TABLE 1.

Localization and annotation of open reading frames and other features of the clc element

ORF no. or featureGene nameCoding regionOrientationSize (aa)Ribosome binding sitePutative productHomology (source)aAccession no.Amino acid identityE valueb
%Range (aa)
tRNA-GlyglyV1-77+26tRNA-GlytRNA-Gly
Repeated regionattR60-7718Right end attachment site
ORF262intB13262-2235+658GGGAAIntegrasePhage-related integrase (Xylella fastidiosa 9a5c)AAF84527916130e-00
ORF28482848-4233462GGAGAAPermeaseCOG0477: permeases of the major facilitator superfamily (Ralstonia eutropha JMP134)ZP_00166365614361e-151
ORF44384438-5157240GAGGGGGAOxidoreductaseCOG1018: flavodoxin reductases (ferredoxin- NADPH reductases) family 1 (Burkholderia cepacia R18194)ZP_00214263562391e-75
ORF55125512-5991160GATGGGGPutative ring dioxygenase small subunitAnthranilate dioxygenase small subunit (Burkholderia cepacia)AAO83640571571e-48
ORF59945994-7256421GGAGALarge subunit aromatic dioxygenaseOrtho-halobenzoate 1,2-dioxygenase alpha-ISPc protein OhbB (Burkholderia mallei ATCC 23344)YP_105030674241e-167
ORF80528052-9035328GAGGHypothetical proteinUnknown (Pseudomonas aeruginosa)AAC69479973270e-00
ORF9151clcE9151-10209353AAGAAGMaleylacetate reductaseMaleylacetate reductaseAAB71540993520e-00
ORF10206clcD10206-10916237GGAGAGDienelactone hydrolaseDienelactone hydrolase (Pseudomonas aeruginosa)AAC69477992361e-134
ORF1093810938-11921328GGGAAHypothetical proteinHypothetical UPF0065 protein in clcB-clcD intergenic region precursorP0A177993261e-180
ORF11948clcB11948-13060371GGAGAChloromuconate cycloisomeraseChloromuconate cycloisomerase (Pseudomonas aeruginosa)AAC69475993700e-00
ORF13057clcA13057-13839261GGAGAChlorocatechol 1,2-dioxygenaseChlorocatechol 1,2-dioxygenase (Ralstonia sp. JS705)CAA06968992581e-148
ORF14009clcR14009-14893+295AGAGGlysR family transcriptional regulatorLys-R type regulatory protein (Pseudomonas aeruginosa)AAC69473992921e-160
ORF1503715037-15387117NoThreonine efflux proteinCOG1280: putative threonine efflux protein (Burkholderia cepacia R18194)ZP_00214880791152e-44
ORF1540515405-1564781GGATHypothetical proteinCOG1280: putative threonine efflux protein (Burkholderia cepacia R18194)ZP_0021488084731e-28
ORF1596215962-16603214NoHypothetical proteinHypothetical protein XF1719 (Xylella fastidiosa 9a5c)NP_299008681412e-65
ORF1677516775-17023+83GGCAHypothetical proteinConserved hypothetical protein (Pseudomonas aeruginosa)AAN6209686502e-17
ORF1716217162-17959266GGGAATranscriptional regulatorPutative transcriptional regulator (Pseudomonas aeruginosa)AAN62138792611e-113
ORF1850218502-19188229GGGAATranscriptional regulatorProbable transcription regulator protein (Ralstonia solanacearum GMI1000)NP_522004572022e-59
ORF1961919619-20563315GGGAAHypothetical proteinHypothetical protein SMc01405 (Sinorhizobium meliloti 1021)NP_386189302853e-27
ORF2070920709-21128140GGAGHypothetical proteinCOG2259: predicted membrane protein (Pseudomonas aeruginosa UCBPP-PA14)ZP_00137687581362e-39
ORF2124121241-21900220GGAGCAtetR-type transcriptional regulatorTranscriptional regulator (Xanthomonas oryzae pv. oryzae KACC10331)YP_199568301982e-21
ORF2192221922-22674251GGAGCAHypothetical proteinCOG2259: predicted membrane protein (Pseudomonas aeruginosa UCBPP-PA14)ZP_00137687381312e-13
ORF22813amnR22813-23430206GGTGAAminophenol repressorNbzR, aminophenol operon repressor (Pseudomonas putida)AAK26517571468e-39
ORF2352623526-23939+138AAAGGAFerredoxin-like proteinPutative ferredoxin (Pseudomonas putida)AAK26518491362e-28
ORF23951amnB23951-24865+305GAGGAGAA2-Aminophenol 1,6-dioxygenase beta subunit2-Aminophenol 1,6-dioxygenase beta subunit (Comamonas testosteroni)AAT35226792985e-163
ORF24910amnA24910-25722+271AGGAGA2-Aminophenol 1,6-dioxygenase alpha subunit2-Aminophenol 1,6-dioxygenase alpha subunit (Comamonas testosteroni)AAT35227592697e-91
ORF25781amnC25781-27259+493AAGAAGG2-Aminomuconic semialdehyde dehydrogenase2-Aminomuconic semialdehyde dehydrogenase (Comamonas testosteroni)AAT35228724850e-00
ORF27249amnD27249-27701+151GCATCC2-Aminomuconate deaminase2-Aminomuconate deaminase (Pseudomonas fluorescens)BAC65310721361e-50
ORF27716amnF27716-28525+270AAGAGG2-Keto-4-pentenoate hydratasePutative hydratase protein (Ralstonia solanacearum GMI1000)NP_522452602593e-82
ORF28522amnE28522-29286+255GGAG4-Oxalocrotonate decarboxylaseProbable 4-oxalocrotonate decarboxylase protein (Ralstonia solanacearum GMI1000)NP_522453662504e-87
ORF29347amnH29347-30288+314GGAGAcetylating aldehyde dehydrogenaseAcetaldehyde dehydrogenase oxidoreductase (Ralstonia oxalatica)CAD61138853125e-163
ORF30304amnG30304-31341+346GAGGAG4-Hydroxy-2-ketovalerate aldolase4-Hydroxy-2-ketovalerate aldolase (Comamonas testosteroni)BAA82884873321e-164
ORF3145331453-31953+167AGCGGTTHypothetical proteinCOG0657: esterase/lipase (Nostoc punctiforme PCC 73102)ZP_00105982351393e-15
ORF3195031950-32345+132CAAGHypothetical proteinCOG0657: esterase/lipase (Nostoc punctiforme PCC 73102)ZP_00105982471262e-25
ORF3296332963-34498+512GGGTGAOuter membrane protein or channel-forming componentProbable channel-forming component of a multidrug resistance efflux pump protein (Ralstonia solanacearum GMI1000)NP_522003544601e-134
ORF3449534495-36069+525GAAGGPermease of the major facilitator superfamilyProbable inner membrane multidrug resistance transmembrane protein (Ralstonia solanacearum GMI1000)NP_522002574781e-159
ORF3607736077-37111+345AAGGAMultidrug efflux pumpPutative multidrug resistance homolog transmembrane protein (Ralstonia solanacearum GMI1000)NP_522001573421e-103
ORF3714337143-37445+101AGGAGAHypothetical proteinHypothetical protein YPTB3109 (Yersinia pseudotuberculosis IP 32953)YP_071613431018e-16
ORF3748937489-38133+215AAAGGAHypothetical proteinHypothetical protein Raeut03005309 (Ralstonia eutropha JMP134)ZP_00166494471178e-18
ORF3818438184-39365+394AGGCEsterase of the alpha-beta hydrolase superfamilyCOG1752: predicted esterase of the alpha-beta hydrolase superfamily (Rubrivivax gelatinosus PM1)ZP_00245180583911e-127
ORF4089439860-40894345GGAGGAHypothetical proteinCOG0823: periplasmic component of the Tol biopolymer transport system (Cytophaga hutchinsonii)ZP_00310748253004e-08
ORF4191740922-41917332AGGAAmidohydrolase/nitrilaseNitA (Pseudomonas fluorescens)AAW79573753131e-137
ORF4197341973-43385471NoAcyl-CoA synthetasePutative long-chain-fatty-acid-CoA ligase (Rhodopseudomonas palustris CGA009)NP_947491284462e-31
ORF4338743387-44967527AGAGGAAGAcyl-CoA synthetasePutative long-chain-fatty-acid-CoA ligase (Rhodopseudomonas palustris CGA009)NP_947491285181e-39
ORF4518045180-46136+319GGAGTranscriptional regulator (AraC-type DNA binding domain-containing protein)COG2207: AraC-type DNA binding domain- containing proteins (Pseudomonas syringae pv. syringae B728a)ZP_00205730303238e-36
ORF4631546315-46698128GGCAGGHypothetical proteinCOG1249: pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes (Polaromonas sp. JS666)ZP_00360452771183e-47
ORF4677746777-4693252GAAGACGGTransposase (fragment)COG2801: transposase and inactivated derivatives (Polaromonas sp. JS666)ZP_0036081574515e-16
ORF4763047630-48811394AGGAATransport proteinCOG2807: cyanate permease (Pseudomonas aeruginosa UCBPP-PA14)ZP_00140706353915e-47
ORF4892248922-49725+268GGAGATranscriptional regulator (AraC-type DNA binding domain-containing protein)Transcriptional regulator, AraC family (Pseudomonas putida KT2440)NP_742746412442e-42
ORF5024050240-52087616AGGAHypothetical proteinConserved hypothetical protein (Pseudomonas aeruginosa)AAN62129806160e-00
ORF5232452324-52710+129GGAGAGHypothetical proteinHypothetical protein NE0293 (Nitrosomonas europaea ATCC 19718)NP_840380751051e-39
ORF5271052710-53168+153GAAGTGGAAHypothetical proteinConserved hypothetical protein (Pseudomonas aeruginosa)AAN62268821501e-71
ORF5319653196-53573+126AGGAGAHypothetical proteinHypothetical protein Reut02005849 (Ralstonia metallidurans CH34)ZP_00271404601229e-33
ORF5358753587-55104506GGGGAGAHypothetical proteinHypothetical protein Reut02005848 (Ralstonia metallidurans CH34)ZP_00271403855020e-00
ORF5512055120-55479120GGGAGGHypothetical proteinHypothetical protein Reut02005847 (Ralstonia metallidurans CH34)ZP_00271402771172e-48
ORF5547655476-56873466GAGGTGGHypothetical proteinHypothetical protein Reut02005846 (Ralstonia metallidurans CH34)ZP_00271401854620e-00
ORF5688356883-57830316GGAGGGHypothetical proteinCOG1154: Deoxyxylulose-5-phosphate synthase (Ralstonia metallidurans CH34)ZP_00271400903131e-170
ORF5782757827-58273149AGGGGHypothetical proteinHypothetical protein (Pseudomonas aeruginosa)AAN62137751486e-61
ORF5843258432-58926165GGAGGDNA repair proteinCOG2003: DNA repair proteins (Ralstonia metallidurans CH34)ZP_00271398821641e-72
ORF5911059110-59874255GGAGAAProtein-disulfide isomeraseConserved hypothetical protein (Pseudomonas aeruginosa)AAN62139822541e-122
ORF5988859888-62755956GGAGGAConserved hypothetical protein VirB4 domainHypothetical protein (Pseudomonas aeruginosa), COG3451AAN62141958850e-00
ORF6275562755-63195147AGGAGAAAHypothetical proteinHypothetical protein (Pseudomonas aeruginosa)AAN62142901463e-71
ORF6317663176-64594473AAGGAGHypothetical proteinHypothetical protein (Pseudomonas aeruginosa)AAN62143924720e-00
ORF6458464584-65516311AAGGAGGAAGHypothetical proteinHypothetical protein Reut02005836 (Ralstonia metallidurans CH34)ZP_00271391843101e-141
ORF6551365513-66205231AAGGGGGHypothetical proteinHypothetical protein Reut02005835 (Ralstonia metallidurans CH34)ZP_00271390942301e-129
ORF6620266202-66612137AGGCGAGGHypothetical proteinHypothetical protein Reut02005834 (Ralstonia metallidurans CH34)ZP_00271389961304e-70
ORF6662566625-66984120GAAAGGHypothetical proteinHypothetical protein (Pseudomonas aeruginosa)AAN62147961192e-59
ORF6700167001-6723478GGAGAACAAGHypothetical proteinHypothetical protein Reut02005832 (Ralstonia metallidurans CH34)ZP_00271387100685e-32
ORF6723167231-67614128AGGAATGGHypothetical proteinCOG0643: chemotaxis protein histidine kinase and related kinases (Ralstonia metallidurans CH34)ZP_00271386851262e-52
ORF6780067800-68204+135GGGGAGAHypothetical proteinHypothetical protein Npun02008345 (Nostoc punctiforme PCC 73102)ZP_0010605338911e-07
ORF6824168241-68990250AACGAGGHypothetical proteinHypothetical protein Reut02005852 (Ralstonia metallidurans CH34)ZP_00271362952491e-133
ORF6898768987-71173729GAAGHypothetical protein, VirD4 domainConserved hypothetical protein (Pseudomonas aeruginosa), COG3505AAN62159967300e-00
ORF7117871178-71726183AGGAGAHypothetical proteinHypothetical protein Reut02005854 (Ralstonia metallidurans CH34)ZP_00271364871822e-84
ORF7172371723-72313197GAGGTGAAHypothetical proteinCOG0741: soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) (Ralstonia metallidurans CH34)ZP_00271365871965e-95
ORF7229572295-73014240GGAGCAHypothetical proteinCOG0695: glutaredoxin and related proteins (Ralstonia metallidurans CH34)ZP_00271366882451e-121
ORF7302973029-73679217GGGAGGHypothetical proteinCOG0845: membrane-fusion protein (Ralstonia metallidurans CH34)ZP_00271367802172e-88
ORF7367673676-74296207GAGGHypothetical proteinHypothetical protein Reut02005858 (Ralstonia metallidurans CH34)ZP_00271368871991e-96
ORF7443674436-75305290AAGGAGAGHypothetical proteinHypothetical protein Rgel02003074 (Rubrivivax gelatinosus PM1)ZP_00242828301088e-03
ORF7541975419-77698760GGAGDNA/RNA helicaseConserved hypothetical plasmid protein (Pseudomonas aeruginosa)AAN62165967590e-00
ORF7779877798-78907370AGGAGAHypothetical proteinConserved hypothetical plasmid protein (Pseudomonas aeruginosa)AAN62168973690e-00
ORF7897278972-79622217GAGGAHypothetical proteinHypothetical protein Reut02005863 (Ralstonia metallidurans CH34)ZP_00271373952161e-116
ORF7969979699-7995987AGGAGGAAHypothetical proteinHypothetical protein XF1757 (Xylella fastidiosa 9a5c)NP_29904690862e-39
ORF7997679976-80383136AGGAGGHypothetical proteinHypothetical protein XF1758 (Xylella fastidiosa 9a5c)NP_299047911343e-68
ORF8048080480-80812111GGAGGHypothetical proteinConserved plasmid protein (Xylella fastidiosa 9a5c)NP_299048651062e-33
ORF8090880908-81597230AAGGAGAAHypothetical proteinHypothetical protein Reut02005867 (Ralstonia metallidurans CH34)ZP_00271377872291e-111
ORF8165581655-82572306GGAGAHypothetical proteinHypothetical protein XF1761 (Xylella fastidiosa 9a5c)NP_299050943051e-160
ORF8335083350-84192281GGAGACGAHypothetical proteinHypothetical protein XF1763 (Xylella fastidiosa 9a5c)NP_299052942801e-158
ORF8433884338-84691118AGGAGAHypothetical proteinHypothetical protein XF1764 (Xylella fastidiosa 9a5c)NP_299053831177e-53
ORF8483584835-85647271AAGGAGAHypothetical proteinHypothetical protein (Pseudomonas aeruginosa)AAN62182872741e-134
ORF8593485934-8621293AGGAGHypothetical proteinCOG0528: uridylate kinase (Ralstonia metallidurans CH34)ZP_0027127989921e-43
ORF8631086310-87047246GGAGAAAHypothetical proteinCOG0834: ABC-type amino acid transport/signal transduction systems, periplasmic component/ domain (Ralstonia metallidurans CH34)ZP_00271280862431e-120
ORF8712787127-87939271GAGAGGGAHypothetical proteinHypothetical protein (Pseudomonas aeruginosa)AAN62185802431e-108
ORF8798687986-88378131GGAGGAAHypothetical proteinHypothetical protein XF1771 (Xylella fastidiosa 9a5c)NP_299060981309e-71
ORF8840088400-8861271AAGGAGHypothetical proteinHypothetical protein XF1772 (Xylella fastidiosa 9a5c)NP_299061100701e-33
ORF8924789247-8950185AGGAHypothetical proteinHypothetical protein XF1773 (Xylella fastidiosa 9a5c)NP_29906296845e-40
ORF8974689746-91347534AGGAGADNA methyltransferaseDNA methyltransferase (Xylella fastidiosa 9a5c)NP_299063895390e-00
ORF9188491884-93896671GGATGGADNA topoisomerase IAPutative DNA topoisomerase III (Pseudomonas aeruginosa)AAN62194906760e-00
ORF9417594175-94615147GGAGASingle-stranded-DNA binding proteinCOG0629: single-stranded DNA-binding protein (Ralstonia metallidurans CH34)ZP_00271286891461e-75
ORF94689inrR94689-95216176GAGGACGAATranscriptional regulatorConserved hypothetical protein (Pseudomonas aeruginosa)AAN62196861755e-82
ORF9521395213-95992260GGGCGGHypothetical proteinConserved hypothetical protein (Pseudomonas aeruginosa)AAN62197912631e-131
ORF9632396323-97567415AAGGAHypothetical proteinHypothetical protein Reut02005948 (Ralstonia metallidurans CH34)ZP_00271289814170e-00
ORF9757197571-98131187GAGGGHypothetical proteinCOG0635: coproporphyrinogen III oxidase and related Fe-S oxidoreductases (Ralstonia metallidurans CH34)ZP_00271290901863e-93
ORF9814798147-99799551AAAGGAAHypothetical proteinConserved hypothetical protein (Pseudomonas aeruginosa), COG1475 ParB domainAAN62200825590e-00
ORF9979299792-10004986GGGAGGHypothetical proteinHypothetical protein Reut02004806 (Ralstonia metallidurans CH34)ZP_0027222778893e-33
ORF100033100033-100908292GGAGAGChromosome partioning-related proteinCOG1192: ATPases involved in chromosome partitioning (Ralstonia metallidurans CH34)ZP_00272228932911e-48
ORF100952100952-10116471AGGAGTGATranscriptional regulatorPhage-related protein (Pseudomonas aeruginosa)AAN6220290704e-30
ORF101284101284-102039252AAGGAGAHypothetical proteinHypothetical protein XF1787 (Xylella fastidiosa 9a5c)NP_299075832491e-117
Repeat regionattL102826-102843Left end attachment site
  • a Due to an almost 100% sequence conservation between the clc element and a chromosomal region in B. xenovorans, homologies between the two are not listed.

  • b E values are based on BLASTP results of the nonredundant NCBI database.

  • c ISP, intracellular serine protease.