Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117766
Name   oriT_pPinheadLarry_05 in_silico
Organism   Klebsiella quasipneumoniae strain Pinhead Larry
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP065472 (51007..51130 [-], 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_pPinheadLarry_05
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11293 GenBank   WP_015059123
Name   traI_I5M56_RS26195_pPinheadLarry_05 insolico UniProt ID   I1WZQ7
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191914.74 Da        Isoelectric Point: 6.1060

>WP_015059123.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

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

(575-627)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   6518 GenBank   WP_001254386
Name   WP_001254386_pPinheadLarry_05 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

ID   6519 GenBank   WP_000124981
Name   WP_000124981_pPinheadLarry_05 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


T4CP

ID   13188 GenBank   WP_000069764
Name   traC_I5M56_RS26280_pPinheadLarry_05 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99302.93 Da        Isoelectric Point: 5.8486

>WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 28582..51702

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I5M56_RS26720 24854..25054 - 201 WP_001408788 hypothetical protein -
I5M56_RS26200 (I5M56_26200) 25121..27078 - 1958 Protein_29 type IV conjugative transfer system coupling protein TraD -
I5M56_RS26205 (I5M56_26205) 27331..28062 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
I5M56_RS26210 (I5M56_26210) 28076..28585 - 510 WP_031943494 conjugal transfer entry exclusion protein TraS -
I5M56_RS26215 (I5M56_26215) 28582..31407 - 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
I5M56_RS26220 (I5M56_26220) 31404..32780 - 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
I5M56_RS26225 (I5M56_26225) 32777..33139 - 363 WP_194425986 P-type conjugative transfer protein TrbJ -
I5M56_RS26230 (I5M56_26230) 33069..33614 - 546 WP_000059821 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
I5M56_RS26235 (I5M56_26235) 33601..33885 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
I5M56_RS26240 (I5M56_26240) 34004..34351 - 348 WP_001287891 conjugal transfer protein TrbA -
I5M56_RS26245 (I5M56_26245) 34367..35110 - 744 WP_001430248 type-F conjugative transfer system pilin assembly protein TraF traF
I5M56_RS26250 (I5M56_26250) 35103..35360 - 258 WP_000864352 conjugal transfer protein TrbE -
I5M56_RS26255 (I5M56_26255) 35387..37195 - 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
I5M56_RS26260 (I5M56_26260) 37192..37830 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
I5M56_RS26265 (I5M56_26265) 37839..38831 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
I5M56_RS26270 (I5M56_26270) 38828..39460 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
I5M56_RS26275 (I5M56_26275) 39457..39843 - 387 WP_172686544 type-F conjugative transfer system protein TrbI -
I5M56_RS26280 (I5M56_26280) 39840..42470 - 2631 WP_000069764 type IV secretion system protein TraC virb4
I5M56_RS26285 (I5M56_26285) 42596..42958 - 363 WP_000836675 hypothetical protein -
I5M56_RS26290 (I5M56_26290) 42986..43200 - 215 Protein_47 hypothetical protein -
I5M56_RS26295 (I5M56_26295) 43280..43756 - 477 WP_194425987 hypothetical protein -
I5M56_RS26300 (I5M56_26300) 43749..43970 - 222 WP_001278695 conjugal transfer protein TraR -
I5M56_RS26305 (I5M56_26305) 44105..44620 - 516 WP_015059130 type IV conjugative transfer system lipoprotein TraV traV
I5M56_RS26310 (I5M56_26310) 44617..44868 - 252 WP_001038342 conjugal transfer protein TrbG -
I5M56_RS26315 (I5M56_26315) 44861..45181 - 321 WP_265087546 conjugal transfer protein TrbD virb4
I5M56_RS26320 (I5M56_26320) 45168..45758 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
I5M56_RS26325 (I5M56_26325) 45748..47175 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
I5M56_RS26330 (I5M56_26330) 47175..47903 - 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
I5M56_RS26335 (I5M56_26335) 47890..48456 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
I5M56_RS26340 (I5M56_26340) 48478..48789 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
I5M56_RS26345 (I5M56_26345) 48804..49163 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
I5M56_RS26350 (I5M56_26350) 49197..49424 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
I5M56_RS26355 (I5M56_26355) 49518..50204 - 687 WP_000332484 PAS domain-containing protein -
I5M56_RS26360 (I5M56_26360) 50395..50778 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
I5M56_RS26365 (I5M56_26365) 51055..51702 + 648 WP_031943493 transglycosylase SLT domain-containing protein virB1
I5M56_RS26370 (I5M56_26370) 51999..52820 - 822 WP_001234469 DUF932 domain-containing protein -
I5M56_RS26375 (I5M56_26375) 52938..53225 - 288 WP_000107544 hypothetical protein -
I5M56_RS26725 53250..53456 - 207 WP_000547968 hypothetical protein -
I5M56_RS26730 53526..53699 + 174 Protein_66 hypothetical protein -
I5M56_RS26735 53697..53927 - 231 WP_001426396 hypothetical protein -
I5M56_RS26380 (I5M56_26380) 54147..54272 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
I5M56_RS26740 54214..54363 - 150 Protein_69 plasmid maintenance protein Mok -
I5M56_RS26385 (I5M56_26385) 54585..55304 - 720 WP_013362833 plasmid SOS inhibition protein A -
I5M56_RS26390 (I5M56_26390) 55301..55735 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   18199 GenBank   NZ_CP065472
Plasmid name   pPinheadLarry_05 Incompatibility group   IncFII
Plasmid size   62418 bp Coordinate of oriT [Strand]   51007..51130 [-]
Host baterium   Klebsiella quasipneumoniae strain Pinhead Larry

Cargo genes

Drug resistance gene   ant(3'')-Ia, sul3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -