Fusobacterium nucleatum comprises thirteen subspecies of which the strain ATCC 25586 is represented herein. The vincentii subspecies sequence as well as a plasmid sequence, pFN1, from strain 12230 (Wadsworth Anaerobe Lab) are available for comparative purposes. F. nucleatum, a gram-negative anaerobe, is a major concern for dental research, although its pathogenicity is effected indirectly insofar as it promotes aggregation and establishment of other dental pathogens.

The 2.17 Mb genome of Fusobacterium nucleatum ATCC 25586, was sequenced in 2002 by a team at Integrated Genomics, Chicago. The key publication describing this newly sequenced genome is Kapatral V., et al., 2002, "Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586"; J.Bact. 184:2005-2018 (PMID: 11889109). A second genomic sequence for the the vincentii subspecies is available in GenBank as contigs and the publication associated with that sequence has been helpful in preparing the annotation herein (Kapatral et al., 2003, Genome Res 13:1180-1189; see the proteome comparison section). Approximately 54 additional and recent references pertaining to F. nucleatum have been extracted from a 2000-2003 molecular subset of PubMed. If we have overlooked any pertinent reference, please inform us (F. nucleatum references).

Three Fusobacteruium nucleatum plasmid sequences, pFN1, pPA52 and pKH9 are included in this section. To access the gene records for these, use the Gene Image Map or Basic Search below with query, "Gene ID" "Contains" "plasmid name".   Publications concerning these plasmids are McKay et al., 1995 (PMID: 7753905), Haake et al., 2000 (PMID: 20115567) and Bachrach et al., 2004 (PMID: 15574887).

The core information in this database is the table of annotated records, 2067 predicted open reading frames taken directly from GenBank; Kapatral et al. 2002 report 2067 ORFs in their original manuscript of which 1394 have identifiable functions. Each gene record is identified by a gene id, FN0001-FN2019. Basic summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record.

For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.17 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the Functional Classes, EC Table, and Biochemical Pathways summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. Fuller analyses of the proteome are underway, for example a table of proteins found in F. nucleatum vincentii and not in other Fusobacterium species, and bi-directional best hits between F. nucleatum ATCC 25586 and F. nucleatum vincentii proteins is presented in the proteome comparison section of the database. Finally, we would encourage anyone with questions or suggestions to contact us at lanl.gov.

User Defined Database Searches
Basic Search
Intermediate Search
Sequence Search
Protein Motif Search
Repeat Search

Predefined Database Searches
Genomic Island Table
Secondary Structure Table
Definition Table
Functional Classes Table
EC Table
PDB Table
Metabolic Pathways
Repeat Table
Codon Usage Table

Specialized Analysis
Phylogenetic Fingerprints
ABC Transporters
Base Composition Analysis

RNA Tables and Maps
Transfer RNA Table
Ribosomal RNA Table
Transfer & Ribosomal RNA Map