Table 1.

Isolated and characterized Paracoccus loci

StrainGene clusterAccession no.Known functionsReference(s)
P. denitrificans71.11 adk U64203 ATP regeneration: adenylate kinase (adk) 66
P. denitrificansPd1222a hemA U12508 Cytochromec biosynthesis: 5-ALA synthase (hemA) 214
P. denitrificansPd1222 secF-hisH-ccmABCDG-ORF36-ORF117 Z71971 Cytochromec biosynthesis: secretory apparatus protein (secF), histidinol phosphate transaminase (hisH) 215
P. denitrificansPd1222 ccmF-ccmH AF023247 Cytochrome cbiosynthesis 216
P. denitrificans LMD 92.63b narGHJI Z26255 Z37158 Denitrification: membrane-bound nitrate reductase α subunit (narG), β subunit (narH), γ subunit (narI) 23
P. denitrificansPd1222 nirISECFD U05002 Denitrification: nitrite reductase transcriptional regulator (nirI), structural gene (nirS), S-adenosyl-l-methionine uroporphyrinogen methyltransferase (nirE), smallc-type cytochrome (nirC) 59
P. denitrificans LMD 92.63b nirSE U75413 Denitrification: nitrite reductase structural gene (nirS) 5,6
P. denitrificansPd1222 nirIX AJ001308 Denitrification: regulation ofnir gene expression 307
P. denitrificans Pd1222 norCBQDEF U28078 Denitrification: nitric oxide reductase large subunit (norB), small subunit (norC) 60
P. denitrificansNCIMB 8944 nosRZD X74792 Denitrification: nitrous oxide reductase transcriptional regulator (nosR), structural gene (nosZ) 125
P. denitrificansc nosZ AF016058 Denitrification: nitrous oxide reductase structural gene (nosZ) 255
P. denitrificansPd1222 nnr U17435 Denitrification: FNR-like transcriptional activator (nnr) 309
P. denitrificans LMD 92.63b pazS Z73141 Denitrification: pseudoazurin structural protein (pazS) 168
P. denitrificansPd1222 cycA-ctaDII Y07533 Electron transport: cytochromec 550 (cycA), iso-cytochromec oxidase subunit II (ctaDII) 235
P. denitrificansPd1222 cycA-ctaDII M27304 Electron transport: cytochromec 550 (cycA), iso-cytochromec oxidase subunit II (ctaDII) 315
P. versutus ATCC 25364 ORF1-cycA-ctaDII X62808 S37058 Electron transport: cytochrome c 550 (cycA), iso-cytochrome c oxidase subunit II (ctaDII) 296, 297
P. denitrificans Pd1235 cycM X70367 Electron transport: cytochrome c 552(cycM) 294
P. denitrificansPd1235 qoxABCD X78196 Electron transport: cytochromeba 3 quinol oxidase subunit II (qoxA), subunit I (qoxB), subunit III (qoxC), subunit IV (qoxD) 244
P. denitrificansATCC 13543 fbcFBC M17522 Electron transport: cytochromebc 1 complex iron sulfur subunit (fbcF), cytochrome b subunit (fbcB), cytochrome c subunit (fbcC) 162
P. denitrificansPd1222 ctaDI X05829 Electron transport: cytochrome oxidase subunit I (ctaDI) 235
P. denitrificans PD 1235 ctaC X05934 Electron transport: cytochrome oxidase subunits II (ctaC) 277
P. denitrificansPd1222 ctaC-ctaB-ORF1-ctaG-ctaE X05828 Electron transport: cytochrome oxidase subunits II (ctaC) and III (ctaE) 234
P. denitrificansS1657c ctaE X04406 Electron transport: cytochrome oxidase subunit III (ctaE) 251
P. denitrificansPd1222 ctaH Y08372 Electron transport: cytochrome coxidase subunit IV (ctaH) 325
P. denitrificans c phaAB D49362 Energy storage: acetoacetyl-CoA reductase (phaA), β-ketothiolase (phaB) 336
P. denitrificans c phaC D43764 Energy storage: poly (3-hydroxyalkanoate) synthase (phaC) 298
P. denitrificansPd1222 pta-ORF3-ORF4-ORF1-ORF2-ORF5 U08864 Insertion sequence IS1248: phosphate acetyltransferase (pta) 311
P. denitrificansPd1222 ORF3-ORF4-ORF1-ORF2-ORF5 U08856 Insertion sequence IS1248b 312
P. denitrificansPd1222 ORF1-ORF2-flhA-clpP-ORF3-fghA-xoxF-cycB-xoxJI-ORF4 U34346 C1metabolism: NAD-GSH-dependent formaldehyde dehydrogenase (flhA), S-formylglutathione hydrolase (fghA), PQQ-dependent dehydrogenase large subunit (xoxF), cytochrome c 553i(cycB) 116, 117, 237, 239, 240
P. denitrificansPd1222 ORF1-flhS-ORF2-flhR-abcABC-pqqE AJ223460 C1metabolism: transcriptional activator proteins (flhS,flhR), ABC transporter-type proteins (abcA,abcB, abcC), coenzyme PQQ synthesis protein E (pqqE) 241
P. denitrificansPd1222 mxaF M17339 Methanol oxidation: methanol dehydrogenase large subunit (mxaF) 114
P. denitrificans Pd1222 mxaGIJ M57684 Methanol oxidation: cytochrome c 551i (mxaG), methanol dehydrogenase β subunit (mxaI) 314
P. denitrificansPd1222 ORF1-cycB-ORF2 M75583 Methanol oxidation: cytochromec 553i(cycB) 239
P. denitrificansPd1222 mxaZYX M92421 Methanol oxidation: two-component regulatory proteins (mxaX,mxaY) 118
P. denitrificansPd1222 ORF1-mxaACKLD-ORF2-ORF3 AJ000884 Methanol oxidation 242
P. versutus ATCC 25364 mauB-ORF1 L08575 Methylamine oxidation: methylamine dehydrogenase α subunit (mauB) 130
P. denitrificans Pd1222 mauB-ami X55665 Methylamine oxidation: methylamine dehydrogenase α subunit (mauB), amicyanin (ami) 317
P. versutus ATCC 25364 ORF1-mauB-ami M58001 Methylamine oxidation: methylamine dehydrogenase α subunit (mauB), amicyanin (ami) 172, 297
P. denitrificans c mauDA M90098 Methylamine oxidation: methylamine dehydrogenase small subunits (mauA,mauD) 49
P. denitrificans c mauFBE M90099 Methylamine oxidation: methylamine dehydrogenase small subunits (mauF,mauB, mauE) 48
P. denitrificans Pd1222 ORF1-mauRFB U12464 Methylamine oxidation: LysR-type transcriptional activator (mauR), methylamine dehydrogenase large subunit (mauB) 313
P. denitrificansPd1222 mauED X98581 Methylamine oxidation 303,304
P. versutus ATCC 25364 mauED L36951 Methylamine oxidation 130,297
P. versutus ATCC 25364 ORF5-mauF L36952 Methylamine oxidation 129
P. versutus ATCC 25364 mauG L36953 Methylamine oxidation 130,297
P. denitrificansPd1222 mauJGMN U15028 Methylamine oxidation: ferredoxin-like proteins (mauM, mauN), cytochrome cperoxidase-like protein (mauG) 304
P. denitrificans NDH-1c nqo1 M64432,J05331 NADH dehydrogenase: 50-kDa subunit (nqo1) 332
P. denitrificansNDH-1c nqo2 M74171, J05337 NADH dehydrogenase: 25-kDa subunit (nqo2) 331
P. denitrificansNDH-1c URF3-nqo3 M84572 NADH dehydrogenase: 66-kDa subunit (nqo3) 334
P. denitrificansNDH-1c uvrA-nqo7-nqo6-nqo5-nqo4 M93015 NADH dehydrogenase: nd3 subunit (nqo7), ndhK subunit (nqo6), 25-kDa subunit (nqo5), 48-kDa subunit (nqo4); DNA repair protein (uvrA) 333
P. denitrificansNDH-1c URF4-nqo8nqo9-URF5-URF6-nqo10-nqo11-nqo12-nqo14-birA L02354,L01096 NADH dehydrogenase: subunit VIII (nqo8), subunit IX (nqo9), subunit X (nqo10), subunit XI (nqo11), subunit XII (nqo12), subunit XIV (nqo14); biotin (acetyl-CoA carboxylase) ligase (birA) 335
P. denitrificansLMD 92.63b dctM-napEDABC Z36773 Nitrate reduction: periplasmic nitrate reductase molybdenum-iron-sulfur-heme subunit (napA), diheme subunit (napB); Membrane transport: integral membrane subunit of a dicarboxylate transporter (dctM) 24, 25, 35
P. versutus ORF1-ORF2 U42228 Plasmid pTAV203 9
P. versutus repABC U60522 Plasmid pTAV203: replication proteins 8
Paracoccus sp. strain 164 ori AF020624 Plasmid pTM164: origin of replication 266
P. denitrificans71.11c secY U64202 Protein translocation: preprotein translocase (secY) 228
P. denitrificansPd1222 ORF1-fnrN-ORF278-ccoNOQPGH U34353 Regulation of anaerobic growth: transcriptional regulator (fnrP) 63
Electron transport: alternative oxidase cytochrome cbb 3monoheme subunit (ccoN), diheme subunit (ccoQ)
P. denitrificans c rrfA X01501 Ribosome assembly: 5S rRNA (rrfA) 181
Paracoccus sp. strain Y4 rrnA AB012914 Ribosome assembly: 16S rRNA (rrnA) 111
P. alcaliphilus JCM 7364 rrnA D32238 Ribosome assembly: 16S rRNA (rrnA) 145
P. alkenifer rrnA Y13827 Ribosome assembly: 16S rRNA (rrnA) 170
P. aminophilus JCM 7686 rrnA D32239 Ribosome assembly: 16S rRNA (rrnA) 145
P. aminovorans JCM 7685 rrnA D32240 Ribosome assembly: 16S rRNA (rrnA) 145
P. denitrificansIAM 12479 rrnA D13480 Ribosome assembly: 16S rRNA (rrnA) 146, 147
P. denitrificans LMG 4218b rrnA X69159 Ribosome assembly: 16S rRNA (rrnA) 178
P. kocurii JCM 7684 rrnA D32241 Ribosome assembly: 16S rRNA (rrnA) 145
P. marcusii rrnA Y12703 Ribosome assembly: 16S rRNA (rrnA) 112
P. solventivoransDSM 6637 rrnA Y07705 Ribosome assembly: 16S rRNA (rrnA) 264
P. solventivorans rrnA Y13826 Ribosome assembly: 16S rRNA (rrnA) 170
P. thiocyanatusTHIO11 rrnA D32242 Ribosome assembly: 16S rRNA (rrnA) 145
P. versutus IAM 12814 rrnA D32243 Ribosome assembly: 16S rRNA (rrnA) 145
P. versutus IAM 12815 rrnA D32244 Ribosome assembly: 16S rRNA (rrnA) 145
P. denitrificansKS1b rrnA U58015 Ribosome assembly: 16S rRNA (rrnA) 139
P. denitrificansKS2b rrnA U58016 Ribosome assembly: 16S rRNA (rrnA) 139
P. denitrificansKL1b rrnA U58017 Ribosome assembly: 16S rRNA (rrnA) 139
P. denitrificans LMG 4218b rrlA X87287 Ribosome assembly: 23S rRNA (rrlA) 179
P. denitrificans71.11c rpsM U64204 Ribosome assembly: ribosomal protein S13 (rpsM) 228
P. denitrificans ATCC 13543c sdhCDAB U31902 Succinate oxidation: succinate dehydrogenase b-type cytochrome subunit (sdhC), hydrophobic membrane anchor (sdhD), flavoprotein subunit (sdhA), iron-sulfur protein subunit (sdhB) 69
P. denitrificansLMD 82.5b soxABCDEF X79242 Sulfur oxidation: protein B (soxB), sulfite oxidase (soxC), cytochrome (soxD), cytochrome (soxE) 326, 327
P. denitrificans Pd1222 porG Y09451 Membrane proteins: porin structural protein (porG) 254
P. denitrificans Pd1222 recA U59631 DNA recombination 75
P. denitrificans IFO 12442c tyrB Y08272 Amino acid biosynthesis: aromatic amino acid transferase (tyrB) 207
  • a P. denitrificans Pd1222 is a derivative of DSM 413.

  • b Now proposed to be P. pantotrophus(233).

  • c Classification as P. denitrificansor P. pantotrophus not yet determined.