Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102498
Name   oriT_pCRKP-12_KPC in_silico
Organism   Klebsiella pneumoniae strain CRKP-12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JANPXN010000003 (40425..40548 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pCRKP-12_KPC
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1855 GenBank   WP_071177725
Name   traI_NVV51_RS27895_pCRKP-12_KPC insolico UniProt ID   A0A7G3L5Q3
Length   1711 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1711 a.a.        Molecular weight: 186716.81 Da        Isoelectric Point: 6.1728

>WP_071177725.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAENRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALLQS

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   766 GenBank   WP_000124981
Name   WP_000124981_pCRKP-12_KPC insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   767 GenBank   WP_001254386
Name   WP_001254386_pCRKP-12_KPC insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   1449 GenBank   WP_059274178
Name   traD_NVV51_RS27900_pCRKP-12_KPC insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83906.57 Da        Isoelectric Point: 5.0504

>WP_059274178.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   1450 GenBank   WP_015059012
Name   traC_NVV51_RS28005_pCRKP-12_KPC insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39853..73282

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NVV51_RS27805 (NVV51_27805) 35825..36259 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
NVV51_RS27810 (NVV51_27810) 36256..36975 + 720 WP_001276217 plasmid SOS inhibition protein A -
NVV51_RS27815 (NVV51_27815) 37197..37346 + 150 Protein_50 plasmid maintenance protein Mok -
NVV51_RS27820 (NVV51_27820) 37288..37413 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NVV51_RS27825 (NVV51_27825) 37732..38028 - 297 Protein_52 hypothetical protein -
NVV51_RS27830 (NVV51_27830) 38328..38624 + 297 WP_001272251 hypothetical protein -
NVV51_RS27835 (NVV51_27835) 38735..39556 + 822 WP_001234445 DUF932 domain-containing protein -
NVV51_RS27840 (NVV51_27840) 39853..40500 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
NVV51_RS27845 (NVV51_27845) 40777..41160 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
NVV51_RS27850 (NVV51_27850) 41351..42037 + 687 WP_015059009 PAS domain-containing protein -
NVV51_RS27855 (NVV51_27855) 42131..42358 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
NVV51_RS27860 (NVV51_27860) 42392..42757 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
NVV51_RS27865 (NVV51_27865) 42772..43083 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
NVV51_RS27870 (NVV51_27870) 43105..43671 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
NVV51_RS27875 (NVV51_27875) 43658..44386 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
NVV51_RS27880 (NVV51_27880) 44386..45813 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
NVV51_RS27885 (NVV51_27885) 45803..46150 + 348 Protein_64 conjugal transfer pilus-stabilizing protein TraP -
NVV51_RS27890 (NVV51_27890) 46214..46918 + 705 WP_001067855 IS6-like element IS26 family transposase -
NVV51_RS27895 (NVV51_27895) 46952..52087 - 5136 WP_071177725 conjugative transfer relaxase/helicase TraI -
NVV51_RS27900 (NVV51_27900) 52087..54303 - 2217 WP_059274178 type IV conjugative transfer system coupling protein TraD virb4
NVV51_RS27905 (NVV51_27905) 54354..55091 - 738 WP_015059020 hypothetical protein -
NVV51_RS27910 (NVV51_27910) 55294..56025 - 732 WP_021559024 conjugal transfer complement resistance protein TraT -
NVV51_RS27915 (NVV51_27915) 56050..56571 - 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
NVV51_RS27920 (NVV51_27920) 56604..59420 - 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
NVV51_RS27925 (NVV51_27925) 59417..60790 - 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
NVV51_RS27930 (NVV51_27930) 60777..61169 - 393 WP_000126338 F-type conjugal transfer protein TrbF -
NVV51_RS27935 (NVV51_27935) 61123..61437 - 315 WP_001384255 P-type conjugative transfer protein TrbJ -
NVV51_RS27940 (NVV51_27940) 61427..61972 - 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NVV51_RS27945 (NVV51_27945) 61959..62195 - 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
NVV51_RS27950 (NVV51_27950) 62356..63105 - 750 WP_072354014 type-F conjugative transfer system pilin assembly protein TraF traF
NVV51_RS27955 (NVV51_27955) 63092..63349 - 258 WP_053913405 conjugal transfer protein TrbE -
NVV51_RS27960 (NVV51_27960) 63376..65226 - 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NVV51_RS27965 (NVV51_27965) 65223..65645 - 423 WP_001229309 HNH endonuclease signature motif containing protein -
NVV51_RS27970 (NVV51_27970) 65671..66042 - 372 WP_000056336 hypothetical protein -
NVV51_RS27975 (NVV51_27975) 66039..66677 - 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
NVV51_RS27980 (NVV51_27980) 66704..67225 - 522 WP_015059014 hypothetical protein -
NVV51_RS27985 (NVV51_27985) 67288..67596 - 309 WP_000412447 hypothetical protein -
NVV51_RS27990 (NVV51_27990) 67623..68615 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NVV51_RS27995 (NVV51_27995) 68612..69244 - 633 WP_001203735 type-F conjugative transfer system protein TraW traW
NVV51_RS28000 (NVV51_28000) 69241..69627 - 387 WP_015059013 type-F conjugative transfer system protein TrbI -
NVV51_RS28005 (NVV51_28005) 69624..72251 - 2628 WP_015059012 type IV secretion system protein TraC virb4
NVV51_RS28010 (NVV51_28010) 72411..72632 - 222 WP_001278692 conjugal transfer protein TraR -
NVV51_RS28015 (NVV51_28015) 72767..73282 - 516 WP_062955122 type IV conjugative transfer system lipoprotein TraV traV
NVV51_RS28020 (NVV51_28020) 73279..73530 - 252 WP_001038341 conjugal transfer protein TrbG -
NVV51_RS28025 (NVV51_28025) 73542..73739 - 198 WP_001324648 conjugal transfer protein TrbD -
NVV51_RS28030 (NVV51_28030) 73726..73974 - 249 Protein_93 conjugal transfer protein TraP -
NVV51_RS28035 (NVV51_28035) 74029..74733 - 705 WP_001067855 IS6-like element IS26 family transposase -
NVV51_RS28040 (NVV51_28040) 74873..75028 + 156 WP_013213988 hypothetical protein -
NVV51_RS28045 (NVV51_28045) 75074..75370 + 297 WP_013213987 transcriptional regulator -
NVV51_RS28050 (NVV51_28050) 75474..76355 + 882 Protein_97 IS1182-like element ISKpn6 family transposase -
NVV51_RS28055 (NVV51_28055) 76605..77486 - 882 WP_004199234 carbapenem-hydrolyzing class A beta-lactamase KPC-2 -

Host bacterium

ID   2942 GenBank   NZ_JANPXN010000003
Plasmid name   pCRKP-12_KPC Incompatibility group   IncFII
Plasmid size   116229 bp Coordinate of oriT [Strand]   40425..40548 [+]
Host baterium   Klebsiella pneumoniae strain CRKP-12

Cargo genes

Drug resistance gene   blaCTX-M-65, fosA3, blaTEM-1B, rmtB, blaKPC-2, catA2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -