Table 3.
Overview of gene inventory involved in nitrogen assimilation, denitrification and ammonification of B. bataviensis LMG 21833T.
| Function | Gene | Gene coordinates | Size (bp) | pBLAST best hit | ORF identifier | ||
|---|---|---|---|---|---|---|---|
| Genbank identifier | % ID | Rel. gene length | |||||
| Cytoplasmic dissimilatory nitrate reduction | narG | contig126_61985_58326a | 3660 | YP_001124778.1 Geobacillus thermodenitrificans NG80-2 | 73 | 99,4 | BABA_18597 |
| narH | contig126_58336_56810 | 1527 | YP_001124779.1 Geobacillus thermodenitrificans NG80-2 | 82 | 99,8 | BABA_18592 | |
| narJ | contig126_56817_56287 | 531 | YP_001124780.1 Geobacillus thermodenitrificans NG80-2 | 44 | 95,2 | BABA_18587 | |
| narI | contig126_56275_55547 | 729 | YP_001124781.1 Geobacillus thermodenitrificans NG80-2 | 66 | 105,7 | BABA_18582 | |
| Periplasmic dissimilatory nitrate reduction | napA | not present | |||||
| napB | not present | ||||||
| napD | not present | ||||||
| napH | contig114_85875_86333 | 459 | AEN91893.1 Bacillus megaterium WSH-002 | 41 | 90,0 | BABA_14547 | |
| napG | not present | ||||||
| Assimilatory nitrate reduction | nasC | contig121_7018_4829 | 2190 | YP_005311789.1 Paenibacillus mucilaginosus 3016 | 80 | 99,5 | BABA_16882 |
| Assimilatory nitrite reduction | nirB | contig05_23966_21540 | 2427 | ZP_09602179.1 Bacillus sp. 1NLA3E | 75 | 100,1 | BABA_00915 |
| nirD | contig05_21543_21223 | 321 | ZP_09602178.1 Bacillus sp. 1NLA3E | 60 | 99,1 | BABA_00910 | |
| Nitrate transport | narK1 | contig115_127063_125732 | 1332 | YP_003562112.1 Bacillus megaterium QM B1551 | 84 | 98,4 | BABA_15587 |
| narK2 | contig126_45914_44613 | 1302 | YP_004643043.1 Paenibacillus mucilaginosus KNP414 | 78 | 99,5 | BABA_18532 | |
| narK3 | contig126_47642_46140 | 1503 | YP_002774204.1 Brevibacillus brevis NBRC 100599 | 65 | 100,4 | BABA_18537 | |
| narK4 | contig135_17368_16046 | 1323 | ZP_08680547.1 Sporosarcina newyorkensis 2681 | 68 | 99,8 | BABA_20711 | |
| Nitrite transport | nirC | contig74_20117_19245 | 816 | ZP_09600582.1 Bacillus sp. 1NLA3E | 73 | 98,6 | BABA_12510 |
| Ammonium transport | amt | contig121_78501_79763 | 561 | ZP_10130407.1 Bacillus methanolicus PB1 | 87 | 97,4 | BABA_17227 |
| Dissimilatory nitrite reduction to ammonium | nrfA | contig123_39386_40837 | 1452 | ZP_09602448.1 Bacillus sp. 1NLA3E | 74 | 102,1 | BABA_17657 |
| nrfH | contig123_38870_39382 | 513 | ZP_09602447.1 Bacillus sp. 1NLA3E | 55 | 98,8 | BABA_17652 | |
| Dissimilatory nitrite reduction to NO | nirK | contig42_38340_38029; contig42_38025_37288 | 1053 | ZP_08007035.1 Bacillus sp. 2_A_57_CT2 | 71 | 99,4 | BABA_p06582 |
| Dissimilatory quinol-dependent nitric oxide reduction | qnorB1 | contig121_76393_77409 | 1017 | ZP_09601292.1 Bacillus sp. 1NLA3E | 79 | 44,7 | BABA_17212 |
| qnorB2 | contig55_76161_75334; contig55_77043_76291 | 1707 | ZP_09599319.1 Bacillus sp. 1NLA3E | 77 | 72,5 | BABA_p08977 | |
| norD | not present | ||||||
| norQ | not present | ||||||
| dnrN/norA | contig134_9390_8692 | 699 | ZP_09599666.1 Bacillus sp. 1NLA3E | 65 | 100,9 | BABA_20471 | |
| Dissimilatory menaquinol/cyt c-dependent nitric oxide reduction (Type I) (qCuANOR, sNOR) | cbaD1 | contig02_44305_43748 | 570 | ZP_08532584.1 Caldalkalibacillus thermarum TA2.A1 | 62 | 95,9 | BABA_00215 |
| senC1 | contig02_44940_44308 | 633 | YP_004095310.1 Bacillus cellulosilyticus DSM 2522 | 65 | 100,0 | BABA_00220 | |
| cbaA1 | contig02_46749_45067 | 1683 | ZP_08008056.1 Bacillus sp. 2_A_57_CT2 | 82 | 99,5 | BABA_00225 | |
| cbaB1 | contig02_47231_46764 | 468 | ZP_08008055.1 Bacillus sp. 2_A_57_CT2 | 66 | 74,3 | BABA_00230 | |
| cbaC1 | contig02_47384_47244 | 138 | YP_004095307.1 Bacillus cellulosilyticus DSM 2522 | 46 | 92,0 | – | |
| ctaB | contig02_48671_47742 | 927 | ZP_9916061.1 Lentibacillus sp. Grbi | 64 | 99,4 | BABA_00235 | |
| Putative dissimilatory menaquinol/cyt c-dependent nitric oxide reduction (Type II) | cbaB2 | contig126_34202_34621 | 420 | ZP_08007586.1 Bacillus sp. 2_A_57_CT2 | 66 | 76,5 | BABA_18497 |
| ccaA2 | contig126_34739_36205 | 1467 | ZP_08007585.1 Bacillus sp. 2_A_57_CT2 | 74 | 100,2 | BABA_18502 | |
| SenC/SCO1-type membrane-bound protein | senC2 | contig36_3182_4066 | 885 | YP_823233.1 bacterium Ellin514 | 28 | 96,1 | BABA_04124 |
| senC3 | contig55_18362_17802 | 561 | EIJ83190.1 Bacillus methanolicus MGA3 | 54 | 97,4 | BABA_08661 | |
| senC4 | contig126_63835_64437 | 603 | ZP_10131691.1 Bacillus methanolicus PB1 | 78 | 58,9 | BABA_18617 | |
Genes are ordered according to their location in the operon when applicable. Gene size is given in absolute numbers as well as relative to that of best pBLAST hit. No ORF identifier is given when ORF was too small to be recognized in initial annotation.
a
The startcodon of BABA_18597 as deposited at DDBJ/EMBL/GenBank, contains a false start codon with an extra 30-bp sequence at the 5′ terminus.