Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103516
Name   oriT_pCRKP-27_KPC in_silico
Organism   Klebsiella pneumoniae strain CRKP-27
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP102632 (81594..81717 [+], 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-27_KPC
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2632 GenBank   WP_071177725
Name   traI_NVS94_RS01645_pCRKP-27_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   1113 GenBank   WP_000124981
Name   WP_000124981_pCRKP-27_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   1114 GenBank   WP_001254386
Name   WP_001254386_pCRKP-27_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   2440 GenBank   WP_021573169
Name   traD_NVS94_RS01650_pCRKP-27_KPC insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83553.19 Da        Isoelectric Point: 5.0504

>WP_021573169.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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   2441 GenBank   WP_015059012
Name   traC_NVS94_RS01755_pCRKP-27_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: 81022..114442

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NVS94_RS01550 (NVS94_01550) 76997..77431 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
NVS94_RS01555 (NVS94_01555) 77428..78189 + 762 Protein_114 plasmid SOS inhibition protein A -
NVS94_RS01560 (NVS94_01560) 78368..78517 + 150 Protein_115 plasmid maintenance protein Mok -
NVS94_RS01565 (NVS94_01565) 78459..78584 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NVS94_RS01570 (NVS94_01570) 78903..79199 - 297 Protein_117 hypothetical protein -
NVS94_RS01575 (NVS94_01575) 79153..79455 - 303 WP_258172015 hypothetical protein -
NVS94_RS01580 (NVS94_01580) 79496..79792 + 297 WP_001272251 hypothetical protein -
NVS94_RS01585 (NVS94_01585) 79903..80724 + 822 WP_001234445 DUF932 domain-containing protein -
NVS94_RS01590 (NVS94_01590) 81022..81669 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
NVS94_RS01595 (NVS94_01595) 81946..82329 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
NVS94_RS01600 (NVS94_01600) 82520..83206 + 687 WP_015059009 PAS domain-containing protein -
NVS94_RS01605 (NVS94_01605) 83300..83527 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
NVS94_RS01610 (NVS94_01610) 83561..83926 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
NVS94_RS01615 (NVS94_01615) 83941..84252 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
NVS94_RS01620 (NVS94_01620) 84274..84840 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
NVS94_RS01625 (NVS94_01625) 84827..85555 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
NVS94_RS01630 (NVS94_01630) 85555..86982 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
NVS94_RS01635 (NVS94_01635) 86972..87319 + 348 Protein_130 conjugal transfer pilus-stabilizing protein TraP -
NVS94_RS01640 (NVS94_01640) 87383..88087 + 705 WP_001067855 IS6-like element IS26 family transposase -
NVS94_RS01645 (NVS94_01645) 88121..93256 - 5136 WP_071177725 conjugative transfer relaxase/helicase TraI -
NVS94_RS01650 (NVS94_01650) 93256..95463 - 2208 WP_021573169 type IV conjugative transfer system coupling protein TraD virb4
NVS94_RS01655 (NVS94_01655) 95514..96251 - 738 WP_015059020 hypothetical protein -
NVS94_RS01660 (NVS94_01660) 96454..97185 - 732 WP_021559024 conjugal transfer complement resistance protein TraT -
NVS94_RS01665 (NVS94_01665) 97210..97731 - 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
NVS94_RS01670 (NVS94_01670) 97764..100580 - 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
NVS94_RS01675 (NVS94_01675) 100577..101950 - 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
NVS94_RS01680 (NVS94_01680) 101937..102329 - 393 WP_000126338 F-type conjugal transfer protein TrbF -
NVS94_RS01685 (NVS94_01685) 102283..102597 - 315 WP_001384255 P-type conjugative transfer protein TrbJ -
NVS94_RS01690 (NVS94_01690) 102587..103132 - 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NVS94_RS01695 (NVS94_01695) 103119..103355 - 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
NVS94_RS01700 (NVS94_01700) 103516..104265 - 750 WP_072354014 type-F conjugative transfer system pilin assembly protein TraF traF
NVS94_RS01705 (NVS94_01705) 104252..104509 - 258 WP_053913405 conjugal transfer protein TrbE -
NVS94_RS01710 (NVS94_01710) 104536..106386 - 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NVS94_RS01715 (NVS94_01715) 106383..106805 - 423 WP_001229309 HNH endonuclease signature motif containing protein -
NVS94_RS01720 (NVS94_01720) 106831..107202 - 372 WP_000056336 hypothetical protein -
NVS94_RS01725 (NVS94_01725) 107199..107837 - 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
NVS94_RS01730 (NVS94_01730) 107864..108385 - 522 WP_015059014 hypothetical protein -
NVS94_RS01735 (NVS94_01735) 108448..108756 - 309 WP_000412447 hypothetical protein -
NVS94_RS01740 (NVS94_01740) 108783..109775 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NVS94_RS01745 (NVS94_01745) 109772..110404 - 633 WP_001203735 type-F conjugative transfer system protein TraW traW
NVS94_RS01750 (NVS94_01750) 110401..110787 - 387 WP_015059013 type-F conjugative transfer system protein TrbI -
NVS94_RS01755 (NVS94_01755) 110784..113411 - 2628 WP_015059012 type IV secretion system protein TraC virb4
NVS94_RS01760 (NVS94_01760) 113571..113735 - 165 WP_096892147 conjugal transfer protein TraR -
NVS94_RS01765 (NVS94_01765) 113675..113818 + 144 WP_258172016 hypothetical protein -
NVS94_RS01770 (NVS94_01770) 113927..114442 - 516 WP_062955122 type IV conjugative transfer system lipoprotein TraV traV
NVS94_RS01775 (NVS94_01775) 114439..114690 - 252 WP_001038341 conjugal transfer protein TrbG -
NVS94_RS01780 (NVS94_01780) 114702..114899 - 198 WP_001324648 conjugal transfer protein TrbD -
NVS94_RS01785 (NVS94_01785) 114886..115134 - 249 Protein_160 conjugal transfer protein TraP -
NVS94_RS01790 (NVS94_01790) 115189..115893 - 705 WP_001067855 IS6-like element IS26 family transposase -
NVS94_RS01795 (NVS94_01795) 116033..116188 + 156 WP_013213988 hypothetical protein -
NVS94_RS01800 (NVS94_01800) 116234..116530 + 297 WP_013213987 transcriptional regulator -
NVS94_RS01805 (NVS94_01805) 116634..117515 + 882 Protein_164 IS1182-like element ISKpn6 family transposase -
NVS94_RS01810 (NVS94_01810) 117765..118646 - 882 WP_004199234 carbapenem-hydrolyzing class A beta-lactamase KPC-2 -

Host bacterium

ID   3959 GenBank   NZ_CP102632
Plasmid name   pCRKP-27_KPC Incompatibility group   IncFII
Plasmid size   153917 bp Coordinate of oriT [Strand]   81594..81717 [+]
Host baterium   Klebsiella pneumoniae strain CRKP-27

Cargo genes

Drug resistance gene   fosA3, blaTEM-1B, rmtB, blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9