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OPENSEQ.org
FEOA_FEOC
Genes: A B A+B
Length: 75 773 784
Sequences: 3624 1540 1191
Seq/Len: 48.32 1.99 1.52
MirrorTree (Pazo et al. 2001) 0.56
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 1.38
2 0.12 0.00 1.40
5 0.12 0.00 1.40
10 0.13 0.00 1.40
20 0.13 0.00 1.41
100 0.13 0.01 1.42
∞ 0.16 0.03 1.44
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 1.35 0.77 0.03
41_R 378_F 1.13 0.58 0.02
56_V 97_N 1.02 0.46 0.01
57_S 272_T 0.98 0.43 0.01
11_I 343_L 0.98 0.43 0.01
14_F 359_M 0.98 0.42 0.01
41_R 279_L 0.95 0.40 0.01
34_G 12_P 0.94 0.38 0.01
62_K 486_V 0.94 0.38 0.01
27_L 407_S 0.90 0.34 0.01
11_I 260_S 0.89 0.33 0.01
23_R 286_P 0.87 0.32 0.01
13_G 238_D 0.86 0.31 0.01
6_D 339_L 0.85 0.30 0.01
10_K 91_N 0.84 0.29 0.01
14_F 52_V 0.83 0.29 0.01
29_L 547_L 0.83 0.29 0.01
12_T 146_I 0.83 0.29 0.01
8_A 90_I 0.83 0.28 0.01
60_L 330_H 0.82 0.27 0.01
53_T 460_M 0.82 0.27 0.01
60_L 254_A 0.81 0.26 0.01
14_F 325_I 0.80 0.26 0.01
51_I 52_V 0.80 0.26 0.01
11_I 225_H 0.80 0.26 0.01
11_I 590_T 0.80 0.25 0.01
50_H 394_F 0.79 0.25 0.01
25_K 73_D 0.79 0.25 0.01
43_A 378_F 0.79 0.25 0.01
53_T 118_A 0.78 0.24 0.01
7_T 235_N 0.77 0.23 0.01
37_F 169_N 0.77 0.23 0.01
55_R 518_V 0.76 0.22 0.01
29_L 103_Y 0.74 0.22 0.01
26_L 439_F 0.74 0.22 0.01
25_K 397_L 0.74 0.21 0.01
16_R 588_L 0.73 0.21 0.01
37_F 550_V 0.73 0.21 0.01
5_P 89_L 0.73 0.21 0.01
10_K 464_V 0.73 0.21 0.01
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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