Table 3.
Annotations of the 79 predicted pseudogenes in HL096PA1.
| Number | ORF | Start | End | Function | Note |
|---|---|---|---|---|---|
| 1 | PAGK_0006 | 7,621 | 6,061 | ABC transporter, ATP-binding protein | Shared with KPA171202 |
| 2 | PAGK_0019 | 23,673 | 23,196 | PTS system, galactitol-specific IIA component | Confirmed by PCR and Sanger sequencing |
| 3 | PAGK_0020 | 24,985 | 23,730 | PTS system, galactitol-specific IIC component | Confirmed by PCR and Sanger sequencing |
| 4 | PAGK_0024 | 25,937 | 27,844 | Hypothetical protein | Shared with KPA171202 |
| 5 | PAGK_0025 | 28,692 | 28,418 | Hypothetical protein | |
| 6 | PAGK_0026 | 29,964 | 29,294 | Hypothetical protein | |
| 7 | PAGK_0089 | 100,317 | 102,505 | Glycosyl hydrolase family protein | |
| 8 | PAGK_0123 | 149,702 | 148,105 | Site-specific recombinase | |
| 9 | PAGK_0193 | 226,656 | 225,834 | Regulator protein | |
| 10 | PAGK_0224 | 266,991 | 265,055 | Putative RHS-related protein | |
| 11 | PAGK_0243 | 289,824 | 290,724 | Putative ABC transporter | |
| 12 | PAGK_0352 | 402,744 | 401,670 | Hypothetical protein | Confirmed by PCR and Sanger sequencing |
| 13 | PAGK_0393 | 441,551 | 441,884 | 2-Hydroxy acid dehydrogenase | |
| 14 | PAGK_0395 | 444,633 | 446,378 | Hypothetical protein | |
| 15 | PAGK_0429 | 474,851 | 476,017 | Putative sensor histidine kinase, two component system | |
| 16 | PAGK_0440 | 487,718 | 487,064 | Hypothetical protein | |
| 17 | PAGK_0463 | 510,587 | 509,659 | Phosphotransferase system protein mannitol/fructose-specific IIA subunit | Confirmed by PCR and Sanger sequencing |
| 18 | PAGK_0482 | 529,279 | 530,146 | Myo-inositol catabolism IolH protein | |
| 19 | PAGK_0573 | 630,324 | 628,497 | Hypothetical protein | |
| 20 | PAGK_0589 | 653,210 | 651,537 | Alpha-glucosidase/amylase family protein | |
| 21 | PAGK_0592 | 657,824 | 655,229 | Aminopeptidase N | |
| 22 | PAGK_0601 | 674,112 | 671,871 | UvrD/Rep helicase | |
| 23 | PAGK_0603 | 685,081 | 680,455 | Hypothetical protein | |
| 24 | PAGK_0604 | 687,943 | 685,068 | Putative helicase | |
| 25 | PAGK_0613 | 702,394 | 698,431 | Hypothetical protein | |
| 26 | PAGK_0720 | 820,262 | 819,153 | Putative peptide ABC transporter, permease component | |
| 27 | PAGK_0757 | 855,259 | 854,123 | Putative lysophospholipase | Confirmed by PCR and Sanger sequencing |
| 28 | PAGK_0811 | 908,541 | 907,748 | Hypothetical protein | |
| 29 | PAGK_0875 | 986,883 | 986,286 | Hypothetical protein | |
| 30 | PAGK_0944 | 1,060,628 | 1,059,358 | Prephenate dehydrogenase | |
| 31 | PAGK_1004 | 1,127,197 | 1,126,813 | Hypothetical protein | |
| 32 | PAGK_1011 | 1,133,493 | 1,133,051 | Hypothetical protein | |
| 33 | PAGK_1158 | 1,298,563 | 1,297,552 | Putative oxidoreductase protein | Confirmed by PCR and Sanger sequencing |
| 34 | PAGK_1160 | 1,299,462 | 1,299,708 | Beta-glucosidase fragment | Confirmed by PCR and Sanger sequencing |
| 35 | PAGK_1181 | 1,318,788 | 1,319,584 | Putative hydrolase | Confirmed by PCR and Sanger sequencing |
| 36 | PAGK_1233 | 1,374,383 | 1,376,290 | PTS system, mannitol-specific IIABC component | Confirmed by PCR and Sanger sequencing |
| 37 | PAGK_1238 | 1,380,347 | 1,381,136 | Putative metallo-beta-lactamase | |
| 38 | PAGK_1242 | 1,386,373 | 1,384,720 | Acetyl-coenzyme A synthetase | |
| 39 | PAGK_1275 | 1,426,760 | 1,425,953 | GntR family regulatory protein | |
| 40 | PAGK_1276 | 1,426,762 | 1,427,445 | Hypothetical protein | |
| 41 | PAGK_1284 | 1,434,222 | 1,434,422 | Hypothetical protein | |
| 42 | PAGK_1285 | 1,434,707 | 1,435,190 | Transposase, Mutator family | |
| 43 | PAGK_1332 | 1,481,350 | 1,482,114 | Hypothetical protein | Confirmed by PCR and Sanger sequencing |
| 44 | PAGK_1344 | 1,496,744 | 1,495,088 | Hypothetical protein | |
| 45 | PAGK_1347 | 1,501,212 | 1,499,580 | ABC transporter ATP-binding protein | Confirmed by PCR and Sanger sequencing |
| 46 | PAGK_1354 | 1,508,597 | 1,511,439 | Oxidoreductase, putative D-lactate | |
| 47 | PAGK_1387 | 1,549,654 | 1,548,834 | Putative GntR-family transcriptional regulator | |
| 48 | PAGK_1407 | 1,567,445 | 1,569,345 | Hypothetical protein | |
| 49 | PAGK_1536 | 1,703,687 | 1,704,612 | Putative lysophospholipase | |
| 50 | PAGK_1586 | 1,764,348 | 1,765,387 | Binding-protein-dependent transport system inner membrane component | Confirmed by PCR and Sanger sequencing and shared with P. acnes J139 |
| 51 | PAGK_1587 | 1,765,384 | 1,766,265 | Binding-protein-dependent transport system inner membrane component | Shared with P. acnes J139 |
| 52 | PAGK_1592 | 1,770,327 | 1,769,760 | Protein associated to putative adhesion protein | |
| 53 | PAGK_1593 | 1,771,040 | 1,770,487 | Protein associated to putative adhesion protein | |
| 54 | PAGK_1594 | 1,773,223 | 1,771,037 | Hypothetical protein | |
| 55 | PAGK_1608 | 1,786,154 | 1,785,310 | Hypothetical protein | |
| 56 | PAGK_1643 | 1,820,268 | 1,818,959 | Transporter (sodium : sulfate symporter) | Shared with KPA171202 |
| 57 | PAGK_1717 | 1,907,494 | 1,905,155 | Putative ABC transporter-associated permease | Confirmed by PCR and Sanger sequencing |
| 58 | PAGK_1730 | 1,924,158 | 1,920,911 | Endo-beta-N-acetylglucosaminidase family protein | |
| 59 | PAGK_1742 | 1,935,480 | 1,935,974 | Hypothetical protein | |
| 60 | PAGK_1744 | 1,936,979 | 1,938,333 | Putative sialidase | |
| 61 | PAGK_1760 | 1,952,431 | 1,951,577 | Glycerophosphoryl diester phosphodiesterase | |
| 62 | PAGK_1793 | 1,981,847 | 1,978,587 | Hypothetical protein | Confirmed by PCR and Sanger sequencing |
| 63 | PAGK_1821 | 2,014,629 | 2,016,701 | Hypothetical protein | Confirmed by PCR and Sanger sequencing |
| 64 | PAGK_1858 | 2,054,370 | 2,056,156 | ABC transporter ATP-binding protein | |
| 65 | PAGK_1895 | 2,103,920 | 2,105,327 | Pyridine nucleotide-disulphide oxidoreductase | |
| 66 | PAGK_1897 | 2,107,483 | 2,109,669 | Hypothetical protein | Shared with P. acnes J139 |
| 67 | PAGK_1966 | 2,185,427 | 2,184,028 | Amidase | |
| 68 | PAGK_1990 | 2,207,618 | 2,209,728 | 5′-Nucleotidase/2′,3′-cyclic phosphodiesterase | |
| 69 | PAGK_1995 | 2,211,776 | 2,211,311 | Hypothetical protein | |
| 70 | PAGK_1997 | 2,212,029 | 2,212,392 | Hypothetical protein | |
| 71 | PAGK_2003 | 2,218,626 | 2,218,090 | Hypothetical protein | |
| 72 | PAGK_2008 | 2,222,549 | 2,223,462 | Putative asparaginase | |
| 73 | PAGK_2023 | 2,236,080 | 2,235,748 | Ornithine carbamoyltransferase, catabolic | |
| 74 | PAGK_2041 | 2,255,990 | 2,257,066 | Putative lysophospholipase | |
| 75 | PAGK_2110 | 2,327,052 | 2,328,480 | Putative adhesion or S-layer protein | Confirmed by PCR and Sanger sequencing |
| 76 | PAGK_2118 | 2,338,399 | 2,337,074 | Hypothetical protein | |
| 77 | PAGK_2159 | 2,375,435 | 2,374,944 | MarR family transcriptional regulator | Confirmed by PCR and Sanger sequencing |
| 78 | PAGK_2189 | 2,405,633 | 2,407,955 | D-ornithine aminomutase E component | |
| 79 | PAGK_2225 | 2,450,551 | 2,449,750 | SorC family transcriptional regulator | Shared with KPA171202 |