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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0281

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

286146-315273

Substrate

exopolysaccharide,lipopolysaccharide,capsule polysaccharide

Loci

Nmul_A0264-Nmul_A0292

Species

Nitrosospira multiformis/1231

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rfbB NMUL_RS01400 WP_011379626.1 0 - 1062 (+) NC_007614.1:286146-287208 4.2.1.46
rfbD NMUL_RS01405 WP_011379627.1 1061 - 1964 (+) NC_007614.1:287207-288110 1.1.1.133
rfbA NMUL_RS01410 WP_011379628.1 1960 - 2848 (+) NC_007614.1:288106-288994 2.7.7.24
rfbC NMUL_RS01415 WP_011379629.1 2844 - 3396 (+) NC_007614.1:288990-289542 5.1.3.13
- NMUL_RS01420 WP_041352320.1 3503 - 4607 (+) NC_007614.1:289649-290753 -
- NMUL_RS01430 WP_041352321.1 5108 - 6389 (+) NC_007614.1:291254-292535 -
tviC NMUL_RS01435 WP_011379633.1 6406 - 7459 (+) NC_007614.1:292552-293605 -
- NMUL_RS01440 WP_011379634.1 7503 - 8118 (-) NC_007614.1:293649-294264 -
- NMUL_RS01445 WP_041352733.1 8359 - 9235 (-) NC_007614.1:294505-295381 -
- NMUL_RS01450 WP_104009691.1 9234 - 10080 (-) NC_007614.1:295380-296226 -
- NMUL_RS01455 WP_011379637.1 10082 - 10334 (-) NC_007614.1:296228-296480 -
- NMUL_RS01465 WP_011379638.1 10737 - 12213 (+) NC_007614.1:296883-298359 -
- NMUL_RS01470 WP_011379639.1 12735 - 13857 (+) NC_007614.1:298881-300003 -
- NMUL_RS01475 WP_104009690.1 14088 - 15381 (+) NC_007614.1:300234-301527 -
- NMUL_RS01480 WP_011379641.1 15587 - 16538 (+) NC_007614.1:301733-302684 -
- NMUL_RS01485 WP_011379642.1 16635 - 17352 (+) NC_007614.1:302781-303498 -
- NMUL_RS01490 WP_011379643.1 17403 - 17829 (+) NC_007614.1:303549-303975 -
- NMUL_RS01495 WP_011379644.1 17844 - 19623 (+) NC_007614.1:303990-305769 -
- NMUL_RS01500 WP_104009564.1 19640 - 19868 (+) NC_007614.1:305786-306014 -
- NMUL_RS01505 WP_011379646.1 19864 - 20545 (+) NC_007614.1:306010-306691 -
- NMUL_RS01510 WP_011379647.1 20557 - 21286 (+) NC_007614.1:306703-307432 -
- NMUL_RS01515 WP_041352737.1 21285 - 21648 (+) NC_007614.1:307431-307794 -
- NMUL_RS01520 WP_041352738.1 21725 - 22523 (+) NC_007614.1:307871-308669 -
rffA NMUL_RS01525 WP_011379650.1 22530 - 23655 (+) NC_007614.1:308676-309801 2.6.1.59
- NMUL_RS01530 WP_011379651.1 23785 - 25003 (+) NC_007614.1:309931-311149 -
- NMUL_RS01535 WP_011379652.1 24999 - 26112 (+) NC_007614.1:311145-312258 -
- NMUL_RS01540 WP_011379653.1 26134 - 27496 (+) NC_007614.1:312280-313642 -
- NMUL_RS01545 WP_011379654.1 27628 - 29128 (+) NC_007614.1:313774-315274 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rfbB 1 - 1062 (+) CDS No
rfbD 1062 - 1964 (+) CDS No
rfbA 1961 - 2848 (+) CDS No
rfbC 2845 - 3396 (+) CDS No
- 3504 - 4607 (+) CDS No
- 5109 - 6389 (+) CDS No
tviC 6407 - 7459 (+) CDS No
- 7504 - 8118 (-) STP: STP|TPR_2 No
- 8360 - 9235 (-) CDS No
- 9235 - 10080 (-) CDS No
- 10083 - 10334 (-) CDS No
- 10738 - 12213 (+) CDS No
- 12736 - 13857 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 14089 - 15381 (+) TC: gnl|TC-DB|A3DDT1|9.B.142.9.3 Yes
- 15588 - 16538 (+) TC: gnl|TC-DB|Q55487|4.D.2.1.9 Yes
- 16636 - 17352 (+) other Yes
- 17404 - 17829 (+) other Yes
- 17845 - 19623 (+) other Yes
- 19641 - 19868 (+) other Yes
- 19865 - 20545 (+) other Yes
- 20558 - 21286 (+) other Yes
- 21286 - 21648 (+) other Yes
- 21726 - 22523 (+) other Yes
rffA 22531 - 23655 (+) other Yes
- 23786 - 25003 (+) CAZyme: GT4 Yes
- 25000 - 26112 (+) CAZyme: GT4 Yes
- 26135 - 27496 (+) CDS No
- 27629 - 29128 (+) CDS No

PUL ID

PUL0281

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.