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. 2016 Jan 22;11(1):e0146796. doi: 10.1371/journal.pone.0146796

Table 3. Functional characterization of non-homologous COPs.

COP Name Subtype COP # Virulent Essential Enzyme Becker 2006
[Citrate (pro-3S)-lyase] ligase   247        
2-(5''-triphosphoribosyl)-3'-dephospho-CoA synthase   432        
2-dehydro-3-deoxyphosphooctonate aldolase   328   Yes Yes Yes
3-deoxy-D-manno-octulosonic-acid transferase   192   Yes Yes Yes
3-deoxy-manno-octulosonate cytidylyltransferase   361   Yes Yes Yes
Acetate kinase   205   Yes Yes  
ADP-heptose—LPS heptosyltransferase I 291   Yes Yes Yes
II 261   Yes Yes Yes
Aerotaxis receptor   104   Yes    
Alanine racemase   245   Yes Yes  
Alkylphosphonate utilization operon protein PhnA   498   Yes Yes  
Anti-sigma-28 factor FlgM 507        
Aspartate racemase   366        
Bifunctional chorismate mutase/prephenate dehydrogenase   227        
Carbon storage regulator   527   Yes    
Chemotaxis methyltransferase CheR 321   Yes Yes  
Chemotaxis protein CheA 49   Yes Yes Dispensable
CheW 276   Yes    
CheZ 409        
CheY 486 Yes Yes    
Chemotaxis-specific methylesterase   259 Yes Yes Yes  
Chromosomal replication initiation protein   136   Yes    
Citrate lyase Gamma 505   Yes Yes  
Colanic acid capsular biosynthesis activation protein A 416        
Cytochrome BD-II ubiquinol oxidase 1 221   Yes Yes  
1 139   Yes Yes  
2 273   Yes Yes  
D-alanyl-D-alanine carboxypeptidase   127   Yes Yes  
  190   Yes Yes  
DNA-binding transcriptional activator DcuR 376   Yes    
KdpE 395   Yes    
SdiA 355        
UhpA 404   Yes    
DNA-binding transcriptional regulator BaeR 374   Yes    
BasR 390 Yes Yes    
CpxR 385   Yes    
PhoP 398 Yes Yes    
QseB 336   Yes    
RstA 368   Yes    
D-ribose transporter RbsB 310   Yes    
Flagella synthesis protein FlgN 478        
Flagellar assembly protein FliH 370        
Flagellar basal body L-ring protein   382 Yes      
Flagellar basal body P-ring biosynthesis protein FlgA 401        
Flagellar basal body rod modification protein   383        
Flagellar basal body rod protein FlgB 479 Yes      
FlgC 484 Yes      
FlgF 354        
FlgG 343 Yes      
Flagellar biosynthesis protein FliJ 471   Yes    
FliO 487   Yes    
FliP 364 Yes      
FliQ 517 Yes      
FliR 340        
FliT 490        
Flagellar hook protein FlgE 201        
Flagellar hook-associated protein FlgL 290   Yes    
Flagellar hook-basal body protein FliE 503        
Flagellar hook-length control protein   199        
Flagellar motor protein MotA 312   Yes    
Flagellar motor switch protein FliM 275 Yes      
Flagellar motor switch protein G 279 Yes      
Flagellar MS-ring protein   68        
Flagellar protein FliS 481 Yes      
Formate dehydrogenase-O Gamma 412        
Fructose 1,6-bisphosphate aldolase   244   Yes Yes  
Fumarate reductase C 485        
D 492   Yes    
Glutamate/aspartate ABC transporter permease GltK 397   Yes    
Hydrogenase 2 Large 72        
Small 230   Yes Yes  
Integral membrane protein MviN 90   Yes    
Invasion protein InvA 48 Yes      
Isochorismatase   326 Yes Yes Yes  
Isochorismate synthase   174   Yes Yes  
Lipid A biosynthesis lauroyl acyltransferase   280   Yes Yes Yes
Lipid-A-disaccharide synthase   218   Yes Yes Yes
Lipopolysaccharide 1,2-glucosyltransferase   272   Yes Yes  
Lipopolysaccharide 1,3-galactosyltransferase   271   Yes Yes  
Lipopolysaccharide core biosynthesis protein   250   Yes Yes  
  339   Yes Yes Yes
  384   Yes Yes  
RfaG 226   Yes Yes  
Maltose ABC transporter substrate-binding protein   132   Yes    
Monofunctional biosynthetic peptidoglycan transglycosylase   369   Yes Yes  
Multidrug efflux system MdtC 12   Yes    
Nitrate reductase 1 Alpha 4   Yes Yes  
Nitrate reductase molybdenum cofactor assembly chaperone 1   381        
Nitrate reductase (81 duplicates of 1 and 2) Beta 98   Yes Yes  
Nitrogen regulation protein NR(I) 135   Yes    
NR(II) 260   Yes Yes  
P-II 1 497   Yes    
O-antigen ligase   166   Yes Yes Yes
Osmolarity response regulator OmpR 367   Yes    
Osmolarity sensor protein EnvZ 160   Yes Yes  
Outer membrane channel protein TolC 120   Yes    
Outer membrane lipoprotein   482        
Outer membrane porin protein C 223   Yes    
Outer membrane protease   293 Yes      
Outer membrane protein F 238   Yes    
Penicillin-binding protein 1b 33   Yes Yes Yes
2 54   Yes    
Peptide transport periplasmic protein SapA 76   Yes    
Peptidoglycan synthetase 1a 31   Yes Yes Yes
FtsI 65   Yes Yes Yes
FtsI 67   Yes Yes
Phosphate ABC transporter substrate-binding protein   251   Yes    
Phosphate acetyltransferase   43   Yes Yes  
Phosphate regulon sensor protein PhoR 186   Yes Yes  
Phosphoenolpyruvate carboxylase   29   Yes Yes  
Phosphoenolpyruvate-protein phosphotransferase   40   Yes Yes  
Phosphoglyceromutase   93   Yes Yes  
Phospho-N-acetylmuramoyl-pentapeptide-transferase   242   Yes Yes Yes
PII uridylyl-transferase   23   Yes Yes  
Preprotein translocase SecA 22   Yes    
SecB 459   Yes    
SecD 60   Yes    
SecE 477   Yes    
SecF 270   Yes    
SecG 439   Yes    
SecY 169   Yes    
YajC 500   Yes    
PTS system ascorbate-specific transporter IIC 129   Yes    
IIC 164   Yes    
PTS system fructose-specific transporter IIBC 74   Yes Yes  
PTS system glucitol/sorbitol-specific transporter IIA 491        
IiB 284        
PTS system glucose-specific transporter IIA 447   Yes Yes  
IIBC 119   Yes Yes  
PTS system lactose/cellobiose-specific transporter IIB 515        
PTS system L-ascorbate-specific transporter IIA 460   Yes Yes  
PTS system mannitol-specific transporter IIA 465   Yes Yes  
IIABC 50   Yes Yes  
PTS system mannose-specific transporter IiAB 285   Yes Yes  
IIC 338        
IID 324        
PTS system N,N'-diacetylchitobiose-specific transporter IIA 496   Yes Yes  
IIB 499   Yes Yes  
IIC 158        
PTS system phosphohistidinoprotein-hexose phosphotransferase Hpr 514   Yes    
Npr 516   Yes    
PTS system transporter subunit IIA-like nitrogen-regulatory protein PtsN 452   Yes Yes  
Purine-binding chemotaxis protein   449 Yes Yes    
Respiratory nitrate reductase 1 Gamma 396        
RNA polymerase sigma factor for flagellar biosynthesis   377 Yes Yes    
RNA polymerase sigma-54 factor   128   Yes    
Sec-independent translocase   434        
Secretion system apparatus protein SsaU 255 Yes      
SsaV 45 Yes      
Sensor protein PhoQ 123 Yes Yes Yes  
BasS/ PmrB 246 Yes Yes Yes  
RstB 179   Yes Yes  
Signal transduction histidine-protein kinase BaeS 140   Yes Yes  
Succinate dehydrogenase cytochrome b556 large membrane   483   Yes K8TKP2  
Surface presentation of antigens protein SpaO 305 Yes      
SpaP 400 Yes      
SpaQ 521 Yes Yes    
SpaS 249 Yes      
Tetraacyldisaccharide 4'-kinase   282   Yes Yes Yes
Tetrathionate reductase complex A 13 Yes      
Transcriptional activator FlhC 423 Yes      
FlhD 494 Yes      
Transcriptional regulator PhoB 387   Yes    
  167   Yes    
  17 Yes Yes    
RcsB 386   Yes    
Tricarboxylate transport membrane protein   109        
  476        
Twin arginine translocase A 522   Yes    
E 525   Yes    
Twin-arginine protein translocation system TatC 345   Yes    
Two component response regulator   410 Yes Yes    
  411 Yes Yes    
  378   Yes    
Two-component sensor kinase protein   152   Yes Yes  
Type III secretion apparatus lipoprotein YscJ/HrcJ family   352 Yes Yes    
Type III secretion apparatus needle protein PrgI 523 Yes      
SsaG 519 Yes      
Type III secretion apparatus protein SpaR 341 Yes Yes    
SpaR 344 Yes Yes    
Type III secretion outer membrane pore   111 Yes      
Type III secretion outer membrane protein YscC/HrcC family   73 Yes      
Type III secretion system protein   286 Yes Yes    
FliP 407 Yes      
InvE 229 Yes      
UDP pyrophosphate phosphatase   333   Yes Yes  
UDP-2,3-diacylglucosamine hydrolase   372   Yes Yes Yes
UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase   265   Yes Yes Yes
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase   301   Yes Yes Yes
UDP-N-acetylenolpyruvoylglucosamine reductase   263   Yes Yes Yes
UDP-N-acetylglucosamine 1-carboxyvinyltransferase   194   Yes Yes Yes
UDP-N-acetylglucosamine acyltransferase   342   Yes Yes Yes
UDP-N-acetylmuramate—L-alanine ligase   121   Yes Yes Yes
UDP-N-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase   113   Yes Yes Yes
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase   177   Yes Yes Yes
UDP-N-acetylmuramoyl-tripeptide—D-alanyl-D-alanine ligase   157   Yes Yes Yes
Virulence membrane protein PagC 430        
Zinc resistance protein   467   Yes