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OPENSEQ.org
cI_F40_cIII_isp_Pdenitr
Genes: A B A+B
Length: 431 190 608
Sequences: 2222 1692 533
Seq/Len: 5.16 8.91 0.88
MirrorTree (Pazo et al. 2001) 0.26
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.01 0.00
10 0.02 0.01 0.01
20 0.02 0.01 0.02
100 0.04 0.01 0.10
∞ 0.12 0.05 0.86
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
260_S 131_V 1.19 0.48 0.00
147_G 127_V 0.98 0.30 0.00
387_E 176_I 0.92 0.25 0.00
261_I 96_Q 0.90 0.24 0.00
162_L 39_V 0.88 0.23 0.00
111_I 39_V 0.83 0.20 0.00
276_G 163_G 0.83 0.20 0.00
262_P 35_A 0.83 0.20 0.00
115_A 26_A 0.82 0.19 0.00
162_L 70_K 0.80 0.18 0.00
72_E 185_T 0.78 0.17 0.00
34_A 175_H 0.78 0.17 0.00
145_D 91_E 0.78 0.17 0.00
406_I 15_R 0.78 0.17 0.00
393_A 170_A 0.77 0.17 0.00
40_R 90_R 0.77 0.17 0.00
117_G 19_L 0.77 0.17 0.00
227_E 95_G 0.77 0.16 0.00
189_M 167_R 0.76 0.16 0.00
49_A 38_L 0.76 0.16 0.00
20_L 32_G 0.76 0.16 0.00
321_M 35_A 0.76 0.16 0.00
294_L 124_E 0.75 0.16 0.00
227_E 31_A 0.75 0.16 0.00
172_I 188_K 0.74 0.15 0.00
105_L 156_G 0.74 0.15 0.00
260_S 189_L 0.74 0.15 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
3026 0.99 cI_F_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2794 0.88 cI_F40_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2793 0.98 cI_F_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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