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OPENSEQ.org
FEOA_FEOC
Genes: A B A+B
Length: 75 773 682
Sequences: 3624 1540 1438
Seq/Len: 48.32 1.99 2.11
MirrorTree (Pazo et al. 2001) 0.59
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 0.11 0.00 1.68
2 0.12 0.00 1.69
5 0.12 0.00 1.70
10 0.13 0.00 1.70
20 0.13 0.00 1.70
100 0.13 0.01 1.71
∞ 0.16 0.03 1.74
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
24_Q 241_A 1.58 0.94 0.66
11_I 302_I 1.07 0.61 0.22
56_V 97_N 1.06 0.60 0.21
57_S 272_T 1.01 0.55 0.18
41_R 378_F 0.94 0.48 0.14
41_R 279_L 0.93 0.46 0.13
2_Q 276_K 0.93 0.46 0.13
12_T 525_F 0.89 0.42 0.11
51_I 52_V 0.87 0.39 0.10
40_V 71_S 0.86 0.39 0.10
11_I 590_T 0.83 0.36 0.09
23_R 286_P 0.83 0.35 0.09
25_K 73_D 0.83 0.35 0.09
35_S 408_V 0.81 0.33 0.08
71_E 110_E 0.81 0.33 0.08
43_A 378_F 0.80 0.33 0.08
11_I 343_L 0.79 0.31 0.07
33_P 242_L 0.79 0.31 0.07
10_K 91_N 0.78 0.30 0.07
28_S 563_V 0.78 0.30 0.07
25_K 22_Q 0.75 0.28 0.06
53_T 311_D 0.75 0.27 0.06
27_L 407_S 0.74 0.26 0.06
40_V 494_V 0.73 0.26 0.06
29_L 408_V 0.72 0.25 0.05
46_G 23_L 0.72 0.25 0.05
60_L 254_A 0.72 0.25 0.05
69_E 146_I 0.72 0.25 0.05
5_P 116_I 0.72 0.25 0.05
60_L 330_H 0.72 0.25 0.05
60_L 242_L 0.72 0.25 0.05
8_A 165_R 0.71 0.24 0.05
28_S 426_M 0.71 0.24 0.05
42_V 145_V 0.71 0.24 0.05
50_H 96_S 0.71 0.24 0.05
24_Q 361_Y 0.71 0.24 0.05
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
4463 2.11 FEOA_FEOC Δgene:(0, 5) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.66 Done - Shared
4462 1.52 FEOA_FEOC Δgene:(1, 5) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4461 0.15 FEOA_FEOC Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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