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OPENSEQ.org
BmdC_BmdB_Alone_Jackhammer
Genes: A B A+B
Length: 481 325 796
Sequences: 39138 721 87
Seq/Len: 81.37 2.22 0.11
MirrorTree (Pazo et al. 2001) 0.55
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 0.36 0.01 0.05
2 0.36 0.01 0.06
5 0.39 0.02 0.08
10 0.40 0.02 0.09
20 0.40 0.02 0.11
100 0.41 0.02 0.17
∞ 0.44 0.02 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
38_T 95_F 1.51 0.22 0.00
207_L 187_L 1.31 0.16 0.00
338_L 247_V 1.27 0.15 0.00
207_L 319_G 1.23 0.14 0.00
381_E 163_S 1.18 0.12 0.00
145_Y 282_V 1.16 0.12 0.00
322_V 138_L 1.14 0.12 0.00
17_F 206_A 1.12 0.11 0.00
452_L 68_L 1.08 0.10 0.00
145_Y 86_E 1.06 0.10 0.00
223_V 271_E 1.06 0.10 0.00
221_R 142_I 1.05 0.10 0.00
75_I 263_A 1.05 0.10 0.00
209_M 256_S 1.04 0.10 0.00
410_L 67_I 1.04 0.10 0.00
228_I 257_M 1.03 0.10 0.00
147_S 320_G 1.03 0.10 0.00
257_V 249_L 1.03 0.10 0.00
15_Q 86_E 1.03 0.10 0.00
148_G 145_R 1.01 0.09 0.00
148_G 273_G 1.01 0.09 0.00
150_T 145_R 1.01 0.09 0.00
150_T 273_G 1.01 0.09 0.00
153_P 145_R 1.01 0.09 0.00
153_P 273_G 1.01 0.09 0.00
286_G 145_R 1.01 0.09 0.00
286_G 273_G 1.01 0.09 0.00
289_E 145_R 1.01 0.09 0.00
289_E 273_G 1.01 0.09 0.00
312_G 145_R 1.01 0.09 0.00
312_G 273_G 1.01 0.09 0.00
349_Y 145_R 1.01 0.09 0.00
349_Y 273_G 1.01 0.09 0.00
373_G 145_R 1.01 0.09 0.00
373_G 273_G 1.01 0.09 0.00
374_D 145_R 1.01 0.09 0.00
374_D 273_G 1.01 0.09 0.00
389_R 145_R 1.01 0.09 0.00
389_R 273_G 1.01 0.09 0.00
398_G 145_R 1.01 0.09 0.00
398_G 273_G 1.01 0.09 0.00
478_K 145_R 1.01 0.09 0.00
478_K 273_G 1.01 0.09 0.00
128_D 196_V 1.00 0.09 0.00
138_E 61_E 1.00 0.09 0.00
358_D 205_K 0.99 0.09 0.00
54_Q 86_E 0.99 0.09 0.00
279_A 130_I 0.98 0.09 0.00
113_L 253_A 0.98 0.09 0.00
269_P 212_N 0.98 0.09 0.00
112_L 307_L 0.97 0.09 0.00
314_P 289_G 0.97 0.09 0.00
474_T 297_N 0.97 0.08 0.00
369_I 55_R 0.97 0.08 0.00
371_K 263_A 0.96 0.08 0.00
75_I 163_S 0.96 0.08 0.00
226_R 177_I 0.96 0.08 0.00
359_A 204_V 0.96 0.08 0.00
448_L 95_F 0.96 0.08 0.00
394_V 299_E 0.95 0.08 0.00
148_G 207_G 0.95 0.08 0.00
150_T 207_G 0.95 0.08 0.00
153_P 207_G 0.95 0.08 0.00
286_G 207_G 0.95 0.08 0.00
289_E 207_G 0.95 0.08 0.00
312_G 207_G 0.95 0.08 0.00
349_Y 207_G 0.95 0.08 0.00
373_G 207_G 0.95 0.08 0.00
374_D 207_G 0.95 0.08 0.00
389_R 207_G 0.95 0.08 0.00
398_G 207_G 0.95 0.08 0.00
478_K 207_G 0.95 0.08 0.00
227_G 192_V 0.95 0.08 0.00
158_I 307_L 0.95 0.08 0.00
91_I 24_G 0.94 0.08 0.00
231_W 77_L 0.94 0.08 0.00
78_L 22_V 0.94 0.08 0.00
288_T 270_I 0.94 0.08 0.00
12_T 192_V 0.93 0.08 0.00
212_D 196_V 0.92 0.08 0.00
353_D 316_A 0.92 0.08 0.00
405_E 284_E 0.92 0.08 0.00
219_L 305_L 0.91 0.08 0.00
410_L 206_A 0.91 0.07 0.00
148_G 185_G 0.90 0.07 0.00
150_T 185_G 0.90 0.07 0.00
153_P 185_G 0.90 0.07 0.00
286_G 185_G 0.90 0.07 0.00
289_E 185_G 0.90 0.07 0.00
312_G 185_G 0.90 0.07 0.00
349_Y 185_G 0.90 0.07 0.00
373_G 185_G 0.90 0.07 0.00
374_D 185_G 0.90 0.07 0.00
389_R 185_G 0.90 0.07 0.00
398_G 185_G 0.90 0.07 0.00
478_K 185_G 0.90 0.07 0.00
26_D 308_E 0.90 0.07 0.00
42_L 320_G 0.90 0.07 0.00
91_I 212_N 0.90 0.07 0.00
461_I 130_I 0.90 0.07 0.00
416_V 182_A 0.90 0.07 0.00
48_Q 193_F 0.89 0.07 0.00
331_P 289_G 0.89 0.07 0.00
420_V 204_V 0.89 0.07 0.00
439_A 90_P 0.89 0.07 0.00
477_G 145_R 0.89 0.07 0.00
477_G 273_G 0.89 0.07 0.00
358_D 63_E 0.89 0.07 0.00
468_L 9_S 0.88 0.07 0.00
394_V 116_E 0.88 0.07 0.00
148_G 149_R 0.88 0.07 0.00
148_G 260_Y 0.88 0.07 0.00
150_T 149_R 0.88 0.07 0.00
150_T 260_Y 0.88 0.07 0.00
153_P 149_R 0.88 0.07 0.00
153_P 260_Y 0.88 0.07 0.00
286_G 149_R 0.88 0.07 0.00
286_G 260_Y 0.88 0.07 0.00
289_E 149_R 0.88 0.07 0.00
289_E 260_Y 0.88 0.07 0.00
312_G 149_R 0.88 0.07 0.00
312_G 260_Y 0.88 0.07 0.00
349_Y 149_R 0.88 0.07 0.00
349_Y 260_Y 0.88 0.07 0.00
373_G 149_R 0.88 0.07 0.00
373_G 260_Y 0.88 0.07 0.00
374_D 149_R 0.88 0.07 0.00
374_D 260_Y 0.88 0.07 0.00
389_R 149_R 0.88 0.07 0.00
389_R 260_Y 0.88 0.07 0.00
398_G 149_R 0.88 0.07 0.00
398_G 260_Y 0.88 0.07 0.00
478_K 149_R 0.88 0.07 0.00
478_K 260_Y 0.88 0.07 0.00
128_D 177_I 0.88 0.07 0.00
38_T 159_F 0.88 0.07 0.00
107_S 135_S 0.88 0.07 0.00
69_K 212_N 0.88 0.07 0.00
212_D 166_L 0.88 0.07 0.00
396_I 78_V 0.88 0.07 0.00
49_V 203_G 0.88 0.07 0.00
204_G 320_G 0.87 0.07 0.00
131_L 242_Q 0.87 0.07 0.00
105_E 263_A 0.87 0.07 0.00
358_D 148_C 0.87 0.07 0.00
76_I 166_L 0.87 0.07 0.00
324_N 24_G 0.87 0.07 0.00
46_S 84_P 0.87 0.07 0.00
422_I 15_R 0.86 0.07 0.00
147_S 145_R 0.86 0.07 0.00
147_S 273_G 0.86 0.07 0.00
212_D 220_L 0.86 0.07 0.00
38_T 76_V 0.86 0.07 0.00
326_D 271_E 0.86 0.07 0.00
22_Q 266_F 0.86 0.07 0.00
336_G 145_R 0.86 0.07 0.00
336_G 273_G 0.86 0.07 0.00
75_I 68_L 0.86 0.07 0.00
39_Y 186_G 0.86 0.07 0.00
64_V 192_V 0.86 0.07 0.00
209_M 130_I 0.86 0.07 0.00
58_I 187_L 0.86 0.07 0.00
105_E 192_V 0.86 0.07 0.00
342_G 145_R 0.85 0.07 0.00
342_G 273_G 0.85 0.07 0.00
333_G 146_R 0.85 0.07 0.00
146_T 132_L 0.85 0.07 0.00
181_R 229_K 0.85 0.07 0.00
221_R 271_E 0.85 0.07 0.00
337_D 149_R 0.85 0.07 0.00
337_D 260_Y 0.85 0.07 0.00
209_M 159_F 0.85 0.07 0.00
215_D 166_L 0.85 0.07 0.00
177_N 194_V 0.85 0.07 0.00
473_L 201_V 0.85 0.07 0.00
440_Q 68_L 0.85 0.07 0.00
241_A 279_L 0.84 0.07 0.00
472_P 145_R 0.84 0.07 0.00
472_P 273_G 0.84 0.07 0.00
58_I 186_G 0.84 0.07 0.00
65_G 130_I 0.84 0.07 0.00
119_E 288_V 0.83 0.07 0.00
437_V 66_E 0.83 0.07 0.00
53_L 132_L 0.83 0.07 0.00
75_I 142_I 0.83 0.07 0.00
351_N 271_E 0.83 0.07 0.00
105_E 319_G 0.83 0.07 0.00
182_I 163_S 0.82 0.06 0.00
465_L 211_F 0.82 0.06 0.00
422_I 194_V 0.82 0.06 0.00
329_M 186_G 0.82 0.06 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
7344 0.11 BmdC_BmdB_Alone_Jackhammer Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7343 0.05 BmdC_BmdB_A2_alone Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
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