18390676, Appl Environ Microbiol. 2008 Jun;74(11):3559-72. doi: 10.1128/AEM.02722-07. Epub 2008 Apr 4.

Characterization method

comparative genomics

Genomic accession number


Nucelotide position range







Nitrosospira multiformis/1231

Degradation or Biosynthesis


Cluster number


Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1842 (-) CDS No
- 1890 - 2585 (-) CDS No
- 2774 - 3715 (-) CDS No
- 3712 - 4674 (-) CDS No
- 4815 - 6758 (-) CDS No
- 6779 - 7984 (-) TC: gnl|TC-DB|P73948|2.A.38.4.5 Yes
xrtA 7968 - 9557 (-) other Yes
- 9612 - 10817 (-) CAZyme: GT4 Yes
- 10822 - 11907 (-) other Yes
- 11904 - 12722 (-) CAZyme: CE0|CE4 Yes
- 12875 - 13879 (-) TC: gnl|TC-DB|P45754|9.B.42.1.1 Yes
- 13893 - 15479 (-) TC: gnl|TC-DB|Q3SF27|1.B.66.5.1 Yes
- 16664 - 18196 (-) other Yes
- 18535 - 19161 (-) TC: gnl|TC-DB|K9TEU5|1.B.18.3.5 Yes
queG 19511 - 20626 (-) CDS No




18390676, Appl Environ Microbiol. 2008 Jun;74(11):3559-72. doi: 10.1128/AEM.02722-07. Epub 2008 Apr 4.


Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.


Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PS, Hauser LJ, Land ML, Larimer FW, Shin MW, Starkenburg SR


The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196(T)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.