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OPENSEQ.org
cI_K_10_cIII_isp_10_Pdenitr
Genes: A B A+B
Length: 101 190 286
Sequences: 4172 1539 573
Seq/Len: 41.31 8.1 2
MirrorTree (Pazo et al. 2001) 0.19
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 0.01 0.00
2 0.00 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.01
20 0.01 0.01 0.04
100 0.03 0.01 0.20
∞ 0.07 0.04 1.97
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
70_A 180_E 1.11 0.64 0.01
55_G 184_D 1.03 0.56 0.01
47_F 39_V 0.97 0.49 0.00
45_I 123_G 0.96 0.48 0.00
9_V 175_H 0.89 0.41 0.00
79_A 174_L 0.89 0.40 0.00
11_G 131_V 0.88 0.39 0.00
29_V 181_F 0.85 0.35 0.00
76_I 148_G 0.84 0.35 0.00
45_I 185_T 0.83 0.34 0.00
17_T 186_T 0.81 0.32 0.00
99_M 153_P 0.81 0.32 0.00
12_A 24_A 0.81 0.32 0.00
8_L 31_A 0.81 0.32 0.00
19_I 121_E 0.80 0.31 0.00
23_F 55_Q 0.80 0.31 0.00
30_I 23_T 0.79 0.30 0.00
17_T 114_D 0.79 0.30 0.00
55_G 29_V 0.78 0.29 0.00
47_F 126_L 0.77 0.28 0.00
61_V 174_L 0.76 0.28 0.00
64_M 19_L 0.76 0.27 0.00
16_V 32_G 0.76 0.27 0.00
18_G 137_C 0.75 0.27 0.00
43_V 99_D 0.75 0.26 0.00
83_V 38_L 0.74 0.26 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
2936 1.01 cI_K_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2935 2 cI_K_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2925 1.52 cI_K_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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