TABLE 1.
Homologies and Shine-Dalgarno analysis of the putative ORFs of the 23.5-kb chromosomal segment
| ORF | Representative homologous protein (sp./accession no.)a | Homologous gene product | Identity (%)/amino acid overlap | SD-initiation codonb |
|---|---|---|---|---|
| xynB2 | XylA (B. stearothermophilus 21/P45702) | β-Xylosidase | 94.2/359 | Incomplete in NH3 end |
| xynA2 | XynA (B. stearothermophilus 21/P45703) | Xylanase | 81.8/336 | GTTGGAGGAGGGGGAATGAAGatg |
| orf1 | ORF HO698 (Halobacterium sp. strain NRC-1/AF016485) | Unknown | 25.5/456 | AATGGGATTGGAGGGAGAAATatg |
| orf2 | LplA (B. subtilis/P37966) | Unknown | 21/381 | AGGGCATTTTTCGATACTGGGatg |
| orf3 | AraP (B. subtilis/X89810) | Integral membrane protein | 25.9/224 | AAGAAGTGAATGAATGGTATCatg |
| orf4 | MsmG (Streptococcus mutans/M77351) | Integral membrane protein | 25.3/217 | TTTTAAAGGGAGGGGAGGTCTatg |
| aguA | AguA (T. maritima/P96105) | α-Glucuronidase | 60.6/578 | GTAACAGGAGGAGAATTCGACatg |
| xynB | XynB (T. saccharolyticum/ P36906) | β-Xylosidase | 64.4/503 | CGGTGAATAGGGGAGAGGAGCatg |
| kdgK | KdgK (E. chrysanthemi/P45416) | KDG kinase | 26.5/223 | AAATGGTTTTGGAGGGACGAGatg |
| kdgA | KdgA (E. chrysanthemi/P38448) | KDGP aldolase | 30.1/196 | CGATAAAGGAGATGAACCTACatg |
| uxuR | UxuR (E. coli/P39161) | Regulatory protein | Partial homology | AAGAAAACGCATGATCATGGatg |
| uxaC | UxaC (E. coli/P42607) | Uronate isomerase | 48.1/420 | GCTTTGCGGGAGGGAGACAGTgtg |
| uxuA | UxuA (E. coli/P24215) | d-Mannonate hydrolase | 47.7/132 | TGAGTGGGGGATGAGATCAGAatg |
| uxuB | YjmF (B. subtilis/AF015825) | Putative d-mannonate oxidoreductase | 59.5/285 | AAGCAGGAAGGTGAGAAGACatg |
| orfA | YteU (B. subtilis/AF008220) | Unknown | 41.5/197 | ACAAGAAAAGGTGGATGAATTatg |
| orfB | Unknown | Unknown | No significant similarities | TCAGAGGAGGGGGAGGAGGACgtg |
| orfC | Rv2812 (Mycobacterium tuberculosis/Z81331) | Unknown | 34.2/374 | CGCGAAGGAGGGAGAACACGgtg |
| orfD | Rv2813 (M. tuberculosis/Z81331) | Unknown | 33.7/261 | TGAGACAAGGAGGAGATTCGAatg |
| xynA | XynA (Bacillus sp. strain C-125/P07528) | Extracellular xylanase | 58.7/375 | TAAAGAATGAGGGGGAATAGTatg |
a
The reported homologous proteins are those showing the highest score among proteins with an experimentally defined function. In the absence of relevant biochemical data, the most similar putative protein was reported.
b
Nucleotides which are complementary to the 3′ end of the 16S rRNA of B. subtilis (3′-UCUUUCCUCCACUAC-5′) are underlined. The ATG and GTG start codons are in lowercase letters. SD, Shine-Dalgarno sequence.