UPGRADE NOTICE:

This version of NaPDoS has been superceded by a newer version called NaPDoS2. We highly recommend that you switch to the new version, which is faster, more accurate, and includes a wider range of reference products:

https://npdomainseeker.sdsc.edu/napdos2

A complete description of the upgrade is provided in the following publication:

Klau LJ, Podell S, Creamer KE, Demko AM, Singh HW, Allen EE, Moore BS, Ziemert N, Letzel AC, Jensen PR. The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function.Journal of Biological Chemistry, 2022, 102480, ISSN 0021-9258, https://doi.org/10.1016/j.jbc.2022.102480.

 

 

PKS/NRPS Domain Search

Choose a domain and query type, then enter your data to identify candidate KS and/or C domains.
Optional Advanced Settings can be used to customize program parameters.

Domain type

    KS domains
    C domains

Query type

    Predicted protein sequences (amino acid)
    Predicted coding sequences or PCR products (DNA)
    Genome or metagenome contigs (DNA)

Query sequence

Enter or paste sequence(s) in FASTA format, or upload a FASTA file. Please avoid using sequence id numbers containing non-standard characters (e.g. commas, slashes, colons, parentheses, ampersands, etc), as well as ambiguity codes "R" and "Y" for nucleic acid sequence files.

Note: Current size limit for uploaded files is 30 MB. For larger files, please consider our suggestions for file size management before submission.

Upload a file:

 
Advanced Settings
Sensitivity may be increased by choosing higher e-values and shorter minimum match lengths, but these adjustments may also increase false positives. Conversely, selectivity can be improved with lower e-values and longer minimum match lengths, at the cost of decresed sensitivity.

KS domain detection
HMM e-value cutoff


 minimum match length

C domain detection
HMM e-value cutoff


 minimum match length

Pathway assignment

BLASTP e-value cutoff


 max db hits per domain