160
Genomic sequencing of representative strains with known and characterized
BGCs can enable the characterization of the basic architecture of related NPRS coding genes (Bills et al. 2014). A single NRPS module in fungi follows certain uniformity in its domain architecture and is found to be consisting of three types of
domains, namely:
(i) ‘A’ domain – The adenylation domain that recognizes and activates a substrate
molecule via adenylation with ATP
(ii) ‘T’ domain – The thiolation domain that binds the substrate to the NRPS
protein
(iii) ‘C’ domain – The condensation domain that helps in linking the two substrates
through a condensation reaction.
The conserved nature of the NRPS modules thus aids in surveying a genome to
identify the encoding genes of known NRPS sequences. This remains true for
siderophore- producing NRPSs as well. Thus, the approaches generally used for NP
and NRPS discovery and annotation are elaborated on to the identification of siderophores also.
Unlike other NRPSs, siderophore synthesizing NRPSs do not follow the colinear structure of the modules whose count and arrangement of domains could be
used to characterize the final product (Mootz et al. 2002). Rather, the modules are
placed iteratively with a single characteristic module with the domains in specific
Table 10.1 Published computational implementations for NRPS analysis
Tool name
Web server address
Reference
SBSPKSv2/
NRPS-PKS
www.nii.ac.in/sbspks2.html
Khater et al. (2017)
antiSMASH
https://antismash.
secondarymetabolites.org/
Blin et al. (2017)
Dereplicator
http://cab.spbu.ru/software/
dereplicator/
Mohimani et al. (2017)
PRISM
http://magarveylab.ca/prism/
Skinnider et al. (2017) and
Skinnider et al. (2015)
CASSIS/SMIPS
https://sbi.hki-jena.de/cassis
Wolf et al. (2015)
GARLIC
http://www.magarveylab.ca/garlic Dejong et al. (2016)
GNPS
http://gnps.ucsd.edu/
Wang et al. (2016)
IMG-ABC
https://img.jgi.doe.gov/abc
Hadjithomas et al. (2015)
SEQL-NRPS
http://services.birc.au.dk/seql-nrps Knudsen et al. (2015)
GNP
https://magarveylab.ca/gnp/
Johnston et al. (2015)
MIBiG
https://mibig.secondarymetabolites.
org/
Medema et al. 2015)
ClusterMine360
http://www.clustermine360.ca/
Conway and Boddy (2012)
Pep2Path
http://pep2path.sourceforge.net/
Medema et al. (2014)
NRPSsp
www.nrpssp.com
Prieto et al. (2011)
NRPSpredictor2
https://bio.tools/NRPSpredictor2
Röttig et al. (2011)
SMURF
https://www.jcvi.org/smurf
Khaldi et al. (2010)
D. Subramanian et al.
Genomic sequencing of representative strains with known and characterized
BGCs can enable the characterization of the basic architecture of related NPRS coding genes (Bills et al. 2014). A single NRPS module in fungi follows certain uniformity in its domain architecture and is found to be consisting of three types of
domains, namely:
(i) ‘A’ domain – The adenylation domain that recognizes and activates a substrate
molecule via adenylation with ATP
(ii) ‘T’ domain – The thiolation domain that binds the substrate to the NRPS
protein
(iii) ‘C’ domain – The condensation domain that helps in linking the two substrates
through a condensation reaction.
The conserved nature of the NRPS modules thus aids in surveying a genome to
identify the encoding genes of known NRPS sequences. This remains true for
siderophore- producing NRPSs as well. Thus, the approaches generally used for NP
and NRPS discovery and annotation are elaborated on to the identification of siderophores also.
Unlike other NRPSs, siderophore synthesizing NRPSs do not follow the colinear structure of the modules whose count and arrangement of domains could be
used to characterize the final product (Mootz et al. 2002). Rather, the modules are
placed iteratively with a single characteristic module with the domains in specific
Table 10.1 Published computational implementations for NRPS analysis
Tool name
Web server address
Reference
SBSPKSv2/
NRPS-PKS
www.nii.ac.in/sbspks2.html
Khater et al. (2017)
antiSMASH
https://antismash.
secondarymetabolites.org/
Blin et al. (2017)
Dereplicator
http://cab.spbu.ru/software/
dereplicator/
Mohimani et al. (2017)
PRISM
http://magarveylab.ca/prism/
Skinnider et al. (2017) and
Skinnider et al. (2015)
CASSIS/SMIPS
https://sbi.hki-jena.de/cassis
Wolf et al. (2015)
GARLIC
http://www.magarveylab.ca/garlic Dejong et al. (2016)
GNPS
http://gnps.ucsd.edu/
Wang et al. (2016)
IMG-ABC
https://img.jgi.doe.gov/abc
Hadjithomas et al. (2015)
SEQL-NRPS
http://services.birc.au.dk/seql-nrps Knudsen et al. (2015)
GNP
https://magarveylab.ca/gnp/
Johnston et al. (2015)
MIBiG
https://mibig.secondarymetabolites.
org/
Medema et al. 2015)
ClusterMine360
http://www.clustermine360.ca/
Conway and Boddy (2012)
Pep2Path
http://pep2path.sourceforge.net/
Medema et al. (2014)
NRPSsp
www.nrpssp.com
Prieto et al. (2011)
NRPSpredictor2
https://bio.tools/NRPSpredictor2
Röttig et al. (2011)
SMURF
https://www.jcvi.org/smurf
Khaldi et al. (2010)
D. Subramanian et al.