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OPENSEQ.org
cI_B_6_cIII_isp_4_Pdenitr
Genes: A B A+B
Length: 175 190 342
Sequences: 1602 1692 541
Seq/Len: 9.15 8.91 1.58
MirrorTree (Pazo et al. 2001) 0.17
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 0.01
5 0.02 0.01 0.02
10 0.02 0.01 0.03
20 0.03 0.01 0.04
100 0.04 0.01 0.19
∞ 0.10 0.05 1.48
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
45_L 22_A 1.13 0.59 0.00
114_I 23_T 1.04 0.50 0.00
160_I 115_E 1.01 0.47 0.00
36_I 40_N 0.93 0.38 0.00
36_I 30_A 0.86 0.32 0.00
85_L 30_A 0.85 0.31 0.00
147_P 73_G 0.85 0.31 0.00
108_P 23_T 0.84 0.30 0.00
38_N 40_N 0.84 0.30 0.00
65_P 59_S 0.84 0.30 0.00
85_L 115_E 0.83 0.29 0.00
85_L 25_G 0.83 0.29 0.00
86_M 30_A 0.82 0.29 0.00
146_V 11_H 0.81 0.28 0.00
160_I 178_V 0.81 0.27 0.00
114_I 115_E 0.81 0.27 0.00
78_A 172_Q 0.80 0.26 0.00
26_K 32_G 0.79 0.26 0.00
157_L 115_E 0.78 0.25 0.00
157_L 15_R 0.78 0.25 0.00
79_S 86_I 0.77 0.24 0.00
72_F 150_W 0.77 0.24 0.00
144_I 39_V 0.77 0.24 0.00
144_I 14_T 0.76 0.23 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
3007 1.51 cI_B_4_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3006 1.58 cI_B_6_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2831 1.6 cI_B_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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