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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0270

PubMed

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

NC_007614.1

Nucelotide position range

2877278-2897903

Substrate

exopolysaccharide,lipopolysaccharide

Loci

Nmul_A2530-Nmul_A2515

Species

Nitrosospira multiformis/1231

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- NMUL_RS13110 WP_011381803.1 0 - 1842 (-) NC_007614.1:2877278-2879120 -
- NMUL_RS13115 WP_104009647.1 1889 - 2585 (-) NC_007614.1:2879167-2879863 -
- NMUL_RS13120 WP_011381805.1 2773 - 3715 (-) NC_007614.1:2880051-2880993 -
- NMUL_RS13125 WP_011381806.1 3711 - 4674 (-) NC_007614.1:2880989-2881952 -
- NMUL_RS13130 WP_011381807.1 4814 - 6758 (-) NC_007614.1:2882092-2884036 -
- NMUL_RS13135 WP_011381808.1 6778 - 7984 (-) NC_007614.1:2884056-2885262 -
xrtA NMUL_RS13140 WP_011381809.1 7967 - 9557 (-) NC_007614.1:2885245-2886835 3.4.22.-
- NMUL_RS13145 WP_011381810.1 9611 - 10817 (-) NC_007614.1:2886889-2888095 -
- NMUL_RS13150 WP_011381811.1 10821 - 11907 (-) NC_007614.1:2888099-2889185 -
- NMUL_RS13155 WP_104009646.1 11903 - 12722 (-) NC_007614.1:2889181-2890000 -
- NMUL_RS13160 WP_011381813.1 12874 - 13879 (-) NC_007614.1:2890152-2891157 -
- NMUL_RS13165 WP_011381814.1 13892 - 15479 (-) NC_007614.1:2891170-2892757 -
- NMUL_RS13170 WP_011633977.1 15465 - 16359 (-) NC_007614.1:2892743-2893637 -
- NMUL_RS13175 WP_011381816.1 16663 - 18196 (-) NC_007614.1:2893941-2895474 -
- NMUL_RS13180 WP_011381817.1 18534 - 19161 (-) NC_007614.1:2895812-2896439 -
queG NMUL_RS13185 WP_049783181.1 19510 - 20626 (-) NC_007614.1:2896788-2897904 1.17.99.6

Cluster number

1

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

PUL ID

PUL0270

PubMed

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

Title

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

Author

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

Abstract

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.