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OPENSEQ.org
cI_H_cIII_ISP_Pdenitr
Genes: A B A+B
Length: 345 190 514
Sequences: 4768 1692 527
Seq/Len: 13.82 8.91 1.03
MirrorTree (Pazo et al. 2001) 0.31
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 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.01 0.01 0.01
20 0.01 0.01 0.02
100 0.02 0.01 0.10
∞ 0.05 0.05 0.99
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
290_M 62_E 1.14 0.47 0.00
75_I 22_A 1.05 0.39 0.00
206_F 128_M 1.02 0.36 0.00
106_E 30_A 1.02 0.36 0.00
17_L 159_Y 1.00 0.34 0.00
27_M 15_R 0.99 0.34 0.00
207_V 22_A 0.93 0.29 0.00
93_M 21_Y 0.92 0.28 0.00
42_A 15_R 0.91 0.28 0.00
80_D 179_A 0.91 0.27 0.00
259_S 51_L 0.88 0.26 0.00
90_L 96_Q 0.88 0.26 0.00
294_V 127_V 0.88 0.25 0.00
73_I 189_L 0.87 0.25 0.00
242_L 90_R 0.86 0.24 0.00
223_A 159_Y 0.86 0.24 0.00
17_L 25_G 0.85 0.23 0.00
263_F 125_W 0.84 0.23 0.00
51_N 22_A 0.84 0.23 0.00
267_L 68_T 0.84 0.23 0.00
274_A 26_A 0.84 0.22 0.00
74_V 22_A 0.84 0.22 0.00
206_F 163_G 0.83 0.22 0.00
110_M 31_A 0.83 0.22 0.00
155_I 13_A 0.82 0.22 0.00
287_W 28_T 0.82 0.21 0.00
75_I 11_H 0.82 0.21 0.00
65_A 42_M 0.81 0.21 0.00
290_M 115_E 0.81 0.20 0.00
123_A 68_T 0.80 0.20 0.00
317_L 19_L 0.80 0.20 0.00
233_T 26_A 0.79 0.20 0.00
131_V 73_G 0.79 0.20 0.00
12_A 65_T 0.79 0.19 0.00
172_T 180_E 0.79 0.19 0.00
86_L 102_A 0.78 0.19 0.00
79_A 76_V 0.78 0.19 0.00
102_I 159_Y 0.78 0.19 0.00
83_V 183_D 0.77 0.18 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
3041 0.92 cI_H_40_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3040 0.94 cI_H_40_cIII_isp_2_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3038 0.95 cI_H_40_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2723 1.03 cI_H_cIII_ISP_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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