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OPENSEQ.org
B-S
Genes: A B A+B
Length: 646 334 965
Sequences: 1735 59249 1150
Seq/Len: 2.69 177.39 1.19
MirrorTree (Pazo et al. 2001) 0.58
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 0.10 0.09 0.04
2 0.11 0.10 0.80
5 0.12 0.13 1.05
10 0.14 0.15 1.11
20 0.15 0.18 1.17
100 0.17 0.25 1.38
∞ 0.21 0.28 1.49
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
108_N 299_A 1.23 0.60 0.00
98_H 271_I 1.22 0.59 0.00
549_K 304_I 1.14 0.51 0.00
550_Q 275_G 1.07 0.45 0.00
298_T 243_I 1.03 0.41 0.00
588_I 271_I 1.03 0.41 0.00
534_L 322_F 1.01 0.39 0.00
592_V 181_I 0.97 0.35 0.00
117_A 229_L 0.96 0.34 0.00
31_L 304_I 0.94 0.33 0.00
21_Y 287_S 0.93 0.32 0.00
162_G 15_A 0.93 0.32 0.00
561_Y 142_E 0.93 0.32 0.00
21_Y 320_L 0.92 0.31 0.00
578_I 301_P 0.92 0.31 0.00
259_I 243_I 0.91 0.30 0.00
437_Y 186_L 0.91 0.30 0.00
567_L 303_L 0.91 0.30 0.00
546_L 233_V 0.90 0.30 0.00
326_A 276_F 0.90 0.30 0.00
532_G 295_A 0.90 0.30 0.00
424_I 307_D 0.90 0.29 0.00
306_L 133_M 0.88 0.28 0.00
547_Y 298_A 0.88 0.28 0.00
533_F 120_M 0.88 0.28 0.00
207_L 300_A 0.88 0.28 0.00
417_V 206_D 0.88 0.28 0.00
136_K 32_S 0.87 0.27 0.00
466_K 54_W 0.87 0.27 0.00
106_A 39_L 0.87 0.27 0.00
272_N 191_I 0.87 0.27 0.00
148_F 299_A 0.86 0.26 0.00
154_V 141_E 0.86 0.26 0.00
406_S 228_L 0.85 0.26 0.00
102_R 142_E 0.85 0.26 0.00
534_L 283_H 0.85 0.26 0.00
503_Q 271_I 0.85 0.26 0.00
103_I 138_D 0.85 0.26 0.00
516_T 149_L 0.85 0.26 0.00
180_I 87_E 0.84 0.25 0.00
210_V 46_I 0.84 0.25 0.00
320_T 243_I 0.84 0.25 0.00
393_V 282_H 0.84 0.25 0.00
14_N 152_E 0.84 0.25 0.00
114_G 256_V 0.84 0.24 0.00
535_G 266_K 0.84 0.24 0.00
57_I 186_L 0.83 0.24 0.00
638_Y 198_C 0.83 0.24 0.00
212_I 29_V 0.83 0.24 0.00
426_V 312_F 0.83 0.24 0.00
344_L 276_F 0.83 0.24 0.00
303_A 233_V 0.83 0.24 0.00
136_K 94_I 0.82 0.24 0.00
388_V 75_D 0.82 0.24 0.00
160_F 277_T 0.82 0.23 0.00
23_F 53_L 0.82 0.23 0.00
148_F 266_K 0.82 0.23 0.00
326_A 270_R 0.82 0.23 0.00
260_S 308_V 0.81 0.23 0.00
88_G 152_E 0.81 0.23 0.00
105_S 276_F 0.81 0.23 0.00
160_F 223_F 0.81 0.23 0.00
299_V 194_L 0.81 0.23 0.00
268_G 48_F 0.81 0.23 0.00
210_V 265_P 0.81 0.23 0.00
526_M 94_I 0.81 0.22 0.00
495_E 92_R 0.81 0.22 0.00
165_L 187_I 0.80 0.22 0.00
67_V 271_I 0.80 0.22 0.00
396_V 53_L 0.80 0.22 0.00
507_K 273_D 0.80 0.22 0.00
591_V 312_F 0.80 0.22 0.00
264_R 178_V 0.80 0.22 0.00
151_Q 228_L 0.80 0.22 0.00
210_V 42_V 0.80 0.22 0.00
392_D 22_L 0.80 0.22 0.00
56_A 256_V 0.79 0.21 0.00
113_F 48_F 0.79 0.21 0.00
44_I 133_M 0.79 0.21 0.00
87_I 268_V 0.79 0.21 0.00
259_I 57_Y 0.79 0.21 0.00
135_F 320_L 0.79 0.21 0.00
180_I 268_V 0.79 0.21 0.00
459_I 298_A 0.78 0.21 0.00
85_K 14_A 0.78 0.21 0.00
594_L 268_V 0.78 0.21 0.00
213_L 205_F 0.78 0.21 0.00
256_V 162_Q 0.78 0.21 0.00
78_I 166_Q 0.78 0.20 0.00
537_T 203_I 0.78 0.20 0.00
617_I 215_L 0.77 0.20 0.00
625_A 21_A 0.77 0.20 0.00
228_K 241_I 0.77 0.20 0.00
67_V 304_I 0.77 0.20 0.00
322_E 44_L 0.77 0.20 0.00
373_P 156_I 0.77 0.20 0.00
130_V 172_I 0.77 0.20 0.00
86_E 288_T 0.77 0.20 0.00
297_T 119_L 0.77 0.20 0.00
217_Y 161_D 0.77 0.20 0.00
232_E 228_L 0.77 0.20 0.00
533_F 165_H 0.76 0.20 0.00
92_L 290_M 0.76 0.20 0.00
468_L 52_F 0.76 0.20 0.00
87_I 176_L 0.76 0.19 0.00
76_N 156_I 0.76 0.19 0.00
553_E 296_K 0.76 0.19 0.00
550_Q 163_Q 0.76 0.19 0.00
162_G 314_A 0.75 0.19 0.00
394_K 266_K 0.75 0.19 0.00
535_G 221_L 0.75 0.19 0.00
110_M 189_K 0.75 0.19 0.00
84_S 271_I 0.75 0.19 0.00
294_T 275_G 0.75 0.19 0.00
642_I 239_S 0.75 0.19 0.00
593_G 125_E 0.75 0.19 0.00
247_G 232_A 0.75 0.19 0.00
514_L 232_A 0.74 0.18 0.00
115_S 228_L 0.74 0.18 0.00
346_E 314_A 0.74 0.18 0.00
612_V 318_F 0.74 0.18 0.00
125_S 43_Y 0.74 0.18 0.00
242_G 68_K 0.73 0.18 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
12032 1.06 BceBS_deltagene100 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.48 Done - Shared
11911 0.98 BceBS Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.60 Done - Shared
10833 0.92 grampos2 Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.73 Done
10832 0.95 grampos Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.63 Done
3615 1.19 B-S Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3614 0.04 B-S Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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