Table 2.
Predicted Functions of Proteins Encoded by 19 Open Reading Frames (ORFs) of the Putative S-Layer Glycosylation Gene Cluster
| ORFa (nt) | Gene | Putative Function | Closest Species Match | GenBank Accession No. | Amino Acid (%) |
GC Content (%) | |
|---|---|---|---|---|---|---|---|
| Identity | Similarity | ||||||
| 1 (408) | … | Hypothetical protein | Clostridium difficile | ZP_05400366.1 | 57 | 84 | 29.9 |
| 2 (1395) | … | Undecaprenyl-phosphate glucose phosphotransferase | Clostridium lentocellum | YP_004310697.1 | 57 | 74 | 23.9 |
| 3 (969) | … | Glycosyl transferase | Lachnospiraceae bacteria | ZP_08602110.1 | 56 | 75 | 24.8 |
| 4 (891) | … | Phosphoribose diphosphate: decaprenyl-phosphate phosphoribosyltransferase | C. difficile | YP_001087463.1 | 65 | 81 | 24.5 |
| 5 (1797) | … | Hypothetical protein | Tolumonas auensis | YP_002893223.1 | 26 | 45 | 26.2 |
| 6 (1332) | … | Glycosyl transferase | Xanthomonas perforans | ZP_08189725.1 | 49 | 65 | 26.6 |
| 7 (3486) | |||||||
| N-terminus | … | Multidomain glycosyl transferase | Bacteroides species | ZP_08584442.1 | 32 | 54 | 26.3b |
| C-terminus | … | Multidomain glycosyl transferase | Polynucleobacter necessarius | YP_001155105.1 | 51 | 68 | 26.3b |
| 8 (1161) | … | Glycosyl transferase | Aromatoleum aromaticum | YP_157889.1 | 50 | 65 | 28.7 |
| 9 (1383) | … | Glycosyl transferase | Clostridium beijerinckii | YP_001311811.1 | 34 | 58 | 22.4 |
| 10 (909) | … | Glycosyl transferase | C. beijerinckii | YP_001311812.1 | 67 | 81 | 22.4 |
| 11 (1283) | wzt | ATP binding cassette (ABC) transporter: ATPase | C. beijerinckii | YP_001311813.1 | 65 | 81 | 26.6 |
| 12 (789) | wzm | ABC transporter: permease | Eubacterium yurii | ZP_07454366.1 | 68 | 84 | 25.6 |
| 13 (1023) | rmlBc | dTDP-glucose 4,6-dehydratase | Turicibacter species | ZP_08166203.1 | 73 | 88 | 27.7 |
| 14 (573) | rmlCc | dTDP-4-dehydrorhamnose 3,5-epimerase | Clostridium perfringens | ZP_02863393.1 | 72 | 86 | 28.0 |
| 15 (924) | … | Phosphogluconolactonase; provisional | Lachnospiraceae bacteria | ZP_08605193.1 | 34 | 59 | 25.4 |
| 16 (879) | rmlAc | Glucose-1-phosphate thymidylyltransferase | Turicibacter species | ZP_08166199.1 | 83 | 93 | 30.3 |
| 17 (681) | rmlDc | dTDP-4-dehydrorhamnose reductase | C. difficile | ZP_05328363.1 | 69 | 86 | 27.2 |
| 18 (816) | rfbNc | Rhamnosyltransferase | Thermoanaerobacter pseudethanolicus | YP_001665609.1 | 50 | 70 | 25.5 |
| 19 (1608) | wzyC | O-Antigen polymerase/ligase | Geobacillus thermoglucosidasius | YP_004586423.1 | 33 | 54 | 23.2 |
C. difficile was found as the closest species match to 3 ORFS. However, although the low level of amino acid identity indicates a similar function for the ORF (eg, an alternative rhamnose pathway in the case of rmlD), the 3 ORFs were widely dispersed in the CD630 reference genome [14]. Thus, these low-level matches do not indicate the presence of another putative S-layer glycosylation cluster. Putative functions of the predicted ORFs were inferred using the entire results of the BLAST query, rather than just the closest match shown in Table 2.
Abbreviations: nt, nucleotide; ORF, open reading frame.
a Numbered as in Figure 3.
b Includes both the N-terminus and C-terminus species matches.
c Rhamnose pathway.