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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0479

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

3677164-3718458

Substrate

pectin

Loci

Fjoh_3109-Fjoh_3128

Species

Flavobacterium johnsoniae/986

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- FJOH_RS16145 WP_012025096.1 0 - 1935 (-) NC_009441.1:3677164-3679099 -
- FJOH_RS16150 WP_012025097.1 1934 - 3296 (-) NC_009441.1:3679098-3680460 -
- FJOH_RS16155 WP_012025098.1 3416 - 5837 (-) NC_009441.1:3680580-3683001 -
- FJOH_RS16160 WP_012025099.1 5868 - 8337 (-) NC_009441.1:3683032-3685501 -
- FJOH_RS16165 WP_012025100.1 8400 - 10386 (-) NC_009441.1:3685564-3687550 -
- FJOH_RS16170 WP_012025101.1 10410 - 11850 (-) NC_009441.1:3687574-3689014 -
- FJOH_RS16175 WP_012025102.1 12061 - 13591 (-) NC_009441.1:3689225-3690755 -
- FJOH_RS16180 WP_044047788.1 13767 - 15405 (-) NC_009441.1:3690931-3692569 -
- FJOH_RS16185 WP_012025104.1 15631 - 16774 (-) NC_009441.1:3692795-3693938 -
- FJOH_RS16190 WP_012025105.1 16877 - 20009 (-) NC_009441.1:3694041-3697173 -
- FJOH_RS16195 WP_012025106.1 20193 - 21081 (-) NC_009441.1:3697357-3698245 1.13.99.1
- FJOH_RS16200 WP_012025107.1 21402 - 25437 (-) NC_009441.1:3698566-3702601 -
- FJOH_RS16205 WP_012025108.1 25489 - 27319 (-) NC_009441.1:3702653-3704483 -
- FJOH_RS16210 WP_012025109.1 27543 - 28395 (-) NC_009441.1:3704707-3705559 -
- FJOH_RS16215 WP_044047789.1 28678 - 29242 (-) NC_009441.1:3705842-3706406 -
- FJOH_RS16220 WP_012025111.1 29256 - 31530 (-) NC_009441.1:3706420-3708694 -
- FJOH_RS16225 WP_012025112.1 31542 - 33849 (-) NC_009441.1:3708706-3711013 -
- FJOH_RS16230 WP_012025113.1 34187 - 35801 (-) NC_009441.1:3711351-3712965 -
- FJOH_RS16235 WP_012025114.1 35820 - 38832 (-) NC_009441.1:3712984-3715996 -
- FJOH_RS16240 WP_012025115.1 39123 - 41295 (-) NC_009441.1:3716287-3718459 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1935 (-) CAZyme: GH43|GH43_34|GH43_19 Yes
- 1935 - 3296 (-) CAZyme: GH27 Yes
- 3417 - 5837 (-) CAZyme: GH2 Yes
- 5869 - 8337 (-) CAZyme: GH95 Yes
- 8401 - 10386 (-) CAZyme: GH51 Yes
- 10411 - 11850 (-) CAZyme: GH28 Yes
- 12062 - 13591 (-) CAZyme: GH28 Yes
- 13768 - 15405 (-) TC: gnl|TC-DB|P96169|2.A.21.3.2 Yes
- 15632 - 16774 (-) other Yes
- 16878 - 20009 (-) CAZyme: GH2 Yes
- 20194 - 21081 (-) other Yes
- 21403 - 25437 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 25490 - 27319 (-) other Yes
- 27544 - 28395 (-) other Yes
- 28679 - 29242 (-) other Yes
- 29257 - 31530 (-) CAZyme: GH92 Yes
- 31543 - 33849 (-) CAZyme: GH92 Yes
- 34188 - 35801 (-) other Yes
- 35821 - 38832 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 39124 - 41295 (-) CAZyme: GH89 Yes

PUL ID

PUL0479

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.