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MFD_SALTY_1_450-UVRA_SALTY_88_595

Genes: A B A+B
Length: 450 507 917
Sequences: 4321 2976 1836
Seq/Len: 9.6 5.87 2
MirrorTree (Pazo et al. 2001) 0.17
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.01 0.45
2 0.03 0.01 0.51
5 0.03 0.01 0.60
10 0.03 0.01 0.69
20 0.03 0.01 0.74
100 0.05 0.02 0.97
0.20 0.06 1.92
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
168_L 87_I 0.84 0.35 0.00
44_L 204_D 0.69 0.22 0.00
350_N 312_F 0.66 0.19 0.00
304_E 453_V 0.64 0.18 0.00
170_D 306_R 0.60 0.15 0.00
218_P 454_I 0.59 0.15 0.00
213_P 247_P 0.59 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
7858 0.78 MFD_SALTY_1_450-UVRA_SALTY_88_595 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7856 2 MFD_SALTY_1_450-UVRA_SALTY_88_595 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7374 MFD_SALTY_1_450-UVRA_SALTY_88_595 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Running - Shared

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