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OPENSEQ.org
ComEA-comEC (A, 35-103)
Genes: A B A+B
Length: 69 752 795
Sequences: 1050 1047 595
Seq/Len: 15.22 1.39 0.75
MirrorTree (Pazo et al. 2001) 0.58
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 0.00 0.21
2 0.00 0.00 0.31
5 0.00 0.00 0.35
10 0.00 0.00 0.35
20 0.00 0.00 0.36
100 0.00 0.00 0.40
∞ 0.01 0.00 0.72
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
29_K 240_I 1.44 0.64 0.00
67_I 632_S 1.27 0.50 0.00
25_I 641_A 1.23 0.46 0.00
56_G 563_G 1.15 0.39 0.00
59_T 390_A 1.09 0.34 0.00
60_V 234_L 1.07 0.34 0.00
32_A 240_I 1.07 0.33 0.00
23_K 405_I 1.06 0.32 0.00
23_K 289_L 1.04 0.31 0.00
49_L 654_L 1.00 0.28 0.00
27_L 598_Q 1.00 0.28 0.00
8_V 275_A 0.98 0.27 0.00
46_I 642_M 0.98 0.27 0.00
8_V 425_A 0.98 0.27 0.00
58_A 245_I 0.97 0.26 0.00
9_N 297_M 0.97 0.26 0.00
28_K 565_W 0.97 0.26 0.00
22_L 219_K 0.96 0.25 0.00
38_E 255_L 0.96 0.25 0.00
29_K 644_E 0.95 0.25 0.00
29_K 407_P 0.95 0.24 0.00
23_K 344_V 0.94 0.24 0.00
48_D 572_W 0.93 0.24 0.00
64_A 711_W 0.93 0.24 0.00
25_I 545_G 0.93 0.24 0.00
34_V 388_V 0.93 0.23 0.00
30_A 406_V 0.91 0.23 0.00
9_N 92_R 0.91 0.22 0.00
40_N 285_A 0.91 0.22 0.00
45_H 546_L 0.90 0.22 0.00
25_I 523_T 0.90 0.22 0.00
35_D 148_P 0.90 0.22 0.00
25_I 468_L 0.89 0.21 0.00
8_V 175_V 0.89 0.21 0.00
47_D 141_E 0.88 0.21 0.00
10_I 285_A 0.88 0.21 0.00
25_I 214_T 0.88 0.20 0.00
25_I 276_L 0.88 0.20 0.00
34_V 139_R 0.88 0.20 0.00
69_L 259_M 0.87 0.20 0.00
45_H 468_L 0.86 0.20 0.00
32_A 239_A 0.86 0.20 0.00
19_A 688_A 0.86 0.20 0.00
5_V 676_A 0.86 0.19 0.00
9_N 379_T 0.85 0.19 0.00
7_T 280_L 0.85 0.19 0.00
23_K 291_T 0.85 0.19 0.00
35_D 361_W 0.85 0.19 0.00
45_H 333_L 0.84 0.18 0.00
36_Y 669_S 0.84 0.18 0.00
9_N 673_E 0.84 0.18 0.00
44_T 395_L 0.83 0.18 0.00
47_D 226_W 0.83 0.18 0.00
63_N 291_T 0.83 0.18 0.00
68_L 617_Q 0.83 0.18 0.00
63_N 715_G 0.83 0.18 0.00
59_T 345_A 0.83 0.18 0.00
16_E 313_A 0.82 0.18 0.00
67_I 255_L 0.82 0.18 0.00
65_A 647_L 0.82 0.17 0.00
32_A 595_W 0.82 0.17 0.00
49_L 395_L 0.82 0.17 0.00
34_V 720_I 0.81 0.17 0.00
51_N 282_A 0.81 0.17 0.00
68_L 580_S 0.81 0.17 0.00
31_Q 658_V 0.81 0.17 0.00
49_L 237_L 0.81 0.17 0.00
42_P 700_V 0.81 0.17 0.00
47_D 479_L 0.81 0.17 0.00
64_A 372_V 0.80 0.17 0.00
22_L 694_N 0.80 0.17 0.00
48_D 496_L 0.80 0.17 0.00
47_D 321_L 0.80 0.16 0.00
25_I 224_Q 0.80 0.16 0.00
29_K 675_I 0.80 0.16 0.00
24_G 286_G 0.80 0.16 0.00
65_A 254_F 0.79 0.16 0.00
61_R 563_G 0.79 0.16 0.00
29_K 375_M 0.79 0.16 0.00
34_V 252_G 0.79 0.16 0.00
16_E 667_K 0.79 0.16 0.00
46_I 485_G 0.78 0.16 0.00
53_K 592_G 0.78 0.16 0.00
52_V 649_R 0.78 0.16 0.00
12_T 708_Q 0.78 0.16 0.00
15_A 258_G 0.78 0.16 0.00
25_I 345_A 0.78 0.16 0.00
59_T 445_D 0.78 0.16 0.00
48_D 260_M 0.78 0.16 0.00
29_K 589_C 0.78 0.15 0.00
58_A 347_V 0.78 0.15 0.00
69_L 299_L 0.78 0.15 0.00
25_I 146_L 0.78 0.15 0.00
25_I 264_A 0.78 0.15 0.00
31_Q 426_Y 0.78 0.15 0.00
63_N 713_D 0.77 0.15 0.00
25_I 249_F 0.77 0.15 0.00
32_A 344_V 0.77 0.15 0.00
9_N 84_G 0.77 0.15 0.00
48_D 149_I 0.77 0.15 0.00
40_N 361_W 0.77 0.15 0.00
60_V 687_V 0.77 0.15 0.00
14_S 390_A 0.77 0.15 0.00
12_T 702_A 0.77 0.15 0.00
56_G 536_V 0.76 0.15 0.00
67_I 437_L 0.76 0.15 0.00
16_E 272_V 0.76 0.15 0.00
24_G 401_F 0.76 0.15 0.00
29_K 371_L 0.76 0.15 0.00
29_K 670_S 0.76 0.15 0.00
18_L 246_G 0.76 0.14 0.00
34_V 624_M 0.76 0.14 0.00
67_I 330_F 0.76 0.14 0.00
58_A 160_L 0.76 0.14 0.00
61_R 633_V 0.75 0.14 0.00
32_A 137_N 0.75 0.14 0.00
50_T 321_L 0.75 0.14 0.00
14_S 607_P 0.75 0.14 0.00
67_I 250_S 0.75 0.14 0.00
65_A 446_V 0.75 0.14 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
0284 0.75 ComEA-comEC (A, 35-103) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0283 0.37 ComEA-comEC (A, 35-103) Δgene:(0, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
0282 0.41 ComEA-comEC (A, 35-103) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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