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cI_B_cIII_isp_Pdenitr
Genes: A B A+B
Length: 175 190 342
Sequences: 1610 1692 546
Seq/Len: 9.2 8.91 1.6
MirrorTree (Pazo et al. 2001) 0.18
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 0.20
∞ 0.10 0.05 1.50
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 1.23 0.69 0.01
114_I 23_T 1.02 0.48 0.01
85_L 30_A 0.95 0.41 0.00
36_I 40_N 0.91 0.37 0.00
146_V 11_H 0.86 0.32 0.00
160_I 115_E 0.85 0.31 0.00
147_P 73_G 0.84 0.31 0.00
160_I 178_V 0.84 0.30 0.00
26_K 32_G 0.84 0.30 0.00
78_A 172_Q 0.81 0.28 0.00
139_I 93_D 0.80 0.27 0.00
36_I 30_A 0.80 0.27 0.00
85_L 25_G 0.80 0.26 0.00
65_P 59_S 0.78 0.25 0.00
85_L 115_E 0.78 0.25 0.00
79_S 86_I 0.78 0.25 0.00
86_M 30_A 0.77 0.25 0.00
160_I 175_H 0.77 0.25 0.00
38_N 40_N 0.77 0.24 0.00
144_I 39_V 0.77 0.24 0.00
112_Y 39_V 0.76 0.24 0.00
108_P 10_D 0.76 0.24 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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