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OPENSEQ.org
ACP_FAAL
Genes: A B A+B
Length: 90 584 642
Sequences: 215 25767 161
Seq/Len: 2.39 44.12 0.25
MirrorTree (Pazo et al. 2001) 0.29
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 0.08 0.09
2 0.01 0.10 0.14
5 0.01 0.13 0.22
10 0.02 0.14 0.23
20 0.02 0.15 0.24
100 0.04 0.20 0.26
∞ 0.11 0.27 0.29
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
16_V 258_I 1.67 0.48 0.00
41_L 244_R 1.63 0.45 0.00
54_L 329_C 1.51 0.37 0.00
57_D 326_M 1.44 0.33 0.00
46_L 504_V 1.38 0.30 0.00
60_E 214_L 1.38 0.30 0.00
47_D 461_H 1.37 0.30 0.00
51_A 53_A 1.34 0.28 0.00
12_T 295_S 1.30 0.26 0.00
35_I 10_S 1.28 0.25 0.00
35_I 82_A 1.18 0.21 0.00
77_L 498_I 1.18 0.20 0.00
74_A 180_K 1.17 0.20 0.00
54_L 84_L 1.16 0.20 0.00
16_V 252_L 1.15 0.19 0.00
57_D 449_F 1.14 0.19 0.00
69_T 326_M 1.14 0.19 0.00
77_L 253_L 1.14 0.19 0.00
75_D 228_L 1.14 0.19 0.00
57_D 532_V 1.13 0.18 0.00
24_V 30_V 1.13 0.18 0.00
16_V 209_G 1.11 0.18 0.00
46_L 521_T 1.09 0.17 0.00
66_V 183_V 1.08 0.17 0.00
86_A 468_Q 1.08 0.17 0.00
76_S 461_H 1.07 0.16 0.00
62_F 163_R 1.05 0.16 0.00
23_R 288_L 1.05 0.16 0.00
28_L 187_G 1.05 0.16 0.00
25_A 23_P 1.04 0.15 0.00
73_E 180_K 1.02 0.15 0.00
81_A 536_V 1.02 0.15 0.00
52_F 312_R 1.01 0.14 0.00
32_A 342_P 1.01 0.14 0.00
76_S 345_R 1.01 0.14 0.00
68_P 89_V 1.01 0.14 0.00
69_T 268_Y 1.00 0.14 0.00
20_L 105_R 1.00 0.14 0.00
65_T 76_F 1.00 0.14 0.00
67_E 526_V 1.00 0.14 0.00
70_L 31_A 0.99 0.14 0.00
37_A 66_V 0.99 0.14 0.00
51_A 12_G 0.99 0.14 0.00
87_L 372_G 0.98 0.13 0.00
65_T 383_I 0.98 0.13 0.00
24_V 315_L 0.97 0.13 0.00
54_L 115_P 0.97 0.13 0.00
60_E 497_R 0.97 0.13 0.00
81_A 122_G 0.97 0.13 0.00
38_D 153_G 0.97 0.13 0.00
35_I 178_S 0.95 0.13 0.00
80_V 335_T 0.95 0.13 0.00
62_F 87_G 0.94 0.12 0.00
77_L 80_Y 0.94 0.12 0.00
72_W 71_P 0.94 0.12 0.00
73_E 52_R 0.94 0.12 0.00
81_A 77_A 0.94 0.12 0.00
25_A 298_I 0.94 0.12 0.00
81_A 144_A 0.94 0.12 0.00
73_E 125_R 0.93 0.12 0.00
38_D 228_L 0.93 0.12 0.00
76_S 558_E 0.93 0.12 0.00
56_G 259_T 0.93 0.12 0.00
66_V 403_R 0.93 0.12 0.00
44_Y 560_F 0.93 0.12 0.00
35_I 498_I 0.93 0.12 0.00
40_P 81_L 0.93 0.12 0.00
25_A 190_L 0.92 0.12 0.00
52_F 435_L 0.92 0.12 0.00
44_Y 442_A 0.92 0.12 0.00
44_Y 451_T 0.92 0.12 0.00
30_C 395_G 0.92 0.12 0.00
20_L 549_G 0.92 0.12 0.00
81_A 458_L 0.92 0.12 0.00
21_V 484_Q 0.92 0.12 0.00
28_L 371_V 0.91 0.11 0.00
77_L 298_I 0.91 0.11 0.00
55_C 491_V 0.90 0.11 0.00
48_S 439_D 0.90 0.11 0.00
48_S 462_G 0.90 0.11 0.00
36_D 400_I 0.90 0.11 0.00
51_A 221_F 0.90 0.11 0.00
36_D 370_M 0.89 0.11 0.00
89_G 300_G 0.89 0.11 0.00
16_V 478_H 0.89 0.11 0.00
19_W 167_A 0.89 0.11 0.00
52_F 270_L 0.89 0.11 0.00
24_V 561_L 0.88 0.11 0.00
73_E 400_I 0.88 0.11 0.00
53_A 244_R 0.88 0.11 0.00
23_R 321_A 0.88 0.11 0.00
81_A 13_E 0.88 0.11 0.00
66_V 189_V 0.88 0.11 0.00
56_G 413_G 0.88 0.11 0.00
19_W 410_G 0.88 0.11 0.00
60_E 532_V 0.88 0.11 0.00
55_C 244_R 0.88 0.11 0.00
79_A 118_V 0.88 0.11 0.00
63_G 541_G 0.87 0.11 0.00
13_P 308_E 0.87 0.10 0.00
89_G 530_V 0.87 0.10 0.00
62_F 12_G 0.87 0.10 0.00
67_E 12_G 0.87 0.10 0.00
23_R 530_V 0.87 0.10 0.00
54_L 344_V 0.87 0.10 0.00
78_A 326_M 0.87 0.10 0.00
41_L 94_P 0.86 0.10 0.00
36_D 397_I 0.86 0.10 0.00
32_A 142_V 0.86 0.10 0.00
16_V 509_P 0.86 0.10 0.00
14_D 491_V 0.86 0.10 0.00
58_I 252_L 0.85 0.10 0.00
51_A 530_V 0.85 0.10 0.00
80_V 224_L 0.85 0.10 0.00
79_A 384_V 0.85 0.10 0.00
36_D 303_M 0.85 0.10 0.00
80_V 426_L 0.85 0.10 0.00
30_C 155_V 0.85 0.10 0.00
21_V 515_G 0.85 0.10 0.00
20_L 463_R 0.85 0.10 0.00
58_I 212_L 0.84 0.10 0.00
22_E 44_E 0.84 0.10 0.00
11_L 530_V 0.84 0.10 0.00
42_T 106_V 0.84 0.10 0.00
57_D 251_R 0.84 0.10 0.00
88_A 180_K 0.84 0.10 0.00
30_C 255_R 0.84 0.10 0.00
35_I 293_N 0.83 0.10 0.00
80_V 257_R 0.83 0.10 0.00
51_A 413_G 0.83 0.10 0.00
85_V 373_V 0.83 0.10 0.00
16_V 321_A 0.83 0.10 0.00
33_E 416_E 0.83 0.10 0.00
71_L 403_R 0.83 0.10 0.00
68_P 224_L 0.83 0.10 0.00
77_L 166_V 0.83 0.10 0.00
43_E 518_S 0.83 0.10 0.00
40_P 353_E 0.83 0.10 0.00
40_P 105_R 0.83 0.10 0.00
21_V 427_A 0.82 0.09 0.00
52_F 258_I 0.82 0.09 0.00
54_L 215_H 0.82 0.09 0.00
29_R 315_L 0.82 0.09 0.00
85_V 143_E 0.82 0.09 0.00
20_L 87_G 0.82 0.09 0.00
17_R 191_D 0.82 0.09 0.00
44_Y 184_L 0.82 0.09 0.00
59_E 529_G 0.82 0.09 0.00
62_F 256_H 0.82 0.09 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
13353 6.25 Lydia Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13352 3.95 ACP_FAAL Δgene:(1, 100) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13350 2.84 ACP_FAAL Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.01 Done - Shared
13346 0 ACP_FAAL Δgene:(1, 20) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
13345 0.25 ACP_FAAL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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