May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIp_4_4_cIV_3_4
Genes: A B A+B
Length: 463 261 655
Sequences: 2150 2465 312
Seq/Len: 4.64 9.44 0.48
MirrorTree (Pazo et al. 2001) 0.53
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 0.01
2 0.00 0.00 0.02
5 0.01 0.00 0.03
10 0.01 0.00 0.05
20 0.02 0.00 0.08
100 0.03 0.00 0.13
∞ 0.09 0.00 0.43
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
412_V 254_V 1.75 0.72 0.01
155_V 131_L 1.65 0.66 0.01
295_G 194_G 1.62 0.64 0.01
182_N 97_F 1.47 0.52 0.01
435_L 258_W 1.37 0.45 0.00
439_S 167_I 1.33 0.42 0.00
106_V 84_I 1.32 0.41 0.00
261_L 170_G 1.31 0.41 0.00
339_Q 123_P 1.30 0.40 0.00
197_M 110_P 1.23 0.35 0.00
227_I 147_A 1.22 0.34 0.00
453_T 28_T 1.16 0.30 0.00
272_T 97_F 1.15 0.30 0.00
200_F 43_L 1.13 0.28 0.00
374_S 136_V 1.13 0.28 0.00
386_T 147_A 1.11 0.27 0.00
264_N 25_L 1.10 0.27 0.00
106_V 135_S 1.09 0.26 0.00
425_K 105_S 1.09 0.26 0.00
293_L 97_F 1.09 0.26 0.00
339_Q 210_I 1.09 0.26 0.00
170_I 226_H 1.07 0.24 0.00
187_V 153_E 1.06 0.24 0.00
339_Q 113_G 1.05 0.24 0.00
292_M 8_Y 1.05 0.23 0.00
186_A 188_I 1.05 0.23 0.00
368_R 18_L 1.04 0.23 0.00
377_S 62_T 1.04 0.23 0.00
454_Q 226_H 1.03 0.23 0.00
315_E 136_V 1.02 0.22 0.00
332_C 48_L 1.02 0.22 0.00
386_T 144_I 1.02 0.22 0.00
293_L 95_A 1.01 0.22 0.00
188_T 81_Y 1.01 0.21 0.00
350_K 210_I 1.01 0.21 0.00
277_V 220_I 0.99 0.21 0.00
101_L 224_M 0.98 0.20 0.00
189_T 53_T 0.98 0.20 0.00
189_T 170_G 0.97 0.20 0.00
108_K 96_G 0.97 0.20 0.00
188_T 120_G 0.97 0.20 0.00
339_Q 132_L 0.97 0.19 0.00
185_M 136_V 0.96 0.19 0.00
152_S 222_Q 0.96 0.19 0.00
227_I 76_Q 0.96 0.19 0.00
429_F 66_T 0.96 0.19 0.00
186_A 107_A 0.96 0.19 0.00
150_A 129_V 0.96 0.19 0.00
279_T 160_I 0.95 0.19 0.00
334_V 151_L 0.95 0.18 0.00
378_L 80_R 0.95 0.18 0.00
332_C 230_K 0.95 0.18 0.00
386_T 206_L 0.95 0.18 0.00
444_L 161_Q 0.94 0.18 0.00
152_S 256_I 0.94 0.18 0.00
318_V 219_F 0.94 0.18 0.00
152_S 147_A 0.93 0.18 0.00
295_G 150_S 0.93 0.18 0.00
105_M 176_L 0.93 0.18 0.00
369_A 198_F 0.93 0.18 0.00
281_E 123_P 0.93 0.18 0.00
309_D 68_Q 0.93 0.17 0.00
222_M 23_S 0.93 0.17 0.00
222_M 194_G 0.93 0.17 0.00
278_V 144_I 0.92 0.17 0.00
365_P 215_L 0.92 0.17 0.00
99_M 64_E 0.92 0.17 0.00
247_F 196_T 0.92 0.17 0.00
315_E 155_N 0.92 0.17 0.00
332_C 259_W 0.92 0.17 0.00
155_V 52_L 0.92 0.17 0.00
81_T 62_T 0.92 0.17 0.00
151_Y 101_F 0.92 0.17 0.00
106_V 178_A 0.92 0.17 0.00
347_C 143_S 0.91 0.17 0.00
247_F 101_F 0.91 0.17 0.00
109_C 184_S 0.91 0.17 0.00
188_T 23_S 0.91 0.17 0.00
344_I 47_L 0.91 0.17 0.00
236_L 247_V 0.91 0.17 0.00
444_L 127_L 0.91 0.17 0.00
174_F 50_N 0.90 0.17 0.00
323_R 219_F 0.90 0.17 0.00
106_V 23_S 0.90 0.17 0.00
218_S 105_S 0.90 0.16 0.00
332_C 39_S 0.90 0.16 0.00
443_M 233_F 0.90 0.16 0.00
453_T 152_M 0.90 0.16 0.00
254_R 82_G 0.89 0.16 0.00
357_K 101_F 0.89 0.16 0.00
108_K 162_A 0.89 0.16 0.00
418_R 43_L 0.89 0.16 0.00
80_I 84_I 0.89 0.16 0.00
126_Y 43_L 0.89 0.16 0.00
305_T 198_F 0.89 0.16 0.00
188_T 110_P 0.89 0.16 0.00
438_M 191_G 0.89 0.16 0.00
334_V 171_L 0.89 0.16 0.00
82_L 217_I 0.89 0.16 0.00
449_A 170_G 0.89 0.16 0.00
418_R 126_P 0.89 0.16 0.00
347_C 176_L 0.88 0.16 0.00
347_C 166_T 0.88 0.16 0.00
259_E 15_P 0.88 0.16 0.00
180_L 224_M 0.88 0.16 0.00
185_M 146_W 0.88 0.16 0.00
441_G 198_F 0.88 0.16 0.00
198_T 118_P 0.88 0.15 0.00
374_S 200_A 0.88 0.15 0.00
106_V 155_N 0.88 0.15 0.00
444_L 5_S 0.88 0.15 0.00
425_K 225_F 0.88 0.15 0.00
151_Y 27_M 0.88 0.15 0.00
349_N 229_S 0.87 0.15 0.00
162_R 222_Q 0.87 0.15 0.00
168_Q 178_A 0.87 0.15 0.00
82_L 54_M 0.87 0.15 0.00
272_T 7_A 0.87 0.15 0.00
253_L 129_V 0.87 0.15 0.00
422_C 59_R 0.86 0.15 0.00
434_G 27_M 0.86 0.15 0.00
444_L 192_I 0.86 0.15 0.00
189_T 20_G 0.86 0.15 0.00
390_Q 135_S 0.86 0.15 0.00
291_V 194_G 0.86 0.15 0.00
386_T 54_M 0.86 0.15 0.00
418_R 168_L 0.86 0.15 0.00
173_L 56_Q 0.86 0.15 0.00
348_L 189_S 0.86 0.15 0.00
82_L 152_M 0.86 0.15 0.00
192_L 19_T 0.85 0.14 0.00
384_L 170_G 0.85 0.14 0.00
317_D 18_L 0.85 0.14 0.00
315_E 33_M 0.85 0.14 0.00
218_S 182_F 0.85 0.14 0.00
275_I 31_L 0.85 0.14 0.00
186_A 170_G 0.84 0.14 0.00
101_L 194_G 0.84 0.14 0.00
151_Y 153_E 0.84 0.14 0.00
213_F 9_H 0.84 0.14 0.00
412_V 12_K 0.84 0.14 0.00
451_I 95_A 0.84 0.14 0.00
367_K 123_P 0.84 0.14 0.00
353_P 192_I 0.83 0.14 0.00
177_I 69_G 0.83 0.14 0.00
332_C 62_T 0.83 0.14 0.00
423_K 100_A 0.83 0.14 0.00
435_L 7_A 0.83 0.14 0.00
252_S 225_F 0.83 0.14 0.00
449_A 38_H 0.83 0.14 0.00
197_M 81_Y 0.82 0.14 0.00
370_E 210_I 0.82 0.14 0.00
107_R 168_L 0.82 0.14 0.00
351_M 28_T 0.82 0.13 0.00
454_Q 66_T 0.82 0.13 0.00
212_E 7_A 0.82 0.13 0.00
132_A 186_F 0.82 0.13 0.00
438_M 114_G 0.82 0.13 0.00
254_R 76_Q 0.82 0.13 0.00
163_P 45_L 0.82 0.13 0.00
349_N 106_L 0.82 0.13 0.00
351_M 21_A 0.82 0.13 0.00
258_L 79_L 0.81 0.13 0.00
425_K 183_E 0.81 0.13 0.00
291_V 153_E 0.81 0.13 0.00
315_E 161_Q 0.81 0.13 0.00
119_G 125_N 0.81 0.13 0.00
124_I 186_F 0.81 0.13 0.00
435_L 68_Q 0.81 0.13 0.00
98_V 230_K 0.81 0.13 0.00
411_L 13_P 0.81 0.13 0.00
165_P 154_N 0.81 0.13 0.00
173_L 129_V 0.81 0.13 0.00
454_Q 170_G 0.81 0.13 0.00
323_R 129_V 0.81 0.13 0.00
150_A 170_G 0.81 0.13 0.00
364_S 220_I 0.81 0.13 0.00
413_S 24_A 0.81 0.13 0.00
274_D 239_A 0.80 0.13 0.00
264_N 206_L 0.80 0.13 0.00
82_L 19_T 0.80 0.13 0.00
259_E 59_R 0.80 0.13 0.00
277_V 254_V 0.80 0.13 0.00
298_I 10_M 0.80 0.13 0.00
150_A 196_T 0.80 0.13 0.00
445_A 210_I 0.80 0.12 0.00
212_E 85_L 0.80 0.12 0.00
334_V 10_M 0.80 0.12 0.00
248_S 33_M 0.80 0.12 0.00
357_K 36_H 0.80 0.12 0.00
101_L 131_L 0.79 0.12 0.00
286_Y 32_T 0.79 0.12 0.00
448_V 97_F 0.79 0.12 0.00
344_I 19_T 0.79 0.12 0.00
453_T 88_T 0.79 0.12 0.00
334_V 187_T 0.79 0.12 0.00
440_K 71_H 0.79 0.12 0.00
410_Y 83_M 0.79 0.12 0.00
150_A 139_A 0.79 0.12 0.00
355_E 229_S 0.79 0.12 0.00
298_I 132_L 0.79 0.12 0.00
359_D 220_I 0.79 0.12 0.00
300_W 240_W 0.79 0.12 0.00
317_D 248_V 0.79 0.12 0.00
353_P 65_S 0.79 0.12 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
4312 0.57 cIp_4_20_cIV_3_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4311 0.48 cIp_4_4_cIV_3_4 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4309 0.65 cIp_4_4_cIV_3_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
Page generated in 0.0974 seconds.