May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIV_A_40_cI_M_40_1_human
Genes: A B A+B
Length: 513 459 967
Sequences: 3245 3931 2297
Seq/Len: 6.33 8.56 2.38
MirrorTree (Pazo et al. 2001) 0.63
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 0.00 0.03
2 0.00 0.00 0.07
5 0.01 0.00 0.24
10 0.01 0.00 1.75
20 0.01 0.00 1.81
100 0.02 0.00 1.88
∞ 0.06 0.01 2.36
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
391_G 195_M 1.20 0.77 0.04
428_Q 285_L 1.12 0.71 0.03
87_I 264_L 1.08 0.66 0.03
265_K 250_L 1.07 0.66 0.03
31_T 278_R 1.04 0.62 0.03
325_A 315_L 1.03 0.61 0.03
356_I 150_L 0.98 0.55 0.02
198_S 291_I 0.97 0.55 0.02
108_S 386_F 0.97 0.54 0.02
69_M 328_C 0.97 0.54 0.02
100_M 335_E 0.96 0.53 0.02
218_T 339_S 0.95 0.52 0.02
500_P 336_R 0.94 0.51 0.02
505_F 336_R 0.93 0.50 0.02
229_I 410_M 0.93 0.49 0.02
7_L 67_M 0.91 0.48 0.02
375_A 341_I 0.91 0.47 0.02
461_S 285_L 0.89 0.45 0.02
220_F 148_Y 0.88 0.43 0.02
509_V 352_L 0.88 0.43 0.02
45_G 266_L 0.88 0.43 0.02
362_S 218_K 0.87 0.43 0.01
161_A 161_L 0.87 0.43 0.01
106_P 278_R 0.87 0.43 0.01
169_I 285_L 0.87 0.42 0.01
397_F 72_L 0.87 0.42 0.01
419_I 243_M 0.86 0.42 0.01
476_F 197_L 0.86 0.41 0.01
443_Y 121_F 0.86 0.41 0.01
318_V 164_L 0.85 0.41 0.01
134_G 348_L 0.85 0.40 0.01
334_W 35_S 0.84 0.39 0.01
350_V 50_F 0.84 0.39 0.01
405_L 126_L 0.83 0.38 0.01
155_V 151_F 0.83 0.38 0.01
391_G 30_H 0.83 0.38 0.01
253_M 120_I 0.83 0.38 0.01
415_T 39_L 0.83 0.38 0.01
299_V 321_L 0.82 0.37 0.01
278_M 406_Y 0.82 0.37 0.01
12_H 239_G 0.82 0.37 0.01
464_A 314_I 0.82 0.37 0.01
356_I 338_H 0.82 0.37 0.01
464_A 201_M 0.82 0.37 0.01
133_A 263_V 0.82 0.36 0.01
282_F 313_V 0.81 0.36 0.01
407_Q 42_F 0.81 0.36 0.01
253_M 404_A 0.81 0.36 0.01
453_L 269_M 0.81 0.36 0.01
83_V 282_L 0.81 0.35 0.01
426_F 221_V 0.81 0.35 0.01
413_H 413_T 0.81 0.35 0.01
117_M 264_L 0.80 0.35 0.01
253_M 424_N 0.80 0.35 0.01
50_N 202_A 0.80 0.35 0.01
258_V 286_I 0.80 0.34 0.01
97_M 414_T 0.80 0.34 0.01
298_D 106_L 0.80 0.34 0.01
231_Y 114_E 0.80 0.34 0.01
89_A 156_G 0.79 0.34 0.01
260_Y 292_S 0.79 0.34 0.01
97_M 280_T 0.79 0.34 0.01
391_G 405_L 0.79 0.34 0.01
401_S 267_W 0.79 0.33 0.01
250_G 333_N 0.78 0.33 0.01
168_I 414_T 0.78 0.33 0.01
141_A 230_V 0.78 0.32 0.01
261_Y 345_S 0.78 0.32 0.01
338_V 202_A 0.78 0.32 0.01
159_L 377_G 0.78 0.32 0.01
392_G 164_L 0.77 0.32 0.01
393_F 402_V 0.77 0.32 0.01
392_G 210_Y 0.77 0.32 0.01
53_I 336_R 0.77 0.32 0.01
36_L 176_I 0.77 0.32 0.01
175_A 295_A 0.77 0.32 0.01
182_P 285_L 0.77 0.31 0.01
395_H 121_F 0.77 0.31 0.01
410_A 211_G 0.77 0.31 0.01
48_L 313_V 0.77 0.31 0.01
189_L 445_L 0.76 0.31 0.01
253_M 300_A 0.76 0.31 0.01
314_I 257_M 0.76 0.31 0.01
196_L 230_V 0.76 0.31 0.01
330_S 270_I 0.76 0.31 0.01
118_V 314_I 0.76 0.31 0.01
482_V 252_P 0.76 0.31 0.01
229_I 198_A 0.76 0.30 0.01
339_L 315_L 0.76 0.30 0.01
359_A 198_A 0.76 0.30 0.01
204_A 325_L 0.75 0.30 0.01
270_Y 149_F 0.75 0.30 0.01
43_Q 160_L 0.75 0.30 0.01
454_S 285_L 0.75 0.30 0.01
5_R 116_I 0.75 0.29 0.01
172_K 140_P 0.74 0.29 0.01
452_T 40_L 0.74 0.29 0.01
467_L 355_M 0.74 0.29 0.01
410_A 267_W 0.74 0.29 0.01
271_M 292_S 0.74 0.28 0.01
85_L 209_L 0.74 0.28 0.01
64_V 207_M 0.74 0.28 0.01
318_V 396_T 0.74 0.28 0.01
299_V 355_M 0.74 0.28 0.01
345_I 60_P 0.74 0.28 0.01
314_I 91_R 0.73 0.28 0.01
188_V 73_L 0.73 0.28 0.01
339_L 326_L 0.73 0.28 0.01
254_I 75_L 0.73 0.28 0.01
166_T 435_T 0.73 0.28 0.01
28_V 151_F 0.73 0.28 0.01
83_V 116_I 0.73 0.28 0.01
87_I 399_N 0.73 0.28 0.01
476_F 101_S 0.73 0.28 0.01
460_I 37_I 0.73 0.28 0.01
473_W 276_C 0.73 0.28 0.01
137_S 124_T 0.73 0.28 0.01
466_M 339_S 0.73 0.27 0.01
189_L 149_F 0.73 0.27 0.01
475_A 226_A 0.72 0.27 0.01
177_T 52_C 0.72 0.27 0.01
339_L 80_S 0.72 0.27 0.01
254_I 77_I 0.72 0.27 0.01
423_L 179_L 0.72 0.27 0.01
472_I 46_N 0.72 0.27 0.01
155_V 250_L 0.72 0.27 0.01
89_A 80_S 0.72 0.27 0.01
455_S 212_L 0.72 0.27 0.01
332_M 117_M 0.72 0.27 0.01
263_G 377_G 0.72 0.26 0.01
21_L 448_S 0.72 0.26 0.01
462_L 448_S 0.72 0.26 0.01
324_L 226_A 0.72 0.26 0.01
404_T 317_I 0.71 0.26 0.01
180_Q 292_S 0.71 0.26 0.01
342_L 99_L 0.71 0.26 0.01
301_T 368_A 0.71 0.26 0.01
492_L 38_P 0.71 0.26 0.01
331_N 368_A 0.71 0.26 0.01
155_V 372_T 0.71 0.26 0.01
189_L 210_Y 0.71 0.26 0.01
289_A 239_G 0.71 0.26 0.01
467_L 259_Y 0.71 0.26 0.01
270_Y 399_N 0.71 0.26 0.01
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
4418 1.62 cIV_A_80_cI_M_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4416 1.15 cIV_A_60_cI_M_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4415 1.17 cIV_A_80_1_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 1) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.30 Done - Shared
4414 1.15 cIV_A_80_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.38 Done - Shared
4413 1.62 cIV_A_60_cI_M_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.17 Done - Shared
4408 2.75 cIV_A_20_cI_M_20_1_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4405 3.06 cIV_A_4_cI_M_4_1_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4398 2.38 cIV_A_40_cI_M_40_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.04 Done - Shared
Page generated in 0.0986 seconds.