Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118058
Name   oriT_pC262205-KPC_101k in_silico
Organism   Klebsiella aerogenes strain C262205
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP139413 (50515..50638 [+], 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_pC262205-KPC_101k
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11459 GenBank   WP_015059021
Name   traI_SM912_RS26695_pC262205-KPC_101k insolico UniProt ID   A0A0X8XR69
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192132.90 Da        Isoelectric Point: 6.0788

>WP_015059021.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Gammaproteobacteria]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAENRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   6581 GenBank   WP_000124981
Name   WP_000124981_pC262205-KPC_101k 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   6582 GenBank   WP_001254386
Name   WP_001254386_pC262205-KPC_101k 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   13389 GenBank   WP_015059012
Name   traC_SM912_RS26585_pC262205-KPC_101k 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   13390 GenBank   WP_320906520
Name   traD_SM912_RS26690_pC262205-KPC_101k 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: 83523.21 Da        Isoelectric Point: 5.1029

>WP_320906520.1 type IV conjugative transfer system coupling protein TraD [Klebsiella aerogenes]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMVQQLPPGISESGEVVDMAAYEAWQ
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: 49943..78113

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SM912_RS26480 (SM912_26480) 45915..46349 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
SM912_RS26485 (SM912_26485) 46346..47065 + 720 WP_001276217 plasmid SOS inhibition protein A -
SM912_RS26490 (SM912_26490) 47287..47436 + 150 Protein_62 plasmid maintenance protein Mok -
SM912_RS26495 (SM912_26495) 47378..47503 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
SM912_RS26500 (SM912_26500) 47822..48118 - 297 Protein_64 hypothetical protein -
SM912_RS26505 (SM912_26505) 48418..48714 + 297 WP_001272251 hypothetical protein -
SM912_RS26510 (SM912_26510) 48825..49646 + 822 WP_001234445 DUF932 domain-containing protein -
SM912_RS26515 (SM912_26515) 49943..50590 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
SM912_RS26520 (SM912_26520) 50867..51250 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
SM912_RS26525 (SM912_26525) 51441..52127 + 687 WP_015059009 PAS domain-containing protein -
SM912_RS26530 (SM912_26530) 52221..52448 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
SM912_RS26535 (SM912_26535) 52482..52847 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
SM912_RS26540 (SM912_26540) 52862..53173 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
SM912_RS26545 (SM912_26545) 53195..53761 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
SM912_RS26550 (SM912_26550) 53748..54476 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
SM912_RS26555 (SM912_26555) 54476..55903 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
SM912_RS26560 (SM912_26560) 55893..56483 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
SM912_RS26565 (SM912_26565) 56470..56667 + 198 WP_001324648 conjugal transfer protein TrbD -
SM912_RS26570 (SM912_26570) 56679..56930 + 252 WP_001038341 conjugal transfer protein TrbG -
SM912_RS26575 (SM912_26575) 56927..57442 + 516 WP_062955122 type IV conjugative transfer system lipoprotein TraV traV
SM912_RS26580 (SM912_26580) 57577..57798 + 222 WP_001278692 conjugal transfer protein TraR -
SM912_RS26585 (SM912_26585) 57958..60585 + 2628 WP_015059012 type IV secretion system protein TraC virb4
SM912_RS26590 (SM912_26590) 60582..60968 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
SM912_RS26595 (SM912_26595) 60965..61597 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
SM912_RS26600 (SM912_26600) 61594..62586 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
SM912_RS26605 (SM912_26605) 62613..62921 + 309 WP_000412447 hypothetical protein -
SM912_RS26610 (SM912_26610) 62984..63505 + 522 WP_015059014 hypothetical protein -
SM912_RS26615 (SM912_26615) 63532..64170 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
SM912_RS26620 (SM912_26620) 64167..64538 + 372 WP_000056336 hypothetical protein -
SM912_RS26625 (SM912_26625) 64564..64986 + 423 WP_001229309 HNH endonuclease -
SM912_RS26630 (SM912_26630) 64983..66833 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SM912_RS26635 (SM912_26635) 66860..67117 + 258 WP_053913405 conjugal transfer protein TrbE -
SM912_RS26640 (SM912_26640) 67104..67853 + 750 WP_072354014 type-F conjugative transfer system pilin assembly protein TraF traF
SM912_RS26645 (SM912_26645) 68014..68250 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
SM912_RS26650 (SM912_26650) 68237..68782 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SM912_RS26655 (SM912_26655) 68772..69086 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
SM912_RS26660 (SM912_26660) 69040..69432 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
SM912_RS26665 (SM912_26665) 69419..70792 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
SM912_RS26670 (SM912_26670) 70789..73605 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
SM912_RS26675 (SM912_26675) 73638..74159 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
SM912_RS26680 (SM912_26680) 74184..74915 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
SM912_RS26685 (SM912_26685) 75118..75855 + 738 WP_015059020 hypothetical protein -
SM912_RS26690 (SM912_26690) 75906..78113 + 2208 WP_320906520 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18491 GenBank   NZ_CP139413
Plasmid name   pC262205-KPC_101k Incompatibility group   IncFII
Plasmid size   101621 bp Coordinate of oriT [Strand]   50515..50638 [+]
Host baterium   Klebsiella aerogenes strain C262205

Cargo genes

Drug resistance gene   blaKPC-2, catA2, rmtB
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -