May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
GTUB_SPC98
Genes: A B A+B
Length: 473 846 1253
Sequences: 982 543 142
Seq/Len: 2.08 0.64 0.11
MirrorTree (Pazo et al. 2001) 0.18
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 0.08 0.01 0.00
2 0.09 0.01 0.00
5 0.10 0.02 0.01
10 0.10 0.02 0.01
20 0.11 0.02 0.01
100 0.12 0.03 0.03
∞ 0.16 0.04 0.11
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
301_P 494_E 1.29 0.15 0.00
223_D 657_I 1.28 0.15 0.00
140_H 590_L 1.25 0.14 0.00
223_D 687_G 1.22 0.14 0.00
8_L 477_L 1.18 0.13 0.00
26_A 385_F 1.14 0.12 0.00
69_M 664_M 1.14 0.12 0.00
79_V 664_M 1.11 0.11 0.00
172_V 644_F 1.07 0.10 0.00
452_D 283_L 1.05 0.10 0.00
94_V 187_Y 1.04 0.10 0.00
223_D 387_Q 1.03 0.10 0.00
62_F 190_Y 0.99 0.09 0.00
452_D 390_V 0.99 0.09 0.00
8_L 522_L 0.99 0.09 0.00
389_N 686_N 0.98 0.09 0.00
141_S 583_Y 0.98 0.09 0.00
221_N 386_N 0.96 0.08 0.00
111_I 677_N 0.96 0.08 0.00
198_S 367_N 0.96 0.08 0.00
234_I 470_Y 0.96 0.08 0.00
151_G 595_K 0.96 0.08 0.00
125_K 208_Q 0.94 0.08 0.00
397_V 344_E 0.94 0.08 0.00
397_V 409_Y 0.93 0.08 0.00
125_K 196_T 0.92 0.08 0.00
448_D 35_L 0.92 0.08 0.00
83_F 186_K 0.92 0.08 0.00
272_F 364_I 0.91 0.08 0.00
382_T 645_N 0.91 0.08 0.00
123_I 350_L 0.90 0.07 0.00
382_T 449_I 0.90 0.07 0.00
223_D 556_D 0.90 0.07 0.00
215_K 111_L 0.89 0.07 0.00
386_V 220_L 0.89 0.07 0.00
438_V 474_V 0.89 0.07 0.00
67_I 284_Y 0.89 0.07 0.00
389_N 69_I 0.89 0.07 0.00
190_A 606_K 0.88 0.07 0.00
444_S 221_L 0.88 0.07 0.00
155_L 193_L 0.88 0.07 0.00
224_L 390_V 0.88 0.07 0.00
271_S 489_M 0.88 0.07 0.00
224_L 3_L 0.87 0.07 0.00
141_S 349_W 0.87 0.07 0.00
172_V 89_L 0.87 0.07 0.00
140_H 583_Y 0.86 0.07 0.00
449_V 451_D 0.86 0.07 0.00
10_A 568_L 0.86 0.07 0.00
67_I 494_E 0.86 0.07 0.00
450_L 559_T 0.86 0.07 0.00
172_V 76_L 0.85 0.07 0.00
315_Y 350_L 0.85 0.07 0.00
141_S 590_L 0.84 0.07 0.00
453_D 280_L 0.84 0.07 0.00
8_L 64_I 0.84 0.07 0.00
338_L 573_N 0.84 0.07 0.00
162_Y 252_A 0.84 0.07 0.00
31_I 556_D 0.84 0.07 0.00
447_D 268_V 0.84 0.07 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
2553 0.11 GTUB_SPC98 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2549 0 GTUB_SPC98 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
2546 0.01 GTUB_SPC98 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
Page generated in 0.7257 seconds.