0.00
302_D 101_D 0.77 0.15 0.00
583_V 151_V 0.77 0.15 0.00
229_I 156_K 0.77 0.14 0.00
546_A 77_V 0.77 0.14 0.00
579_G 27_L 0.76 0.14 0.00
413_L 26_K 0.76 0.14 0.00
578_K 36_L 0.76 0.14 0.00
306_L 80_V 0.76 0.14 0.00
648_L 74_Q 0.76 0.14 0.00
239_T 150_A 0.76 0.14 0.00
723_A 31_G 0.76 0.14 0.00
376_A 80_V 0.76 0.14 0.00
481_L 21_F 0.76 0.14 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
4961 0.72 cI_3_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4960 0.78 cI_3_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
Page generated in 0.1533 seconds.