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OPENSEQ.org
4FXE_Jackhmmer
Genes: A B A+B
Length: 79 95 164
Sequences: 1168 3484 615
Seq/Len: 14.78 36.67 3.75
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.00 3.53
2 0.00 0.01 3.53
5 0.01 0.02 3.62
10 0.01 0.03 3.67
20 0.02 0.03 3.74
100 0.03 0.07 4.01
∞ 0.06 0.12 4.56
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
55_D 77_S 1.53 0.98 0.83
63_K 50_C 1.44 0.96 0.78
63_K 65_Q 1.40 0.95 0.75
59_V 50_C 1.34 0.94 0.70
65_R 8_D 1.25 0.90 0.62
52_S 77_S 1.17 0.86 0.54
62_V 8_D 1.05 0.76 0.42
54_E 10_R 1.00 0.71 0.36
62_V 76_I 0.99 0.70 0.35
28_S 5_L 0.95 0.66 0.32
72_V 15_W 0.94 0.64 0.30
52_S 14_E 0.93 0.63 0.29
46_F 56_R 0.92 0.62 0.28
57_E 3_Y 0.88 0.57 0.25
63_K 49_D 0.85 0.53 0.22
65_R 14_E 0.84 0.51 0.21
75_T 15_W 0.83 0.51 0.21
45_P 64_Y 0.81 0.48 0.19
8_I 9_E 0.79 0.45 0.18
75_T 7_F 0.74 0.38 0.14
54_E 77_S 0.72 0.36 0.13
64_E 5_L 0.72 0.36 0.13
56_A 47_M 0.70 0.34 0.12
48_Q 28_K 0.70 0.34 0.12
58_L 42_N 0.69 0.33 0.11
26_T 72_V 0.68 0.31 0.10
62_V 74_F 0.67 0.30 0.10
23_M 64_Y 0.67 0.30 0.10
17_Y 24_E 0.67 0.30 0.10
55_D 42_N 0.66 0.30 0.10
55_D 55_L 0.66 0.29 0.09
68_N 8_D 0.65 0.28 0.09
57_E 29_K 0.65 0.28 0.09
28_S 76_I 0.65 0.28 0.09
5_N 15_W 0.65 0.28 0.09
78_E 88_S 0.64 0.27 0.09
21_E 10_R 0.64 0.27 0.09
71_P 12_L 0.64 0.27 0.09
58_L 81_R 0.64 0.27 0.08
17_Y 34_L 0.64 0.27 0.08
32_R 47_M 0.64 0.27 0.08
66_L 65_Q 0.64 0.27 0.08
61_I 8_D 0.63 0.26 0.08
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
4762 4.1 TA_fifteen Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.93 Done - Shared
0725 3.75 4FXE_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.83 Done
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