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OPENSEQ.org
cIV_A_80_cI_M_60_1_human
Genes: A B A+B
Length: 513 459 968
Sequences: 3020 2643 1572
Seq/Len: 5.89 5.76 1.62
MirrorTree (Pazo et al. 2001) 0.75
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 0.00
2 0.00 0.00 0.02
5 0.01 0.00 0.13
10 0.01 0.00 1.52
20 0.01 0.00 1.55
100 0.02 0.00 1.57
∞ 0.05 0.00 1.62
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 1.50 0.87 0.22
43_Q 160_L 1.36 0.79 0.15
500_P 336_R 1.27 0.73 0.12
134_G 348_L 1.21 0.68 0.10
87_I 264_L 1.20 0.66 0.10
504_T 125_T 1.19 0.66 0.10
419_I 243_M 1.19 0.66 0.10
253_M 120_I 1.18 0.65 0.09
4_D 339_S 1.18 0.65 0.09
43_Q 235_L 1.14 0.61 0.08
325_A 315_L 1.12 0.59 0.08
509_V 352_L 1.12 0.59 0.08
359_A 388_W 1.10 0.56 0.07
475_A 226_A 1.10 0.56 0.07
69_M 328_C 1.07 0.54 0.06
108_S 386_F 1.07 0.54 0.06
97_M 163_A 1.06 0.53 0.06
36_L 348_L 1.06 0.53 0.06
115_S 402_V 1.05 0.52 0.06
320_V 267_W 1.05 0.51 0.06
356_I 234_V 1.05 0.51 0.06
36_L 388_W 1.05 0.51 0.06
253_M 214_L 1.04 0.51 0.06
260_Y 292_S 1.04 0.50 0.06
265_K 250_L 1.03 0.50 0.06
87_I 399_N 1.03 0.49 0.06
229_I 410_M 1.03 0.49 0.06
229_I 198_A 1.03 0.49 0.06
298_D 106_L 1.03 0.49 0.06
133_A 263_V 1.03 0.49 0.05
32_A 321_L 1.03 0.49 0.05
97_M 82_R 1.01 0.48 0.05
253_M 404_A 1.01 0.47 0.05
97_M 280_T 1.01 0.47 0.05
410_A 267_W 1.00 0.46 0.05
391_G 249_I 1.00 0.46 0.05
32_A 381_V 0.99 0.46 0.05
223_A 411_F 0.99 0.45 0.05
489_S 105_S 0.99 0.45 0.05
161_A 161_L 0.98 0.44 0.04
475_A 314_I 0.97 0.43 0.04
260_Y 196_W 0.96 0.42 0.04
470_F 275_I 0.96 0.42 0.04
390_M 76_T 0.96 0.42 0.04
97_M 315_L 0.95 0.41 0.04
333_K 154_L 0.95 0.41 0.04
175_A 295_A 0.94 0.40 0.04
108_S 95_Y 0.94 0.40 0.04
328_H 76_T 0.93 0.39 0.04
507_E 125_T 0.93 0.39 0.04
155_V 372_T 0.93 0.39 0.04
505_F 336_R 0.93 0.39 0.04
146_T 286_I 0.93 0.39 0.04
357_V 439_M 0.93 0.39 0.04
286_I 261_F 0.93 0.39 0.04
155_V 348_L 0.92 0.38 0.04
36_L 115_L 0.92 0.38 0.04
324_L 397_G 0.92 0.38 0.04
339_L 80_S 0.91 0.37 0.04
89_A 156_G 0.91 0.37 0.04
356_I 150_L 0.91 0.37 0.04
87_I 358_W 0.91 0.37 0.04
83_V 395_L 0.91 0.37 0.04
53_I 336_R 0.91 0.37 0.04
5_R 116_I 0.90 0.36 0.03
341_A 226_A 0.90 0.36 0.03
392_G 210_Y 0.90 0.36 0.03
141_A 230_V 0.90 0.36 0.03
455_S 173_S 0.90 0.36 0.03
31_T 278_R 0.90 0.36 0.03
423_L 95_Y 0.89 0.35 0.03
472_I 356_A 0.89 0.35 0.03
87_I 61_L 0.89 0.35 0.03
189_L 445_L 0.89 0.35 0.03
87_I 441_L 0.89 0.35 0.03
472_I 173_S 0.89 0.35 0.03
391_G 270_I 0.88 0.34 0.03
83_V 116_I 0.88 0.34 0.03
33_L 307_W 0.88 0.34 0.03
296_G 288_Y 0.88 0.34 0.03
434_S 406_Y 0.87 0.34 0.03
223_A 328_C 0.87 0.33 0.03
467_L 259_Y 0.87 0.33 0.03
508_P 149_F 0.87 0.33 0.03
215_L 415_Q 0.87 0.33 0.03
139_P 210_Y 0.87 0.33 0.03
286_I 356_A 0.86 0.33 0.03
405_L 296_L 0.86 0.32 0.03
231_Y 409_Y 0.86 0.32 0.03
267_P 363_S 0.86 0.32 0.03
416_I 402_V 0.86 0.32 0.03
434_S 445_L 0.86 0.32 0.03
400_F 269_M 0.86 0.32 0.03
468_M 326_L 0.85 0.32 0.03
417_M 207_M 0.85 0.32 0.03
181_T 212_L 0.85 0.32 0.03
87_I 212_L 0.85 0.31 0.03
26_A 179_L 0.85 0.31 0.03
266_E 71_W 0.85 0.31 0.03
64_V 255_K 0.85 0.31 0.03
289_A 324_S 0.85 0.31 0.03
449_T 339_S 0.85 0.31 0.03
117_M 418_S 0.85 0.31 0.03
57_I 279_Q 0.84 0.31 0.03
500_P 377_G 0.84 0.31 0.03
337_A 420_T 0.84 0.31 0.03
404_T 61_L 0.84 0.30 0.03
168_I 200_T 0.84 0.30 0.03
391_G 30_H 0.84 0.30 0.03
278_M 116_I 0.84 0.30 0.03
476_F 197_L 0.84 0.30 0.03
187_S 56_F 0.84 0.30 0.03
176_M 373_I 0.84 0.30 0.03
265_K 175_N 0.84 0.30 0.03
182_P 226_A 0.84 0.30 0.03
134_G 342_M 0.84 0.30 0.03
391_G 449_L 0.84 0.30 0.03
391_G 423_I 0.84 0.30 0.03
500_P 433_E 0.83 0.30 0.03
389_I 433_E 0.83 0.30 0.03
297_M 119_Y 0.83 0.30 0.03
198_S 291_I 0.83 0.30 0.03
511_M 69_T 0.83 0.30 0.03
477_A 176_I 0.83 0.29 0.03
363_L 155_V 0.83 0.29 0.03
115_S 134_T 0.83 0.29 0.03
325_A 292_S 0.83 0.29 0.03
407_Q 42_F 0.83 0.29 0.03
413_H 269_M 0.83 0.29 0.03
119_E 140_P 0.83 0.29 0.03
122_A 398_L 0.83 0.29 0.03
215_L 102_L 0.83 0.29 0.03
502_Y 413_T 0.82 0.29 0.03
43_Q 81_Q 0.82 0.29 0.03
253_M 300_A 0.82 0.29 0.03
350_V 50_F 0.82 0.29 0.03
423_L 179_L 0.82 0.29 0.03
341_A 235_L 0.82 0.29 0.03
162_I 292_S 0.82 0.29 0.03
114_A 162_I 0.82 0.28 0.02
356_I 392_T 0.82 0.28 0.02
118_V 399_N 0.81 0.28 0.02
363_L 318_A 0.81 0.28 0.02
21_L 39_L 0.81 0.28 0.02
334_W 282_L 0.81 0.28 0.02
423_L 34_I 0.81 0.28 0.02
356_I 273_S 0.81 0.28 0.02
478_S 115_L 0.81 0.28 0.02
334_W 35_S 0.81 0.28 0.02
174_P 72_L 0.81 0.28 0.02
97_M 414_T 0.81 0.28 0.02
190_I 179_L 0.81 0.28 0.02
333_K 198_A 0.81 0.28 0.02
357_V 255_K 0.81 0.28 0.02
400_F 262_L 0.81 0.27 0.02
83_V 302_L 0.80 0.27 0.02
475_A 312_A 0.80 0.27 0.02
356_I 428_P 0.80 0.27 0.02
5_R 395_L 0.80 0.27 0.02
7_L 452_D 0.80 0.27 0.02
100_M 335_E 0.80 0.27 0.02
133_A 278_R 0.80 0.27 0.02
57_I 367_L 0.80 0.27 0.02
159_L 377_G 0.80 0.27 0.02
7_L 162_I 0.80 0.27 0.02
223_A 278_R 0.80 0.27 0.02
410_A 211_G 0.80 0.27 0.02
415_T 39_L 0.79 0.27 0.02
334_W 131_A 0.79 0.26 0.02
394_I 311_G 0.79 0.26 0.02
50_N 201_M 0.79 0.26 0.02
109_L 72_L 0.79 0.26 0.02
403_Y 246_L 0.79 0.26 0.02
133_A 163_A 0.79 0.26 0.02
403_Y 39_L 0.79 0.26 0.02
87_I 267_W 0.79 0.26 0.02
397_F 72_L 0.79 0.26 0.02
398_P 142_R 0.79 0.26 0.02
417_M 323_S 0.79 0.26 0.02
215_L 125_T 0.79 0.26 0.02
392_G 274_S 0.79 0.26 0.02
116_A 115_L 0.79 0.26 0.02
83_V 403_T 0.79 0.26 0.02
342_L 330_A 0.79 0.26 0.02
258_V 134_T 0.78 0.26 0.02
420_G 245_R 0.78 0.26 0.02
83_V 210_Y 0.78 0.26 0.02
473_W 276_C 0.78 0.25 0.02
299_V 295_A 0.78 0.25 0.02
188_V 384_T 0.78 0.25 0.02
145_L 343_I 0.78 0.25 0.02
342_L 146_G 0.78 0.25 0.02
500_P 444_I 0.78 0.25 0.02
166_T 435_T 0.78 0.25 0.02
467_L 355_M 0.78 0.25 0.02
168_I 414_T 0.78 0.25 0.02
182_P 286_I 0.78 0.25 0.02
215_L 414_T 0.78 0.25 0.02
274_V 138_S 0.78 0.25 0.02
511_M 60_P 0.78 0.25 0.02
180_Q 164_L 0.78 0.25 0.02
366_V 332_S 0.78 0.25 0.02
507_E 408_L 0.78 0.25 0.02
180_Q 24_W 0.78 0.25 0.02
469_I 377_G 0.77 0.25 0.02
479_K 296_L 0.77 0.25 0.02
507_E 421_H 0.77 0.25 0.02
26_A 291_I 0.77 0.25 0.02
461_S 96_L 0.77 0.25 0.02
106_P 367_L 0.77 0.25 0.02
356_I 338_H 0.77 0.25 0.02
484_M 339_S 0.77 0.25 0.02
481_K 336_R 0.77 0.24 0.02
472_I 352_L 0.77 0.24 0.02
416_I 337_T 0.77 0.24 0.02
404_T 317_I 0.77 0.24 0.02
504_T 403_T 0.77 0.24 0.02
82_L 411_F 0.77 0.24 0.02
318_V 396_T 0.77 0.24 0.02
21_L 266_L 0.77 0.24 0.02
215_L 408_L 0.77 0.24 0.02
505_F 95_Y 0.77 0.24 0.02
49_G 102_L 0.77 0.24 0.02
83_V 271_M 0.76 0.24 0.02
363_L 312_A 0.76 0.24 0.02
405_L 192_N 0.76 0.24 0.02
485_V 330_A 0.76 0.24 0.02
20_L 313_V 0.76 0.24 0.02
460_I 414_T 0.76 0.24 0.02
476_F 396_T 0.76 0.24 0.02
23_G 238_L 0.76 0.24 0.02
405_L 126_L 0.76 0.24 0.02
166_T 104_I 0.76 0.24 0.02
181_T 403_T 0.76 0.24 0.02
502_Y 121_F 0.76 0.24 0.02
173_P 163_A 0.76 0.24 0.02
117_M 272_T 0.76 0.24 0.02
133_A 384_T 0.76 0.23 0.02
7_L 164_L 0.76 0.23 0.02
389_I 292_S 0.76 0.23 0.02
434_S 330_A 0.76 0.23 0.02
115_S 350_T 0.76 0.23 0.02
324_L 367_L 0.75 0.23 0.02
446_A 104_I 0.75 0.23 0.02
182_P 62_T 0.75 0.23 0.02
278_M 309_F 0.75 0.23 0.02
465_V 394_L 0.75 0.23 0.02
327_L 169_N 0.75 0.23 0.02
5_R 345_S 0.75 0.23 0.02
299_V 77_I 0.75 0.23 0.02
307_S 98_M 0.75 0.23 0.02
229_I 104_I 0.75 0.23 0.02
8_F 409_Y 0.75 0.23 0.02
190_I 302_L 0.75 0.23 0.02
341_A 9_I 0.75 0.23 0.02
262_S 138_S 0.75 0.23 0.02
456_V 256_H 0.75 0.23 0.02
345_I 60_P 0.75 0.23 0.02
266_E 329_L 0.75 0.23 0.02
443_Y 121_F 0.75 0.23 0.02
448_T 395_L 0.75 0.23 0.02
461_S 285_L 0.75 0.23 0.02
21_L 277_L 0.75 0.23 0.02
333_K 147_T 0.75 0.23 0.02
419_I 188_N 0.75 0.23 0.02
476_F 423_I 0.75 0.23 0.02
146_T 190_W 0.75 0.23 0.02
5_R 235_L 0.75 0.23 0.02
463_T 195_M 0.75 0.23 0.02
466_M 339_S 0.75 0.23 0.02
176_M 449_L 0.74 0.23 0.02
472_I 46_N 0.74 0.23 0.02
253_M 424_N 0.74 0.23 0.02
48_L 292_S 0.74 0.23 0.02
476_F 193_N 0.74 0.23 0.02
401_S 125_T 0.74 0.23 0.02
216_N 148_Y 0.74 0.23 0.02
153_A 240_G 0.74 0.23 0.02
169_I 80_S 0.74 0.23 0.02
134_G 69_T 0.74 0.23 0.02
311_I 343_I 0.74 0.22 0.02
406_D 362_A 0.74 0.22 0.02
97_M 169_N 0.74 0.22 0.02
135_N 211_G 0.74 0.22 0.02
106_P 141_E 0.74 0.22 0.02
265_K 179_L 0.74 0.22 0.02
175_A 243_M 0.74 0.22 0.02
496_Y 234_V 0.74 0.22 0.02
318_V 149_F 0.74 0.22 0.02
510_Y 317_I 0.74 0.22 0.02
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
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