TABLE 3.
Comparison of products from the van-iva locus to entries in the GenBank, Pfam, or COG databasea
| Product | Sizeb (aa) | MMb (kDa) | GenBank, Pfam, or COG entryc | Description of homologued |
|---|---|---|---|---|
| Ctb1 | 170 | 18.6 | Pfam03061 | Thioesterase superfamily |
| Ctb2 | 166 | 18.3 | Rv3701c (33) NP_218218 | Hypothetical protein from Mycobacterium tuberculosis strain H37Rv (13) |
| Ctb3 | 609 | 107.3 | COG5265 | Group ATM1 of the ATP-binding cassette transporters. Permease and ATPase components. Involved in Fe-S cluster assembly |
| VanR | 254 | 27.9 | VanR (38) AAC27105 | Repressor of vanAB in Acinetobacter sp. strain ADP1 (25) |
| VanA | 358 | 40.1 | VanA (72) AF009672 | Van monooxygenase from Acinetobacter sp. strain ADP1 (35) |
| IvaR | 159 | 17.9 | Pfam01047 | MarR-like transcriptional regulator |
| IvaK | 451 | 47.3 | VanK (46) YP_045696 | Mediates uptake of Pca and Van in Acinetobacter sp. strain ADP1 (17) |
| IvaA | 359 | 40.3 | TsaM (37) AF311437 | 4-Toluene sulfonate/carboxylate methyl monooxygenase from C. testosteroni strain T-2 (20) |
| IvaB | 322 | 35.1 | VanB (55) AF009672 | Oxidoreductase for VanA in Acinetobacter sp. strain ADP1 (35) |
| IvaC | 313 | 32.7 | Pfam00389 (aa 48 and 97) | Catalytic domain of d-isomer-specific dehydrogenases for 2-hydroxy acids |
| Pfam02826 (aa 106 to 280) | NAD-binding domain of d-isomer-specific dehydrogenases for 2-hydroxy acids | |||
| Ctb4 | 345 | 37.2 | COG1638 | DctP, the periplasmic component of the tripartite ATP-independent periplasmic (TRAP)-type C4-dicarboxylate transport system involved in carbohydrate transport and metabolism |
| Ctb5 | 432 | 45.2 | COG1593 | DctQ, large permease component of the TRAP-type C4-dicarboxylate transport system involved in carbohydrate transport and metabolism |
Functionally characterized GenBank homologues are shown for VanA, IvaA, and IvaB because the latter three are the focus of this study, and for VanR and IvaK because the latter show identity to proteins known to be involved in Van metabolism. Otherwise, homologues in the Pfam (Protein Family) database (4) or COG database (Clusters of Orthologous Groups) of proteins (37) are shown, except for Ctb2, which is not described in the latter two databases.
The size (in amino acids [aa]) and molecular mass (MM) (in kilodaltons) of the products are based on a conceptual translation of the genes.
For GenBank homologues, the percent identity is shown in parentheses. During analyses, more than one homologue in the Pfam or COG database was often uncovered. For the sake of brevity, only the entry with the lowest E value (i.e., highest significant match) is listed. E values were ≤4e−8, except for Ctb2 (E = 0.1).
Numbers in parentheses are references.