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Figure 1 | Cell & Bioscience

Figure 1

From: Transport genes and chemotaxis in Laribacter hongkongensis: a genome-wide analysis

Figure 1

Homology model of DctP_00983 (panel A) and DctP_01394 (panel B), putative DctP TRAP transporters for C 4 -dicarboxylate in L. hongkongensis. For DctP_00983, the C-score of the model was 1.49, which approximately corresponded to an expected TM-score of 0.92 ± 0.06 and an expected root-mean-square deviation (RMSD) of 3.2 ± 2.3 Å from the native structure. The Ramachandran plot showed that 99.6% of aa are in the favored and allowed regions. Calculated G-factors for dihedral angles and main-chain covalent forces are 0.11 and -0.17 respectively, with an overall average of 0.01. The Z-score of the model is -7.84, which is comparable to other experimentally determined protein chains of a similar size in the PDB. Local model quality analysis by plot of residue scores in ProSA-web did not reveal any problematic regions in the structure. The quality analysis results suggested that the homology model is mostly reliable with good structural qualities. For DctP_01394, the C-score of the model was 1.36, which approximately corresponded to an expected TM-score of 0.90 ± 0.06 and an expected RMSD of 3.5 ± 2.4 Å from the native structure. The Ramachandran plot showed that 99.0% of aa are in the favored and allowed regions. Calculated G-factors for dihedral angles and main-chain covalent forces are 0.09 and -0.17 respectively, with an overall average of 0.00. The Z-score of the model is -8.15, which is comparable to other experimentally determined protein chains of a similar size in the PDB. Local model quality analysis by plot of residue scores in ProSA-web did not reveal any problematic regions in the structure. The quality analysis results suggested that the homology model of DctP_01394 is also reliable with good structural qualities.

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