Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101432
Name   oriT_pCRE31_3 in_silico
Organism   Klebsiella pneumoniae strain S30_CRE31
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAHBNY010000006 (69745..70096 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 70..75, 80..85  (ATAAAT..ATTTAT)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_pCRE31_3
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGATTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1299 GenBank   WP_046788513
Name   traI_KIN66_RS27215_pCRE31_3 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191885.66 Da        Isoelectric Point: 5.7009

>WP_046788513.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRSSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQILITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSYDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGIHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRIVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIHPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERDRAAITEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   460 GenBank   WP_001151524
Name   WP_001151524_pCRE31_3 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22

ID   461 GenBank   WP_001309237
Name   WP_001309237_pCRE31_3 insolico UniProt ID   A0A5W1N5T0
Length   131 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 131 a.a.        Molecular weight: 15183.38 Da        Isoelectric Point: 9.9240

>WP_001309237.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(70-117)

TraY domain (TraY)

(16-59)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W1N5T0


T4CP

ID   913 GenBank   WP_050195440
Name   traC_KIN66_RS27135_pCRE31_3 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: 99240.86 Da        Isoelectric Point: 5.8486

>WP_050195440.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPFEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-763)

  Protein structure



No available structure.



ID   914 GenBank   WP_000009364
Name   traD_KIN66_RS27210_pCRE31_3 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: 83567.22 Da        Isoelectric Point: 5.0524

>WP_000009364.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
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: 69174..94444

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KIN66_RS27030 (KIN66_26930) 65137..65571 + 435 WP_000845901 conjugation system SOS inhibitor PsiB -
KIN66_RS27035 (KIN66_26935) 65568..66330 + 763 Protein_86 plasmid SOS inhibition protein A -
KIN66_RS27040 (KIN66_26940) 66509..66721 + 213 WP_001825191 plasmid maintenance protein Mok -
KIN66_RS27045 66945..67175 + 231 WP_001426396 hypothetical protein -
KIN66_RS27050 67173..67346 - 174 Protein_89 hypothetical protein -
KIN66_RS27055 (KIN66_26945) 67416..67622 + 207 WP_000547939 hypothetical protein -
KIN66_RS27060 (KIN66_26950) 67647..67934 + 288 WP_000107535 hypothetical protein -
KIN66_RS27065 (KIN66_26955) 68056..68877 + 822 WP_001234469 DUF932 domain-containing protein -
KIN66_RS27070 (KIN66_26960) 69174..69764 - 591 WP_000252680 transglycosylase SLT domain-containing protein virB1
KIN66_RS27075 (KIN66_26965) 70097..70480 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
KIN66_RS27080 (KIN66_26970) 70667..71356 + 690 WP_000283380 conjugal transfer transcriptional regulator TraJ -
KIN66_RS27085 (KIN66_26975) 71466..71861 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
KIN66_RS27090 (KIN66_26980) 71894..72253 + 360 WP_000994781 type IV conjugative transfer system pilin TraA -
KIN66_RS27095 (KIN66_26985) 72268..72579 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
KIN66_RS27100 (KIN66_26990) 72601..73167 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
KIN66_RS27105 (KIN66_26995) 73154..73882 + 729 WP_001230798 type-F conjugative transfer system secretin TraK traK
KIN66_RS27110 (KIN66_27000) 73882..75309 + 1428 WP_000146657 F-type conjugal transfer pilus assembly protein TraB traB
KIN66_RS27115 (KIN66_27005) 75299..75889 + 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
KIN66_RS27120 (KIN66_27010) 75876..76193 + 318 WP_001057308 conjugal transfer protein TrbD -
KIN66_RS27125 (KIN66_27015) 76193..76633 + 441 WP_268202835 type IV conjugative transfer system lipoprotein TraV traV
KIN66_RS27130 (KIN66_27020) 76768..76989 + 222 WP_000064029 conjugal transfer protein TraR -
KIN66_RS27135 (KIN66_27025) 77149..79776 + 2628 WP_050195440 type IV secretion system protein TraC virb4
KIN66_RS27140 (KIN66_27030) 79773..80159 + 387 WP_000214096 type-F conjugative transfer system protein TrbI -
KIN66_RS27145 (KIN66_27035) 80156..80788 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
KIN66_RS27150 (KIN66_27040) 80785..81777 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
KIN66_RS27155 (KIN66_27045) 81786..82424 + 639 WP_000777702 type-F conjugative transfer system pilin assembly protein TrbC trbC
KIN66_RS27160 (KIN66_27050) 82421..84271 + 1851 WP_032283054 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KIN66_RS27165 (KIN66_27055) 84298..84555 + 258 WP_000864341 conjugal transfer protein TrbE -
KIN66_RS27170 (KIN66_27060) 84542..85291 + 750 WP_077942049 type-F conjugative transfer system pilin assembly protein TraF traF
KIN66_RS27175 (KIN66_27065) 85452..85688 + 237 WP_001346259 type-F conjugative transfer system pilin chaperone TraQ -
KIN66_RS27180 (KIN66_27070) 85675..86220 + 546 WP_044804936 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KIN66_RS27185 (KIN66_27075) 86150..86512 + 363 WP_072078458 P-type conjugative transfer protein TrbJ -
KIN66_RS27190 (KIN66_27080) 86512..87885 + 1374 WP_050195262 conjugal transfer pilus assembly protein TraH traH
KIN66_RS27195 (KIN66_27085) 87882..90704 + 2823 WP_046788512 conjugal transfer mating-pair stabilization protein TraG traG
KIN66_RS27200 (KIN66_27090) 90719..91222 + 504 WP_000605510 hypothetical protein -
KIN66_RS27205 (KIN66_27095) 91254..91985 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
KIN66_RS27210 (KIN66_27100) 92237..94444 + 2208 WP_000009364 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1876 GenBank   NZ_JAHBNY010000006
Plasmid name   pCRE31_3 Incompatibility group   IncFII
Plasmid size   103447 bp Coordinate of oriT [Strand]   69745..70096 [+]
Host baterium   Klebsiella pneumoniae strain S30_CRE31

Cargo genes

Drug resistance gene   floR
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -