TABLE 1.

Predicted F. johnsoniae glycohydrolases involved in chitin digestion

Gene	Predicted functiona	Homologsb	Predicted localizationc	Molecular mass (kDa)d	Enzymatic and other domainse
Fjoh_0674	Candidate β-N-acetylglucosaminidase	P. gingivalis NahA (38% identity over 774 amino acids [52])	Periplasmic	87.6	GH20
Fjoh_2039	Candidate β-N-acetylglucosaminidase	P. gingivalis NahA (40% identity over 610 amino acids [52])	Periplasmic	87.3	GH20
Fjoh_2118	Candidate β-glycosidase, related to N-acetylglucosaminidases	Pseudoalteromonas piscicida Cht60 (30% identity over 389 amino acids [91])	Cytoplasmic	59.9	GH3
Fjoh_2608	Distantly related to plant chitinases	Solanum tuberosum (potato) CHTB2 endochitinase 2 (24% identity over 231 amino acids [12])	Unknown	90.8	GH19
Fjoh_4175	Candidate chitinase	Bacillus circulans ChiA1 (26% identity over 317 amino acids [94])	Unknown	57.8	GH18-CBM6-D5
Fjoh_4555	Candidate chitinase	B. circulans ChiA1 (33% identity over 513 amino acids [94]), B. circulans ChiD (37% identity over 353 amino acids [93])	Outer membrane or extracellular	168.9	GH18-GH18
Fjoh_4556	Candidate β-N-acetylglucosaminidase	P. gingivalis NahA (36% identity over 447 amino acids [52])	Periplasmic	77.3	GH20
Fjoh_4560	Candidate chitinase	Bos taurus (bovine) ChiA (25% identity over 244 amino acids [89])	Lipoprotein	38.1	GH18
Fjoh_4757	Candidate chitinase	B. circulans ChiA1 (37% identity over 298 amino acids [94])	Unknown, not cytoplasmic	41.2	GH18
Fjoh_4808	Candidate β-N-acetylglucosaminidase	P. gingivalis NahA (32% identity over 633 amino acids [52])	Periplasmic	94.8	GH20

^aPredicted functions were assigned by routines used for updating the Carbohydrate Active Enzymes database (http://www.cazy.org/) using the following criteria: typically, 70% or greater amino acid identity with a protein domain with a biochemically determined function at the time of analysis resulted in “candidate” status; 30% to 70% amino acid identity with a protein domain with a known function resulted in “related to” status; and less than 30% amino acid identity with a protein domain with a known function resulted in “distantly related to” status. Because the threshold of similarity that correlates with a change of substrate specificity is variable from one glycoside hydrolase family to another, the criteria were tightened or loosened appropriately for several families. All analyses were conducted domain by domain to avoid problems arising from the modular structure of many of the proteins.

^bHomologs were identified by a BlastP search with the Swiss-Prot database. Fjoh_4555 has two catalytic domains, so a homolog for each domain is listed. ChiA1 is similar to the N-terminal GH18 domain, and ChiD is similar to the C-terminal GH18 domain. The numbers in brackets are reference numbers.

^cLocalization was predicted using the default settings of PSORTb (26). Predicted lipoproteins were identified using LipoP (42).

^dPredicted molecular mass of the primary product of translation, including any predicted signal peptide.

^eCBM6, family 6 CBM, as assigned by CAZY; D5, carboxy-terminal domain of R. marinus xylanases predicted to be involved in attachment to the cell surface (43); GH, glycoside hydrolase as assigned by CAZY (the numbers indicate families).