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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0482

PubMed

19717629, Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.

Characterization method

growth assay

Genomic accession number

NC_009441.1

Nucelotide position range

4877994-4935368

Substrate

pectin

Loci

Fjoh_4080-Fjoh_4106

Species

Flavobacterium johnsoniae/986

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- FJOH_RS21090 WP_012026054.1 0 - 2751 (-) NC_009441.1:4877994-4880745 -
- FJOH_RS21095 WP_044047975.1 2937 - 4026 (-) NC_009441.1:4880931-4882020 -
- FJOH_RS21100 WP_012026056.1 4099 - 5668 (-) NC_009441.1:4882093-4883662 -
- FJOH_RS21105 WP_012026057.1 5854 - 8305 (-) NC_009441.1:4883848-4886299 -
- FJOH_RS21110 WP_012026058.1 8580 - 9999 (-) NC_009441.1:4886574-4887993 -
- FJOH_RS21120 WP_012026059.1 10149 - 12930 (-) NC_009441.1:4888143-4890924 -
- FJOH_RS21125 WP_012026060.1 13079 - 14942 (-) NC_009441.1:4891073-4892936 -
- FJOH_RS21130 WP_012026061.1 15237 - 16155 (-) NC_009441.1:4893231-4894149 -
- FJOH_RS21135 WP_012026062.1 16253 - 17822 (-) NC_009441.1:4894247-4895816 -
- FJOH_RS21140 WP_012026063.1 18052 - 19459 (-) NC_009441.1:4896046-4897453 -
- FJOH_RS21145 WP_052295204.1 19615 - 22711 (-) NC_009441.1:4897609-4900705 -
- FJOH_RS21150 WP_012026065.1 22953 - 24660 (-) NC_009441.1:4900947-4902654 -
- FJOH_RS21155 WP_012026066.1 24868 - 25537 (-) NC_009441.1:4902862-4903531 -
- FJOH_RS21160 WP_012026067.1 25720 - 27433 (-) NC_009441.1:4903714-4905427 -
- FJOH_RS21165 WP_012026068.1 27537 - 29538 (-) NC_009441.1:4905531-4907532 -
- FJOH_RS21170 WP_012026069.1 29556 - 32928 (-) NC_009441.1:4907550-4910922 -
- FJOH_RS21175 WP_012026070.1 33595 - 34582 (-) NC_009441.1:4911589-4912576 3.1.1.11
- FJOH_RS21180 WP_012026071.1 34797 - 36816 (-) NC_009441.1:4912791-4914810 -
- FJOH_RS21185 WP_012026072.1 36994 - 39454 (-) NC_009441.1:4914988-4917448 -
- FJOH_RS21190 WP_044048487.1 39469 - 41797 (-) NC_009441.1:4917463-4919791 -
- FJOH_RS21195 WP_012026074.1 41958 - 43383 (-) NC_009441.1:4919952-4921377 3.1.1.53
- FJOH_RS21200 WP_012026075.1 43648 - 47038 (-) NC_009441.1:4921642-4925032 -
- FJOH_RS21205 WP_123875727.1 47289 - 50541 (-) NC_009441.1:4925283-4928535 -
- FJOH_RS21210 WP_012026077.1 50846 - 51971 (-) NC_009441.1:4928840-4929965 -
- FJOH_RS21215 WP_012026078.1 52091 - 53768 (-) NC_009441.1:4930085-4931762 -
- FJOH_RS21220 WP_012026079.1 53941 - 56128 (-) NC_009441.1:4931935-4934122 -
- FJOH_RS21225 WP_012026080.1 56556 - 57375 (-) NC_009441.1:4934550-4935369 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2751 (-) CAZyme: GH78|CBM67 Yes
- 2938 - 4026 (-) other Yes
- 4100 - 5668 (-) CAZyme: GH142 Yes
- 5855 - 8305 (-) CAZyme: GH95 Yes
- 8581 - 9999 (-) other Yes
- 10150 - 12930 (-) CAZyme: GH78|CBM67 Yes
- 13080 - 14942 (-) CAZyme: GH143 Yes
- 15238 - 16155 (-) CAZyme: GH43_18|GH43 Yes
- 16254 - 17822 (-) CAZyme: GH28 Yes
- 18053 - 19459 (-) CAZyme: GH140 Yes
- 19616 - 22711 (-) other Yes
- 22954 - 24660 (-) CAZyme: PL1|CE8|PL1_2 Yes
- 24869 - 25537 (-) other Yes
- 25721 - 27433 (-) CAZyme: PL1|CE8|PL1_2 Yes
- 27538 - 29538 (-) other Yes
- 29557 - 32928 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 33596 - 34582 (-) CAZyme: CE8 Yes
- 34798 - 36816 (-) CAZyme: GH127 Yes
- 36995 - 39454 (-) CAZyme: PL1|PL1_2 Yes
- 39470 - 41797 (-) CAZyme: GH139 Yes
- 41959 - 43383 (-) other Yes
- 43649 - 47038 (-) CAZyme: GH106 Yes
- 47290 - 50541 (-) CAZyme: GH2 Yes
- 50847 - 51971 (-) CAZyme: GH137 Yes
- 52092 - 53768 (-) other Yes
- 53942 - 56128 (-) CAZyme: GH78 Yes
- 56557 - 57375 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0482

PubMed

19717629, Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.

Title

Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis.

Author

McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ, Stein JL

Abstract

The 6.10-Mb genome sequence of the aerobic chitin-digesting gliding bacterium Flavobacterium johnsoniae (phylum Bacteroidetes) is presented. F. johnsoniae is a model organism for studies of bacteroidete gliding motility, gene regulation, and biochemistry. The mechanism of F. johnsoniae gliding is novel, and genome analysis confirms that it does not involve well-studied motility organelles, such as flagella or type IV pili. The motility machinery is composed of Gld proteins in the cell envelope that are thought to comprise the "motor" and SprB, which is thought to function as a cell surface adhesin that is propelled by the motor. Analysis of the genome identified genes related to sprB that may encode alternative adhesins used for movement over different surfaces. Comparative genome analysis revealed that some of the gld and spr genes are found in nongliding bacteroidetes and may encode components of a novel protein secretion system. F. johnsoniae digests proteins, and 125 predicted peptidases were identified. F. johnsoniae also digests numerous polysaccharides, and 138 glycoside hydrolases, 9 polysaccharide lyases, and 17 carbohydrate esterases were predicted. The unexpected ability of F. johnsoniae to digest hemicelluloses, such as xylans, mannans, and xyloglucans, was predicted based on the genome analysis and confirmed experimentally. Numerous predicted cell surface proteins related to Bacteroides thetaiotaomicron SusC and SusD, which are likely involved in binding of oligosaccharides and transport across the outer membrane, were also identified. Genes required for synthesis of the novel outer membrane flexirubin pigments were identified by a combination of genome analysis and genetic experiments. Genes predicted to encode components of a multienzyme nonribosomal peptide synthetase were identified, as were novel aspects of gene regulation. The availability of techniques for genetic manipulation allows rapid exploration of the features identified for the polysaccharide-digesting gliding bacteroidete F. johnsoniae.