TABLE 1.
F. columnare genes encoding proteins predicted to function in siderophore biosynthesis, export, and uptakea
| Locus tag | Protein name | NCBI product name | Conserved domainsb | Predicted functionc | Protein localizationd |
|---|---|---|---|---|---|
| C6N29_04150 | MFS transporter | Macrolide efflux protein A and similar major facilitator superfamily transporters (cd06173, pfam07690) | Siderophore export | Cytoplasmic membrane | |
| C6N29_04155 | IucX | Hypothetical protein | RhbC (rhizobactin IucA/IucC-like siderophore biosynthesis protein) super family (cl34746, COG4264, pfam04183, pfam06276) | Siderophore biosynthesis | Cytoplasm |
| C6N29_04160 | Hypothetical protein | PRK14016 super family, cyanophycin synthetase, provisional (cl36324), RimK-like ATP grasp domain (pfam08443) | Siderophore biosynthesis | Cytoplasm | |
| C6N29_04165 | TonB-dependent siderophore receptor | OM channel superfamily, possible TonB-dependent siderophore receptor (cl21487 cl21470, TIGR01783, pfam00593, pfam07715) | Siderophore uptake | Outer membrane | |
| C6N29_09920 | MATE family efflux transporter | MATE_like_14 (cd13139, TIGR00797, pfam01554) | Siderophore export | Cytoplasmic membrane | |
| C6N29_09925 | IucA | IucA/IucC family siderophore biosynthesis protein | IucA/IucC family siderophore biosynthesis protein (COG4264, pfam04183, pfam06276) | Siderophore biosynthesis | Cytoplasm |
| C6N29_09930 | IucB | N-Acetyltransferase | Acetyltransferase (GNAT) domain (pfam13523) | Siderophore biosynthesis | Cytoplasm |
| C6N29_09935 | IucC | GNAT family N-acetyltransferase | Acetyltransferase (GNAT) domain (pfam13523), IucA/IucC family siderophore biosynthesis protein (COG 4264, pfam04183, pfam06276) | Siderophore biosynthesis | Cytoplasm |
| C6N29_09940e | DUF1624 domain-containing protein | Acyl_transf_3 super family (cl21495, pfam07786) | Cytoplasmic membrane | ||
| C6N29_09945 | IucD | Alcaligin biosynthesis protein | Lysine/ornithine N-monooxygenase (COG3486, pfam13434) | Siderophore biosynthesis | Cytoplasm |
| C6N29_09950e | Aspartate aminotransferase family protein | Glutamate or tyrosine decarboxylase or related PLP-dependent protein (COG0076, pfam00282) | Cytoplasm | ||
| C6N29_09955 | SidR | LuxR family transcriptional regulator | HTH_LUXR (smart00421, COG2197, pfam00196) | Regulation of siderophore synthesis | Cytoplasm |
| C6N29_09960e | Hypothetical protein | Cytoplasm | |||
| C6N29_09965e | Peptidase M4 | PepSY_TM (pfam03929) | Cytoplasmic membrane | ||
| C6N29_09970 | IutA | TonB-dependent siderophore receptor | TonB-dependent siderophore receptor (cl21487, TIGR01783, pfam00593, pfam07715) | Siderophore uptake | Outer membrane |
MATE, multidrug and toxic compound extrusion; MFS, major facilitator superfamily; OM, outer membrane; GNAT, Gcn5-related N-acetyltransferase.
Conserved domains as assigned by NCBI and by the Joint Genome Institute Integrated Microbial Genomes and Microbiomes (IMG/M version 6.0, https://img.jgi.doe.gov/m) (53). TIGRFAM, pfam, smart, cl, cd, or COG numbers are indicated.
Function predicted based on conserved domains and gene organization.
Location of each protein was predicted using psortb 3.0 (65).
C6N29_09940, C6N29_09950, C6N29_09960, and C6N29_09965 did not have predicted functions but were included in this table because they were part of the sidL locus and were conserved in the seven genomes analyzed in Table S1.