Table 2.
Overview of gene inventory involved in nitrogen assimilation, denitrification and ammonification of B. azotoformans LMG 9581T.
| Function | Gene | Gene coordinates | Size (bp) | pBLAST best hit | ORF identifier | ||
|---|---|---|---|---|---|---|---|
| Genbank identifier | % ID | Rel. gene length | |||||
| Cytoplasmic dissimilatory nitrate reduction | narG1 | contig48_8658_4975 | 3684 | ABO66033 Geobacillus thermodenitrificans NG80-2 | 73 | 100,1 | BAZO_08891 |
| narH1 | contig48_4985_3435 | 1551 | ABO66034.1 Geobacillus thermodenitrificans NG80-2 | 73 | 101,4 | BAZO_08886 | |
| narJ1 | contig48_3463_2900 | 564 | ABO66035 Geobacillus thermodenitrificans NG80-2 | 46 | 101,1 | BAZO_08881 | |
| narI1 | contig48_2856_2140 | 717 | YP_001124781.1 Geobacillus thermodenitrificans NG80-2 | 65 | 103,9 | BAZO_08876 | |
| narG2 | contig69_15227_11544 | 3684 | EEL50916 Bacillus cereus Rock3-44 | 80 | 98,0 | BAZO_10677 | |
| narH2 | contig69_11554_10088 | 1467 | EID44195 Geobacillus thermoglucosidans TNO-09.020 | 84 | 99,8 | BAZO_10672 | |
| narJ2 | contig69_10009_9455 | 555 | YP_005422967 Bacillus amyloliquefaciens subsp. plantarum YAU B9601-Y2 | 46 | 100,0 | BAZO_10667 | |
| narI2 | contig69_9458_8769 | 690 | YP_002949597.1 Geobacillus sp. WCH70 | 69 | 98,3 | BAZO_10662 | |
| Periplasmic dissimilatory nitrate reduction | napG1 | contig124_32161_32757 | 597 | ZP_07949106.1 Eggerthella sp. 1_3_56FAA | 57 | 97,5 | BAZO_15064 |
| napA | contig124_32833_35370 | 2538 | YP_004710008.1 Eggerthella sp. YY7918 | 61 | 99,3 | BAZO_15069 | |
| napB | contig124_35383_35802 | 420 | YP_003303796.1 Sulfurospirillum deleyianum DSM 6946 | 28 | 80,9 | BAZO_15074 | |
| napD | contig124_35847_36104 | 258 | ZP_07949109.1 Eggerthella sp. 1_3_56FAA | 38 | 101,2 | BAZO_15079 | |
| napH | contig121_9516_10421 | 906 | ZP_07949110.1 Eggerthella sp. 1_3_56FAA | 40 | 101,3 | BAZO_14359 | |
| napG2 | contig124_36110_36679 | 570 | ZP_09635522 Desulfitobacterium dehalogenans ATCC 51507 | 36 | 101,6 | BAZO_15084 | |
| Assimilatory nitrate reduction | nasC | Not present | |||||
| Assimilatory nitrite reduction | nirB | Not present | |||||
| nirD | Not present | ||||||
| Nitrate transport | narK | contig69_15531_17030 | 1500 | ZP_08006147.1 Bacillus sp. 2_A_57_CT2 | 66 | 99,6 | BAZO_10682 |
| Nitrite transport | nirC1 | contig05_16758_15988 | 768 | ZP_09351718.1 Bacillus smithii 7_3_47FAA | 62 | BAZO_00505 | |
| nirC2 | contig107_<1_505 | 505 | YP_005876144.1 Lactococcus lactis subsp. cremoris A76 | 97 | BAZO_11644 | ||
| Ammonium transport | Not present | ||||||
| Dissimilatory nitrite reduction to ammonium | nrfH | contig37_9421_9936 | 516 | YP_002435907.1 Desulfovibrio vulgaris str. 'Miyazaki F' | 46 | 108,2 | BAZO_03250 |
| nrfA | contig37_9926_11395 | 1469 | ZP_09602448.1 Bacillus sp. 1NLA3E | 65 | 103,1 | BAZO_03255 | |
| Dissimilatory nitrite reduction to NO | nirK | contig38_30517_31578 | 1062 | ZP_08007035.1 Bacillus sp. 2_A_57_CT2 | 74 | 100,3 | BAZO_03565 |
| Dissimilatory quinol-dependent nitric oxide reduction | qnorB1 | contig04_38763_36502 | 2262 | ZP_09601292.1 Bacillus sp. 1NLA3E | 82 | 99,3 | BAZO_00190 |
| qnorB2 | contig48_12741_10378 | 2364 | ZP_09599319.1 Bacillus sp. 1NLA3E | 77 | 100,5 | BAZO_08916 | |
| norD/yojO | contig15_10303_8381 | 1923 | AEN89960.1 Bacillus megaterium WSH-002 | 58 | 100,5 | BAZO_01537 | |
| norQ/yojN | contig15_11194_10313 | 882 | YP_003597326.1 Bacillus megaterium DSM 319 | 73 | 96,7 | BAZO_01542 | |
| dnrN/norA | contig39_94731_95435 | 705 | ZP_08532570.1 Caldalkalibacillus thermarum TA2.A1 | 56 | 98,7 | BAZO_04395 | |
| Dissimilatory menaquinol/cyt c-dependent nitric oxide reduction (Type I) (qCuANOR, sNOR) | cbaC1 | contig42_104893_105033 | 138 | ZP_08784194.1 Ornithinibacillus scapharcae TW25 | 38 | 102,2 | – |
| cbaB1 | contig42_105051_105512 | 462 | YP_004095308.1 Bacillus cellulosilyticus DSM 2522 | 70 | 99,4 | BAZO_06394 | |
| cbaA1 | contig42_105527_107233 | 1707 | ZP_08532586.1 Caldalkalibacillus thermarum TA2.A1 | 71 | 100,9 | BAZO_06399 | |
| senC1 | contig42_107320_107955 | 636 | YP_004095310.1 Bacillus cellulosilyticus DSM | 62 | 100,5 | BAZO_06404 | |
| cbaD1 | contig42_107955_108527 | 570 | ZP_08008054.1 Bacillus sp. 2_A_57_CT2 | 69 | 102.1 | BAZO_06409 | |
| Putative dissimilatory menaquinol/cyt c-dependent nitric oxide reduction (Type II) | cbaC2 | contig40_60717_60133 | 582 | ZP_03146936.1 Geobacillus sp. G11MC16 | 44 | 101.0 | BAZO_04695 |
| senC2 | contig40_61349_60744 | 606 | ABO66889.1 Geobacillus thermodenitrificans NG80-2 | 44 | 95,7 | BAZO_04700 | |
| cbaA2 | contig40_62823_61342 | 1482 | ABO66888.1 Geobacillus thermodenitrificans NG80-2 | 65 | 102,5 | BAZO_04705 | |
| cbaB2 | contig40_63368_62850 | 519 | ZP_03146939.1 Geobacillus sp. G11MC16 | 58 | 96,6 | BAZO_04710 | |
| Dissimilatory nitrous oxide reduction | nosF0 | contig04_11581_12357 | 777 | ZP_07028021.1 Afipia sp. 1NLS2 | 52 | 101,2 | BAZO_00080 |
| nosC1 | contig04_19964_20425 | 459 | ZP_08982140.1 Desulfosporosinus meridiei DSM 13257 | 36 | 104,1 | BAZO_00115 | |
| nosZ1 | contig04_20450_22300 | 1851 | YP_00454079.1 Desulfotomaculum ruminis DSM 2154 | 66 | 97,3 | BAZO_00120 | |
| nosD1 | contig04_22977_24377 | 1401 | AEG59795.1 Desulfotomaculum ruminis DSM 2154 | 36 | 95,3 | BAZO_00130 | |
| nosL1 | contig04_24398_24883 | 485 | ZP_09074493.1 Paenibacillus elgii B69 | 36 | 83,8 | BAZO_00135 | |
| nosY1 | contig04_24858_25700 | 843 | YP_002456717.1 Desulfitobacterium hafniense DCB-2 | 45 | 101,1 | BAZO_00140 | |
| nosF1 | contig04_25697_26614 | 918 | ZP_09636992.1 Desulfitobacterium dehalogenans | 43 | 100,0 | BAZO_00145 | |
| nosC2 | contig41_6372_6797 | 423 | YP_001125844.1 Geobacillus thermodenitrificans NG80-2 | 48 | 93,4 | BAZO_05335 | |
| nosZ2 | contig41_6822_8702 | 1881 | YP_001125843.1 Geobacillus thermodenitrificans NG80-2 | 76 | 100,8 | BAZO_05340 | |
| nosD2 | contig41_9319_10644 | 1326 | YP_001125841.1 Geobacillus thermodenitrificans NG80-2 | 48 | 102,1 | BAZO_05350 | |
| nosC3 | contig147_57854_58288 | 432 | YP_001125844.1 Geobacillus thermodenitrificans NG80-2 | 51 | 95,4 | BAZO_18221 | |
| nosZ3 | contig147_58304_60181 | 1878 | YP_001125843.1 Geobacillus thermodenitrificans NG80-2 | 78 | 100,6 | BAZO_18226 | |
| nosD3 | contig147_60810_62126 | 1317 | YP_001125841.1 Geobacillus thermodenitrificans NG80-2 | 55 | 101,4 | BAZO_18236 | |
| nosY3 | contig147_62126_62923 | 798 | YP_001125840.1 Geobacillus thermodenitrificans NG80-2 | 48 | 100,4 | BAZO_18241 | |
| nosF3 | contig147_62920_63591 | 672 | YP_001125839.1 Geobacillus thermodenitrificans NG80-2 | 65 | 101,8 | BAZO_18246 | |
| nosD4 | contig147_26847_28190 | 1344 | YP_002315691.1 Anoxybacillus flavithermus DSM 21510 / WK1 | 37 | 100,7 | BAZO_18066 | |
| nosL4 | contig147_28190_28672 | 482 | YP_002315692.1 Anoxybacillus flavithermus DSM 21510 / WK1 | 45 | 108,6 | BAZO_18071 | |
| nosY4 | contig147_28713_29543 | 831 | YP_002315693.1 Anoxybacillus flavithermus DSM 21510 / WK1 | 43 | 103,0 | BAZO_18076 | |
| nosF4 | contig147_29548_30279 | 732 | YP_002315694.1 Anoxybacillus flavithermus DSM 21510 / WK1 | 53 | 104,7 | BAZO_18081 | |
| nosD5 | contig120_85053_86486 | 1434 | YP_003570259.1 Salinibacter ruber M8 | 28 | 102,8 | BAZO_14249 | |
| nosL5 | contig120_86476_86982 | 506 | ZP_08007037.1 Bacillus sp. 2_A_57_CT2 | 41 | 107,4 | BAZO_14254 | |
| nosY5 | contig120_87020_87985 | 966 | ZP_08007038.1 Bacillus sp. 2_A_57_CT2 | 52 | 115,4 | BAZO_14259 | |
| SenC/SCO1-type membrane-bound protein | senC3 | contig09_37800_37213 | 522 | YP_002316585.1 Anoxybacillus flavithermus WK1 | 55 | 88,8 | BAZO_01207 |
| senC4 | contig147_56968_57558 | 591 | ZP_01173458.1 Bacillus sp. NRRL B-14911 | 53 | 101,5 | BAZO_18216 | |
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.