So, basically it can be said that the carbon assimilation pathways, membrane
morphology, presence of specific genes guide a cell to uptake specific pathway to
perform the bio transformation process.
8.8
Biological Databases Relevant to Environmental Studies
There are a number of biological databases which have been able to provide
information about the metabolic pathways, about the bio geochemical pathways
which include various levels of microbial interactions among the different
microorganisms (Lovely 2003; Perez-Garcia et al. 2014a). It will also be able to
define the link between the sequence and the annotated genome using tools like
Pathway Tools, which allow prediction of metabolic network with the help of
Pathway/Genome Database (PGDB).
8.8.1 BioSurfDb
This is one databank providing information about different microorganisms,
metagenomes, biodegradation related genes, specific proteins, and even the
pathways associated with the same, it also includes the number of experiments
with pollutants and their respective treatments. This curated database also provides
information about the biosurfactant: name, class, and also references related to it
(http://www.biosurfdb.org/#/getstarted).
8.8.2 MetaCyc
Databases like MetaCyc (metacyc.org) allow non-redundant databases, which
contains information like metabolic pathways and even the respective enzymes
involved. Kyoto Encyclopedia of Genes and Genomes (KEGG) also provides
information giving interrelation of genes and genomes, with the number of enzymes,
reactions, chemical compounds.
8.8.3 MetaRouter
This allows one to have dataset providing relevant information in context to bioremediation. It provides information in terms of enzymes involved, compounds,
microorganisms, and the framework in which it is involved (Pazos et al. 2005).
8.8.4 Biodegradation Probability Program (BIODEG)
BIODEG enables to calculate the rate of biodegradation using microorganisms. This
software gives the probability of rapid degradation under aerobic conditions.
174
J. Tomar
morphology, presence of specific genes guide a cell to uptake specific pathway to
perform the bio transformation process.
8.8
Biological Databases Relevant to Environmental Studies
There are a number of biological databases which have been able to provide
information about the metabolic pathways, about the bio geochemical pathways
which include various levels of microbial interactions among the different
microorganisms (Lovely 2003; Perez-Garcia et al. 2014a). It will also be able to
define the link between the sequence and the annotated genome using tools like
Pathway Tools, which allow prediction of metabolic network with the help of
Pathway/Genome Database (PGDB).
8.8.1 BioSurfDb
This is one databank providing information about different microorganisms,
metagenomes, biodegradation related genes, specific proteins, and even the
pathways associated with the same, it also includes the number of experiments
with pollutants and their respective treatments. This curated database also provides
information about the biosurfactant: name, class, and also references related to it
(http://www.biosurfdb.org/#/getstarted).
8.8.2 MetaCyc
Databases like MetaCyc (metacyc.org) allow non-redundant databases, which
contains information like metabolic pathways and even the respective enzymes
involved. Kyoto Encyclopedia of Genes and Genomes (KEGG) also provides
information giving interrelation of genes and genomes, with the number of enzymes,
reactions, chemical compounds.
8.8.3 MetaRouter
This allows one to have dataset providing relevant information in context to bioremediation. It provides information in terms of enzymes involved, compounds,
microorganisms, and the framework in which it is involved (Pazos et al. 2005).
8.8.4 Biodegradation Probability Program (BIODEG)
BIODEG enables to calculate the rate of biodegradation using microorganisms. This
software gives the probability of rapid degradation under aerobic conditions.
174
J. Tomar