Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105026
Name   oriT_pC2414-2-KPC in_silico
Organism   Klebsiella pneumoniae strain C2414
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039820 (41625..41748 [+], 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_pC2414-2-KPC
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3517 GenBank   WP_071177725
Name   traI_FA958_RS28615_pC2414-2-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   1564 GenBank   WP_000124981
Name   WP_000124981_pC2414-2-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   1565 GenBank   WP_001254386
Name   WP_001254386_pC2414-2-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   3478 GenBank   WP_015059012
Name   traC_FA958_RS28500_pC2414-2-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   3479 GenBank   WP_021573169
Name   traD_FA958_RS28610_pC2414-2-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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 41053..70289

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FA958_RS28400 (FA958_28590) 36256..36975 + 720 WP_001276217 plasmid SOS inhibition protein A -
FA958_RS30330 37197..37346 + 150 Protein_49 plasmid maintenance protein Mok -
FA958_RS28405 (FA958_28595) 37288..37413 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
FA958_RS30050 37732..38028 - 297 Protein_51 hypothetical protein -
FA958_RS28415 (FA958_28615) 38328..38624 + 297 WP_001272251 hypothetical protein -
FA958_RS28420 (FA958_28620) 38805..39785 + 981 WP_000019473 IS5-like element ISKpn26 family transposase -
FA958_RS28425 (FA958_28625) 39935..40756 + 822 WP_001234445 DUF932 domain-containing protein -
FA958_RS28430 (FA958_28630) 41053..41700 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
FA958_RS28435 (FA958_28635) 41977..42360 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
FA958_RS28440 (FA958_28640) 42551..43237 + 687 WP_015059009 PAS domain-containing protein -
FA958_RS28445 (FA958_28645) 43331..43558 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
FA958_RS28450 (FA958_28650) 43592..43957 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
FA958_RS28455 (FA958_28655) 43972..44283 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
FA958_RS28460 (FA958_28660) 44305..44871 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
FA958_RS28465 (FA958_28665) 44858..45586 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
FA958_RS28470 (FA958_28670) 45586..47013 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
FA958_RS28475 (FA958_28675) 47003..47593 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
FA958_RS28480 (FA958_28680) 47580..47777 + 198 WP_001324648 conjugal transfer protein TrbD -
FA958_RS28485 (FA958_28685) 47789..48040 + 252 WP_001038341 conjugal transfer protein TrbG -
FA958_RS28490 (FA958_28690) 48037..48552 + 516 WP_062955122 type IV conjugative transfer system lipoprotein TraV traV
FA958_RS28495 (FA958_28695) 48687..48908 + 222 WP_001278692 conjugal transfer protein TraR -
FA958_RS28500 (FA958_28700) 49068..51695 + 2628 WP_015059012 type IV secretion system protein TraC virb4
FA958_RS28505 (FA958_28705) 51692..52078 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
FA958_RS28510 (FA958_28710) 52075..52707 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
FA958_RS28515 (FA958_28715) 52704..53696 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
FA958_RS28520 (FA958_28720) 53723..54031 + 309 WP_000412447 hypothetical protein -
FA958_RS28525 (FA958_28725) 54094..54615 + 522 WP_015059014 hypothetical protein -
FA958_RS28530 (FA958_28730) 54642..55280 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
FA958_RS28535 (FA958_28735) 55277..55648 + 372 WP_000056336 hypothetical protein -
FA958_RS28540 (FA958_28740) 55674..56096 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
FA958_RS28545 (FA958_28745) 56093..57943 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FA958_RS28550 (FA958_28750) 57970..58227 + 258 WP_053913405 conjugal transfer protein TrbE -
FA958_RS28555 (FA958_28755) 58214..58963 + 750 WP_072354014 type-F conjugative transfer system pilin assembly protein TraF traF
FA958_RS28560 (FA958_28760) 59124..59360 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
FA958_RS28565 (FA958_28765) 59347..59892 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
FA958_RS28570 (FA958_28770) 59882..60196 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
FA958_RS28575 (FA958_28775) 60150..60542 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
FA958_RS28580 (FA958_28780) 60529..61902 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
FA958_RS28585 (FA958_28785) 61899..64715 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
FA958_RS28590 (FA958_28790) 64748..65077 + 330 WP_227650653 hypothetical protein -
FA958_RS28595 (FA958_28800) 65095..66063 + 969 WP_013362812 IS5-like element IS903B family transposase -
FA958_RS28600 (FA958_28810) 66360..67091 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
FA958_RS28605 (FA958_28815) 67294..68031 + 738 WP_015059020 hypothetical protein -
FA958_RS28610 (FA958_28820) 68082..70289 + 2208 WP_021573169 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5464 GenBank   NZ_CP039820
Plasmid name   pC2414-2-KPC Incompatibility group   IncR
Plasmid size   172001 bp Coordinate of oriT [Strand]   41625..41748 [+]
Host baterium   Klebsiella pneumoniae strain C2414

Cargo genes

Drug resistance gene   blaCTX-M-65, fosA3, blaTEM-1B, rmtB, blaKPC-2, catA2
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9