TABLE 4.
Nitrobacter subcore genesa
| Category and putative function | Gene(s) in:
|
||
|---|---|---|---|
| N. hamburgensis | N. winogradskyi | NB311A | |
| Polysaccharide biosynthesis | |||
| Lipopolysaccharide biosynthesis protein | Nham_1054 | Nwi_0538 | NB311A03749 |
| Glycosyl transferase, family 2 | Nham_1055 | Nwi_0539 | NB311A03744 |
| Glycosyl transferase | Nham_3303 | Nwi_0540 | NB311A03739 |
| Capsule polysaccharide biosynthesis protein | Nham_1195 | Nwi_0641 | NB311A16262 |
| Acylneuraminate cytidylyltransferase | Nham_1201 | Nwi_0645 | NB311A16252 |
| Hypothetical protein | Nham_1200 | Nwi_0646 | NB311A16247 |
| NUDIX hydrolase | Nham_1197 | Nwi_0648 | NB311A16237 |
| Haloacid dehalogenase-like hydrolase | Nham_1198 | Nwi_0649 | NB311A16232 |
| NUDIX hydrolase | Nham_1199 | Nwi_0650 | NB311A16227 |
| Nitrite metabolism, transport | |||
| Hypothetical protein | Nham_3451 | Nwi_0772 | NB311A09094 |
| Cytochrome c, class I | Nham_3450 | Nwi_0773 | NB311A09084 |
| nxrA1; nitrite oxidoreductase, alpha subunit | Nham_3449 | Nwi_0774 | NB311A09079 |
| nxrX; nitrite oxidoreductase, subunit X | Nham_3448 | Nwi_0775 | NB311A09069 |
| nxrB1; nitrite oxidoreductase, beta subunit | Nham_3447 | Nwi_0776 | NB311A09069 |
| nxrD; nitrite oxidoreductase, delta subunit | Nham_3446 | Nwi_0777 | NB311A09054 |
| nxrG; nitrite oxidoreductase, gamma subunit | Nham_3445 | Nwi_0778 | NB311A09049 |
| narK; nitrite/nitrate major facilitator superfamily transporter | Nham_3444 | Nwi_0779 | NB311A09044 |
| TDT family transport protein | Nham_3443 | Nwi_0780 | NB311A09039 |
| Cytochrome c, class IC (adjacent to nirK) | Nham_3282 | Nwi_2649 | NB311A15177 |
| Cytochrome c, class I | Nham_3283 | Nwi_2650 | NB311A15182 |
| Cytochrome c biogenesis factor | Nham_3285 | Nwi_2652 | NB311A15192 |
| nsrR; transcriptional regulator, BadM/Rrf2 family | Nham_3286 | Nwi_2653 | NB311A15197 |
| Nitrite reductase [NAD(P)H] large subunit, NirD | Nham_2964 | Nwi_0720 | NB311A01969 |
| nxrB homolog | Nham_3289 | Nwi_0965 | NB311A10815 |
| nxrA homolog(s) | Nham_0951, Nham_2961 | Nwi_2068 | NB311A17691 |
| Regulatory genes | |||
| PII-like regulatory protein | Nham_4043, Nham_4324, Nham_4330 | Nwi_1989, Nwi_2931 | NB311A00865 |
| Transcriptional regulator, LuxR family | Nham_2943 | Nwi_0957 | NB311A10770 |
| Transcription regulatory protein GAL11 domain | Nham_2946 | Nwi_0960 | NB311A10785 |
| Transcription factor jumonji/aspartyl beta-hydroxylase | Nham_1520 | Nwi_1272 | NB311A10046 |
| Miscellaneous | |||
| Sulfite reductase (NADPH) hemoprotein, beta subunit | Nham_0683 | Nwi_0591 | NB311A03464 |
| Major facilitator superfamily MFS_1 | Nham_1829 | Nwi_1437 | NB311A17399 |
| Polyphosphate glucokinase | Nham_2098 | Nwi_1575 | NB311A17319 |
| Phosphoesterase, PA-phosphatase related | Nham_2161 | Nwi_1638 | NB311A18878 |
| Isoprenylcysteine carboxyl methyltransferase | Nham_1746 | Nwi_1821 | NB311A06266 |
| Luciferase-like protein | Nham_0958 | Nwi_2071 | NB311A16699 |
| TonB-dependent receptor | Nham_0957 | Nwi_2072 | NB311A16694 |
| TadE-like protein | Nham_3156 | Nwi_2536 | NB311A14567 |
| Cupin 2, conserved barrel | Nham_3657 | Nwi_0906 | NB311A18960 |
| Na+/H+ antiporter NhaA | Nham_4598 | Nwi_2853 | NB311A16719 |
| Putative serine/threonine protein phosphatase | Nham_3383 | Nwi_3015 | NB311A06978 |
| Nucleoside phosphorylase | Nham_3696 | Nwi_3067 | NB311A02747 |
| Additional hypothetical proteins (75) | |||
| Phage genes (6) | |||
a
All of the genes with a functional annotation had at least one homolog (E value of ≤1e−5) in a genome other than R. palustris or B. japonicum. Of the 75 hypothetical proteins, 41 had no match to any peptide in the KEGG genome database (see Table S2 in the supplemental material).