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cI_K_cIV_cyoc20_Ecoli
Genes: A B A+B
Length: 100 204 296
Sequences: 1292 4430 865
Seq/Len: 12.92 21.72 2.92
MirrorTree (Pazo et al. 2001) 0.27
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 0.03 0.02
2 0.00 0.03 0.06
5 0.00 0.03 0.19
10 0.01 0.03 0.29
20 0.01 0.04 0.43
100 0.02 0.05 0.73
∞ 0.03 0.08 2.85
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
100_G 33_L 1.03 0.67 0.01
11_A 189_V 0.99 0.62 0.01
63_I 108_F 0.96 0.59 0.01
78_A 89_A 0.96 0.59 0.01
9_I 110_A 0.94 0.57 0.01
84_H 161_M 0.94 0.56 0.01
63_I 194_V 0.93 0.56 0.01
80_L 51_V 0.92 0.54 0.01
42_S 195_F 0.91 0.53 0.01
94_S 140_F 0.90 0.51 0.01
78_A 195_F 0.89 0.51 0.01
79_L 106_W 0.85 0.45 0.01
52_Y 75_L 0.84 0.45 0.01
44_L 62_D 0.84 0.44 0.01
43_A 38_I 0.83 0.43 0.01
60_V 162_V 0.82 0.42 0.01
40_N 80_S 0.81 0.41 0.01
73_A 31_I 0.81 0.41 0.01
26_R 61_K 0.81 0.41 0.01
33_I 194_V 0.81 0.41 0.01
90_L 77_L 0.81 0.41 0.01
100_G 102_L 0.80 0.40 0.01
26_R 144_G 0.79 0.39 0.01
19_L 100_S 0.79 0.38 0.01
84_H 105_T 0.78 0.37 0.01
12_A 51_V 0.78 0.37 0.01
13_I 172_T 0.77 0.36 0.01
5_Q 47_Y 0.77 0.36 0.01
17_L 106_W 0.77 0.36 0.01
65_A 92_K 0.76 0.35 0.01
45_A 86_A 0.76 0.35 0.01
1_M 88_I 0.76 0.35 0.01
83_L 140_F 0.76 0.35 0.01
67_S 43_L 0.76 0.35 0.01
10_L 96_S 0.75 0.34 0.01
73_A 190_V 0.74 0.33 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
2763 9.88 cI_K_cIV_cyoc2_2_Ecoli Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
2762 9.81 cI_K_cIV_cyoc2_Ecoli Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
2760 2.92 cI_K_cIV_cyoc20_Ecoli Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2751 9.4 cI_K_cIV_cyoc_Ecoli Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
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