Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103507
Name   oriT_pCRKP-30_KPC in_silico
Organism   Klebsiella pneumoniae strain CRKP-30
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP102634 (115343..115466 [+], 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-30_KPC
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2628 GenBank   WP_071177725
Name   traI_NVS92_RS01005_pCRKP-30_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   1110 GenBank   WP_000124981
Name   WP_000124981_pCRKP-30_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   1111 GenBank   WP_001254386
Name   WP_001254386_pCRKP-30_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   2435 GenBank   WP_015059012
Name   traC_NVS92_RS00895_pCRKP-30_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.



ID   2436 GenBank   WP_000009363
Name   traD_NVS92_RS01000_pCRKP-30_KPC insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84259.95 Da        Isoelectric Point: 5.0504

>WP_000009363.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 114771..142959

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NVS92_RS00790 (NVS92_00790) 110743..111177 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
NVS92_RS00795 (NVS92_00795) 111174..111893 + 720 WP_001276217 plasmid SOS inhibition protein A -
NVS92_RS00800 (NVS92_00800) 112115..112264 + 150 Protein_161 plasmid maintenance protein Mok -
NVS92_RS00805 (NVS92_00805) 112206..112331 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NVS92_RS00810 (NVS92_00810) 112650..112946 - 297 Protein_163 hypothetical protein -
NVS92_RS00815 (NVS92_00815) 113246..113542 + 297 WP_001272251 hypothetical protein -
NVS92_RS00820 (NVS92_00820) 113653..114474 + 822 WP_001234445 DUF932 domain-containing protein -
NVS92_RS00825 (NVS92_00825) 114771..115418 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
NVS92_RS00830 (NVS92_00830) 115695..116078 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
NVS92_RS00835 (NVS92_00835) 116269..116955 + 687 WP_015059009 PAS domain-containing protein -
NVS92_RS00840 (NVS92_00840) 117049..117276 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
NVS92_RS00845 (NVS92_00845) 117310..117675 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
NVS92_RS00850 (NVS92_00850) 117690..118001 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
NVS92_RS00855 (NVS92_00855) 118023..118589 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
NVS92_RS00860 (NVS92_00860) 118576..119304 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
NVS92_RS00865 (NVS92_00865) 119304..120731 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
NVS92_RS00870 (NVS92_00870) 120721..121311 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
NVS92_RS00875 (NVS92_00875) 121298..121495 + 198 WP_001324648 conjugal transfer protein TrbD -
NVS92_RS00880 (NVS92_00880) 121507..121758 + 252 WP_001038341 conjugal transfer protein TrbG -
NVS92_RS00885 (NVS92_00885) 121755..122270 + 516 WP_062955122 type IV conjugative transfer system lipoprotein TraV traV
NVS92_RS00890 (NVS92_00890) 122405..122626 + 222 WP_001278692 conjugal transfer protein TraR -
NVS92_RS00895 (NVS92_00895) 122786..125413 + 2628 WP_015059012 type IV secretion system protein TraC virb4
NVS92_RS00900 (NVS92_00900) 125410..125796 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
NVS92_RS00905 (NVS92_00905) 125793..126425 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
NVS92_RS00910 (NVS92_00910) 126422..127414 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NVS92_RS00915 (NVS92_00915) 127441..127749 + 309 WP_000412447 hypothetical protein -
NVS92_RS00920 (NVS92_00920) 127812..128333 + 522 WP_015059014 hypothetical protein -
NVS92_RS00925 (NVS92_00925) 128360..128998 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
NVS92_RS00930 (NVS92_00930) 128995..129366 + 372 WP_000056336 hypothetical protein -
NVS92_RS00935 (NVS92_00935) 129392..129814 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
NVS92_RS00940 (NVS92_00940) 129811..131661 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NVS92_RS00945 (NVS92_00945) 131688..131945 + 258 WP_053913405 conjugal transfer protein TrbE -
NVS92_RS00950 (NVS92_00950) 131932..132681 + 750 WP_202157635 type-F conjugative transfer system pilin assembly protein TraF traF
NVS92_RS00955 (NVS92_00955) 132842..133078 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
NVS92_RS00960 (NVS92_00960) 133065..133610 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NVS92_RS00965 (NVS92_00965) 133600..133914 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
NVS92_RS00970 (NVS92_00970) 133868..134260 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
NVS92_RS00975 (NVS92_00975) 134247..135620 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
NVS92_RS00980 (NVS92_00980) 135617..138433 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
NVS92_RS00985 (NVS92_00985) 138466..138987 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
NVS92_RS00990 (NVS92_00990) 139012..139743 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
NVS92_RS00995 (NVS92_00995) 139946..140683 + 738 WP_015059020 hypothetical protein -
NVS92_RS01000 (NVS92_01000) 140734..142959 + 2226 WP_000009363 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3950 GenBank   NZ_CP102634
Plasmid name   pCRKP-30_KPC Incompatibility group   IncFII
Plasmid size   158524 bp Coordinate of oriT [Strand]   115343..115466 [+]
Host baterium   Klebsiella pneumoniae strain CRKP-30

Cargo genes

Drug resistance gene   blaTEM-1B, rmtB, blaKPC-2
Virulence gene   -
Metal resistance gene   merR, merT, merP, merE, merD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9