We present a systematic analysis of molecular level alignments and electron transport characteristics based on the nonequilibrium Green's function (NEGF) approach combined with density functional theory (DFT) for six conjugated molecules (PTP, CPTP, NiPTP, CoPTP4, CoPTP5, and FePTP) containing different types of conjugated frameworks. The conjugated molecules are classified into three groups according to the incorporated component into the conjugated framework where group I, group II, and group III contain antiaromatic, nonaromatic, and aromatic units, respectively. The results show that the combining of non- and antiaromatic components increases the conductance due to the close alignment of the HOMO level relative to the Fermi level. Consequently, the order of current follows the manner of group I > group II > group III ([NiPTP > CoPTP4 > CPTP] > [CoPTP5 > FePTP] > [PTP]). The important feature emerging from this work is that the distinct response of each group to molecule-contact coupling and applied bias voltage causes distinguishable features of electron transport characteristics and these factors may give an insight into the design of new nanoscale molecular electronic devices.