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 subunitConfirmed 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 componentConfirmed 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 componentShared 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