May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIV_A_4_cI_Ld500_560_4_1_Pdenitr
Genes: A B A+B
Length: 538 642 1141
Sequences: 4477 2008 1119
Seq/Len: 8.32 3.13 0.98
MirrorTree (Pazo et al. 2001) 0.08
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 0.01 0.00 0.01
2 0.01 0.00 0.03
5 0.02 0.00 0.09
10 0.03 0.00 0.20
20 0.03 0.01 0.26
100 0.05 0.01 0.36
∞ 0.08 0.03 0.95
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
417_G 119_F 1.08 0.40 0.00
475_I 209_L 0.99 0.33 0.00
102_L 527_L 0.99 0.33 0.00
179_L 393_F 0.97 0.31 0.00
28_L 14_L 0.96 0.31 0.00
182_I 557_L 0.95 0.29 0.00
32_C 308_L 0.94 0.29 0.00
71_W 307_G 0.93 0.28 0.00
182_I 187_I 0.93 0.28 0.00
410_A 480_I 0.93 0.28 0.00
48_Y 422_A 0.91 0.26 0.00
135_A 84_L 0.90 0.26 0.00
30_S 449_T 0.89 0.25 0.00
99_F 38_L 0.89 0.25 0.00
479_I 613_V 0.89 0.25 0.00
472_I 297_A 0.89 0.25 0.00
277_V 591_I 0.89 0.25 0.00
312_Y 139_L 0.87 0.24 0.00
519_P 96_M 0.87 0.24 0.00
21_F 415_A 0.86 0.23 0.00
240_F 453_K 0.84 0.22 0.00
473_S 316_V 0.84 0.22 0.00
333_V 175_V 0.84 0.22 0.00
128_L 385_F 0.84 0.22 0.00
277_V 286_P 0.84 0.22 0.00
129_G 406_G 0.84 0.22 0.00
438_I 530_I 0.83 0.21 0.00
378_S 160_Y 0.82 0.21 0.00
117_L 582_L 0.82 0.21 0.00
7_F 198_Q 0.82 0.21 0.00
35_V 340_A 0.82 0.21 0.00
240_F 234_G 0.82 0.21 0.00
218_S 433_I 0.81 0.20 0.00
282_A 68_F 0.81 0.20 0.00
483_S 394_A 0.81 0.20 0.00
207_S 571_F 0.80 0.19 0.00
182_I 139_L 0.80 0.19 0.00
302_L 162_K 0.80 0.19 0.00
28_L 24_G 0.79 0.19 0.00
312_Y 553_L 0.78 0.18 0.00
130_V 589_A 0.78 0.18 0.00
488_I 494_F 0.78 0.18 0.00
279_S 471_M 0.78 0.18 0.00
488_I 522_F 0.77 0.18 0.00
361_F 15_I 0.77 0.18 0.00
472_I 508_D 0.77 0.18 0.00
477_A 463_H 0.77 0.18 0.00
33_F 217_L 0.77 0.18 0.00
333_V 297_A 0.77 0.17 0.00
364_L 34_G 0.77 0.17 0.00
273_I 19_G 0.76 0.17 0.00
36_Y 411_L 0.76 0.17 0.00
442_L 408_A 0.76 0.17 0.00
182_I 74_I 0.76 0.17 0.00
240_F 528_G 0.76 0.17 0.00
364_L 342_F 0.75 0.17 0.00
380_A 374_Y 0.75 0.17 0.00
32_C 480_I 0.75 0.17 0.00
298_A 135_A 0.75 0.17 0.00
182_I 341_M 0.74 0.17 0.00
67_N 383_L 0.74 0.16 0.00
376_V 13_S 0.74 0.16 0.00
168_F 253_E 0.74 0.16 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
3324 0.98 cIV_A_4_cI_Ld500_560_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3323 0.98 cIV_A_4_cI_Ld500_560_4_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
Page generated in 0.1636 seconds.