Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0484

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

5124512-5142865

Substrate

pectin

Loci

Fjoh_4246-Fjoh_4257

Species

Flavobacterium johnsoniae/986

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- FJOH_RS21960 WP_012026220.1 0 - 657 (-) NC_009441.1:5124512-5125169 -
- FJOH_RS21965 WP_012026221.1 757 - 2104 (-) NC_009441.1:5125269-5126616 -
pelA FJOH_RS21970 WP_012026222.1 2229 - 4230 (-) NC_009441.1:5126741-5128742 4.2.2.2
- FJOH_RS21975 WP_012026223.1 4239 - 5838 (-) NC_009441.1:5128751-5130350 -
- FJOH_RS21980 WP_044048002.1 6008 - 7229 (-) NC_009441.1:5130520-5131741 -
- FJOH_RS21985 WP_012026225.1 7251 - 8457 (-) NC_009441.1:5131763-5132969 -
- FJOH_RS21990 WP_012026226.1 8469 - 9669 (-) NC_009441.1:5132981-5134181 -
- FJOH_RS21995 WP_012026227.1 9710 - 10667 (-) NC_009441.1:5134222-5135179 -
- FJOH_RS22000 WP_012026228.1 10771 - 12445 (-) NC_009441.1:5135283-5136957 -
- FJOH_RS22005 WP_012026229.1 12457 - 15562 (-) NC_009441.1:5136969-5140074 -
- FJOH_RS22010 WP_012026230.1 15607 - 17035 (-) NC_009441.1:5140119-5141547 -
- FJOH_RS22015 WP_012026231.1 17325 - 18354 (+) NC_009441.1:5141837-5142866 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 657 (-) CAZyme: CE12 Yes
- 758 - 2104 (-) CAZyme: GH28 Yes
pelA 2230 - 4230 (-) CAZyme: PL10|CE8|PL10_1 Yes
- 4240 - 5838 (-) CAZyme: GH43_10|GH43 Yes
- 6009 - 7229 (-) CAZyme: GH105 Yes
- 7252 - 8457 (-) CAZyme: GH105 Yes
- 8470 - 9669 (-) CAZyme: GH105 Yes
- 9711 - 10667 (-) other Yes
- 10772 - 12445 (-) TC: gnl|TC-DB|G0IYY9|8.A.46.1.6 Yes
- 12458 - 15562 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 15608 - 17035 (-) CAZyme: GH28 Yes
- 17326 - 18354 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 No

PUL ID

PUL0484

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.