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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0259

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

254443-284481

Substrate

exopolysaccharide

Loci

Nmul_A0238-Nmul_A0262

Species

Nitrosospira multiformis/1231

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

epsA NMUL_RS01260 WP_011379600.1 0 - 804 (+) NC_007614.1:254443-255247 -
- NMUL_RS01265 WP_011379601.1 796 - 2215 (+) NC_007614.1:255239-256658 2.7.8.31
epsL NMUL_RS01270 WP_104009692.1 2429 - 3662 (+) NC_007614.1:256872-258105 -
epsD NMUL_RS01275 WP_011379603.1 3903 - 4896 (+) NC_007614.1:258346-259339 5.2.1.8
epsE NMUL_RS01280 WP_011379604.1 4924 - 5719 (+) NC_007614.1:259367-260162 -
epsF NMUL_RS01285 WP_011379605.1 5733 - 7125 (+) NC_007614.1:260176-261568 -
epsG NMUL_RS01290 WP_011379606.1 7145 - 8075 (+) NC_007614.1:261588-262518 -
- NMUL_RS01295 WP_080557660.1 8251 - 8695 (-) NC_007614.1:262694-263138 -
xrtB NMUL_RS01300 WP_011379608.1 8630 - 9545 (+) NC_007614.1:263073-263988 -
epsI NMUL_RS01305 WP_041352730.1 9547 - 10225 (+) NC_007614.1:263990-264668 -
- NMUL_RS01310 WP_011379610.1 10285 - 11749 (+) NC_007614.1:264728-266192 -
- NMUL_RS01315 WP_011379611.1 11796 - 13275 (+) NC_007614.1:266239-267718 -
- NMUL_RS01320 WP_011379612.1 13271 - 14396 (+) NC_007614.1:267714-268839 -
- NMUL_RS01325 WP_011379613.1 14659 - 16978 (+) NC_007614.1:269102-271421 -
- NMUL_RS01330 WP_011379614.1 17230 - 18052 (+) NC_007614.1:271673-272495 -
- NMUL_RS01335 WP_011379615.1 18591 - 19668 (+) NC_007614.1:273034-274111 -
- NMUL_RS01340 WP_011379616.1 20054 - 20888 (+) NC_007614.1:274497-275331 -
- NMUL_RS01345 WP_011379617.1 21032 - 22055 (+) NC_007614.1:275475-276498 -
- NMUL_RS01350 WP_011379618.1 22077 - 23184 (+) NC_007614.1:276520-277627 -
- NMUL_RS01355 WP_011379619.1 23214 - 24081 (+) NC_007614.1:277657-278524 -
- NMUL_RS01360 WP_004180929.1 24099 - 24942 (+) NC_007614.1:278542-279385 -
- NMUL_RS01365 WP_011379621.1 25229 - 26345 (+) NC_007614.1:279672-280788 5.1.3.14
galE NMUL_RS01370 WP_011379622.1 26648 - 27710 (+) NC_007614.1:281091-282153 5.1.3.2
- NMUL_RS01375 WP_011379623.1 27811 - 29257 (+) NC_007614.1:282254-283700 2.7.7.13, 5.3.1.8
- NMUL_RS15145 WP_074705642.1 29919 - 30039 (+) NC_007614.1:284362-284482 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

epsA 1 - 804 (+) TF: DBD-Pfam|GerE No
- 797 - 2215 (+) TC: gnl|TC-DB|G0CIY2|9.B.18.1.1 Yes
epsL 2430 - 3662 (+) other Yes
epsD 3904 - 4896 (+) other Yes
epsE 4925 - 5719 (+) other Yes
epsF 5734 - 7125 (+) other Yes
epsG 7146 - 8075 (+) STP: STP|CbiA Yes
- 8252 - 8695 (-) other Yes
xrtB 8631 - 9545 (+) other Yes
epsI 9548 - 10225 (+) other Yes
- 10286 - 11749 (+) other Yes
- 11797 - 13275 (+) other Yes
- 13272 - 14396 (+) CAZyme: GT4 Yes
- 14660 - 16978 (+) CAZyme: PL15 Yes
- 17231 - 18052 (+) other Yes
- 18592 - 19668 (+) CAZyme: GT4 Yes
- 20055 - 20888 (+) CDS No
- 21033 - 22055 (+) CDS No
- 22078 - 23184 (+) CDS No
- 23215 - 24081 (+) CDS No
- 25230 - 26345 (+) CDS No
galE 26649 - 27710 (+) CDS No
- 27812 - 29257 (+) STP: STP|AraC_binding No
- 29920 - 30039 (+) CDS No

PUL ID

PUL0259

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.