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OPENSEQ.org
J F no SP unlimited
Genes: A B A+B
Length: 537 306 818
Sequences: 109 1030 73
Seq/Len: 0.2 3.37 0.09
MirrorTree (Pazo et al. 2001) 0.53
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.01
2 0.00 0.06 0.01
5 0.00 0.08 0.01
10 0.00 0.09 0.01
20 0.00 0.10 0.02
100 0.00 0.14 0.04
∞ 0.00 0.19 0.09
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
257_D 288_F 1.89 0.33 0.00
41_V 99_L 1.50 0.19 0.00
478_T 217_F 1.50 0.19 0.00
144_N 198_Y 1.28 0.13 0.00
275_S 165_N 1.25 0.12 0.00
48_M 21_P 1.20 0.12 0.00
151_F 143_I 1.19 0.11 0.00
97_T 32_I 1.17 0.11 0.00
478_T 156_F 1.14 0.10 0.00
321_Y 11_Y 1.14 0.10 0.00
11_R 161_V 1.13 0.10 0.00
55_V 251_G 1.13 0.10 0.00
482_D 91_L 1.11 0.10 0.00
48_M 84_S 1.10 0.10 0.00
361_Q 191_A 1.09 0.10 0.00
328_L 265_Y 1.07 0.09 0.00
317_A 38_T 1.06 0.09 0.00
506_Y 150_K 1.05 0.09 0.00
480_I 107_F 1.05 0.09 0.00
376_V 67_S 1.04 0.09 0.00
506_Y 261_F 1.04 0.09 0.00
353_D 252_P 1.04 0.09 0.00
357_Y 260_K 1.03 0.09 0.00
157_D 284_V 1.03 0.09 0.00
248_A 84_S 1.03 0.09 0.00
90_L 36_G 1.03 0.09 0.00
510_D 190_D 1.03 0.09 0.00
480_I 88_H 1.02 0.08 0.00
319_K 154_I 1.01 0.08 0.00
379_A 44_K 1.01 0.08 0.00
420_D 180_Y 1.01 0.08 0.00
326_F 113_D 1.00 0.08 0.00
357_Y 141_F 1.00 0.08 0.00
506_Y 103_L 0.99 0.08 0.00
531_R 17_F 0.99 0.08 0.00
363_A 72_K 0.98 0.08 0.00
257_D 55_D 0.98 0.08 0.00
326_F 53_Y 0.98 0.08 0.00
248_A 21_P 0.97 0.08 0.00
195_S 113_D 0.97 0.08 0.00
445_K 43_I 0.97 0.08 0.00
478_T 224_Y 0.96 0.08 0.00
291_L 252_P 0.96 0.08 0.00
481_D 128_P 0.96 0.08 0.00
195_S 208_A 0.94 0.07 0.00
41_V 210_D 0.93 0.07 0.00
430_Q 284_V 0.92 0.07 0.00
453_S 72_K 0.92 0.07 0.00
357_Y 271_F 0.92 0.07 0.00
94_F 103_L 0.91 0.07 0.00
532_R 165_N 0.91 0.07 0.00
185_F 151_N 0.90 0.07 0.00
481_D 138_N 0.90 0.07 0.00
316_N 158_A 0.90 0.07 0.00
480_I 223_R 0.90 0.07 0.00
396_L 44_K 0.89 0.07 0.00
351_A 252_P 0.89 0.07 0.00
258_V 175_D 0.89 0.07 0.00
420_D 270_M 0.89 0.07 0.00
311_G 217_F 0.89 0.07 0.00
21_N 184_T 0.88 0.07 0.00
482_D 103_L 0.88 0.07 0.00
34_A 255_G 0.88 0.07 0.00
177_N 192_E 0.88 0.07 0.00
425_R 10_Q 0.88 0.07 0.00
480_I 132_D 0.87 0.07 0.00
109_S 218_N 0.87 0.07 0.00
126_T 148_R 0.87 0.06 0.00
326_F 56_F 0.87 0.06 0.00
417_S 195_R 0.87 0.06 0.00
257_D 219_F 0.86 0.06 0.00
291_L 92_D 0.85 0.06 0.00
316_N 266_S 0.85 0.06 0.00
311_G 100_S 0.85 0.06 0.00
256_A 64_V 0.85 0.06 0.00
287_R 255_G 0.84 0.06 0.00
357_Y 79_T 0.84 0.06 0.00
193_S 161_V 0.84 0.06 0.00
39_V 128_P 0.84 0.06 0.00
248_A 53_Y 0.84 0.06 0.00
255_A 252_P 0.84 0.06 0.00
144_N 297_C 0.84 0.06 0.00
39_V 34_A 0.84 0.06 0.00
461_D 72_K 0.83 0.06 0.00
172_K 206_Y 0.83 0.06 0.00
157_D 290_F 0.83 0.06 0.00
256_A 165_N 0.83 0.06 0.00
64_T 59_L 0.83 0.06 0.00
291_L 217_F 0.83 0.06 0.00
374_E 32_I 0.83 0.06 0.00
291_L 223_R 0.83 0.06 0.00
106_E 181_Q 0.83 0.06 0.00
120_G 101_F 0.83 0.06 0.00
346_I 145_A 0.82 0.06 0.00
478_T 38_T 0.82 0.06 0.00
301_Y 186_M 0.82 0.06 0.00
319_K 209_S 0.82 0.06 0.00
493_R 73_N 0.82 0.06 0.00
326_F 221_Y 0.82 0.06 0.00
355_N 74_G 0.82 0.06 0.00
95_P 47_P 0.81 0.06 0.00
475_K 91_L 0.81 0.06 0.00
447_D 113_D 0.81 0.06 0.00
390_K 192_E 0.81 0.06 0.00
64_T 8_F 0.81 0.06 0.00
76_T 288_F 0.81 0.06 0.00
76_T 74_G 0.81 0.06 0.00
256_A 72_K 0.81 0.06 0.00
20_Q 192_E 0.81 0.06 0.00
191_V 301_Q 0.81 0.06 0.00
94_F 5_L 0.81 0.06 0.00
274_W 144_S 0.80 0.06 0.00
109_S 288_F 0.80 0.06 0.00
421_N 19_L 0.80 0.06 0.00
248_A 144_S 0.80 0.06 0.00
506_Y 17_F 0.80 0.06 0.00
441_E 92_D 0.80 0.06 0.00
94_F 165_N 0.80 0.06 0.00
7_S 116_E 0.80 0.06 0.00
375_I 253_M 0.80 0.06 0.00
405_V 281_T 0.80 0.06 0.00
396_L 198_Y 0.80 0.06 0.00
291_L 44_K 0.80 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
11635 0.09 J F no SP unlimited Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11633 0.02 J F no SP Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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