Molecular Systems Engineering Lab

(Genomic Energy of Bioresources)

Department of bioinformatics

CPSIR-CM: Cyanobacterial Protein Structure Information Resource for C1Metabolisms

Cyanobacteria are capable of degrading both naturally occurring aliphatic and aromatic hydrocarbons. In this study, database structure is organized for completed cyanobacterial genomes comprising information to 9 metabolic pathways. Protein structural information for starvation induced proteins, C1 transporters and assimilation pathways to methane, aliphatic, nitrogenated, halogenated and sulfated C1 compounds have incorporated in this database. Structural information for more than 500 functional proteins has included individually describing their features at primary, secondary and tertiary levels. Along with NCBI accession we have also given unique number to retrieve enzyme of interest in specified pathways of genus alone. Protein 3D models of each entry are implemented in this resource in PDB format that would be supporting for molecular modeling, dynamics and docking studies on understanding the structure-function relationships. NCBI accession, pathway, names of enzymes and organism are assigned as search forms in a search engine supported by this database. Click Here

GSMMM Portel: Genome-Scale Microbial Metabolic Models Portel

A central goal of molecular systems biology is the elucidation of cell function and physiology through the integrated use of broad based genomic and physiological data. Genome-scale models of microbial organisms, comprising different levels of information, are primarily on the stoichiometry of many different reactions. Some information about metabolic regulation could offer a suitable platform for developing systems level tools for analyzing and engineering metabolism. The in silico model has also been used to predict the metabolic adaptation to several environmental perturbations. These predictions are currently being compared with experimental data, including physiological measurements and global gene expression data, to achieve the goal of improvement in our understanding on the metabolism of microorganisms under non-optimal but environmentally relevant conditions. In our lab, we are constructing genome-scale models for Methanobrevibacter ruminantium M1, Methanosarcina mazei GO1, Methanothermobacter thermautotrophicus delta H, Methanothermococcus okinawensis, Clostridium sticklandii HF, Clostridium botulinum type A and type B. Click Here

Structural genes


Accession Gene Organism
EU826071 16S rRNA Ochrobactrum anthropi strain SRK5
EU826070 16S rRNA Ignatzschineria larvae strain SRK4
EU826069 16S rRNA Ochrobactrum cytisi strain SRK3
EU513181 16S rRNA Photorhabdus luminescens subsp. laumondii strain SRK 2
EU513180 16S rRNA Xenorhabdus poinarii strain SRK 1
EU159696 16S rRNA Leptospira interrogans serovar Bataviae strain Swart
EU159695 16S rRNA Leptospira santarosai serovar Sarmin strain CZ390
EU159694 16S rRNA Leptospira borgpetersenii serovar Javanica strain Poi
EU159693 16S rRNA Leptospira interrogans serovar Autumnalis strain N2
EU159692 16S rRNA Leptospira biflexa serovar Patoc strain Patoc 1
EU159691 16S rRNA Leptospira interrogans serovar Hardjo strain Hardjoprajitno
EU159690 16S rRNA Leptospira noguchii serovar Louisiana strain LSU1945
EU159689 16S rRNA Leptospira sp. G6
EU159688 16S rRNA Leptospira sp. G3
EU159687 16S rRNA Leptospira interrogans serovar Australis strain Ballico
EU159686 16S rRNA Leptospira borgpetersenii serovar Javanica strain R1R
EU159685 16S rRNA Leptospira borgpetersenii serovar Javanica strain R1L

Functional genes


Accession Gene Organism
EU091296 OmpL41 Leptospira interrogans serovar Grippotyphosa
EU091295 OmpL41 Leptospira interrogans serovar Autumnalis
EU091294 OmpLL1 Leptospira interrogans serovar Autumnalis
EU091293 OmpLL1 Leptospira interrogans serovar Grippotyphosa
ACB12047 OmpL32 Leptospira interrogans serovar Autumnalis
ACB12046 OmpL32 Leptospira borgpetersenii serovar Javanica
ACB12045 OmpL32 Leptospira borgpetersenii serovar Javanica
ABX83722 OmpL32 Leptospira borgpetersenii serovar Javanica
ABX83723 OmpL32 Leptospira interrogans serovar Autumnalis
EU526391 OmpL32 Leptospira interrogans serovar Autumnalis strain N2
EU526390 OmpL32 Leptospira borgpetersenii serovar Javanica strain R1L
EU526389 OmpL32 Leptospira borgpetersenii serovar Javanica strain R1R
EU293442 OmpL32 Leptospira borgpetersenii serovar Javanica strain R1L
EU293441 OmpL32 Leptospira borgpetersenii serovar Javanica strain R1L
EU293443 OmpL32 Leptospira interrogans serovar Autumnalis strain N2
FJ434139 SecY Uncultured Leptospira sp.
FJ434138 SecY Uncultured Leptospira sp.
FJ434137 SecY Uncultured Leptospira sp.
FJ755847 Collagen type II Gallus gallus.