Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102908
Name   oriT_pDT1 in_silico
Organism   Klebsiella pneumoniae strain DT1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP019078 (12641..12746 [+], 106 nt)
oriT length   106 nt
IRs (inverted repeats)      30..35, 41..46  (CCGCCG..CGGCGG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 106 nt

>oriT_pDT1
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2185 GenBank   WP_004187323
Name   Relaxase_BVU42_RS25645_pDT1 insolico UniProt ID   A0A3U8KUL3
Length   659 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 659 a.a.        Molecular weight: 75179.89 Da        Isoelectric Point: 9.9948

>WP_004187323.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(86-334)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U8KUL3


T4CP

ID   1855 GenBank   WP_004206885
Name   t4cp2_BVU42_RS25760_pDT1 insolico UniProt ID   _
Length   695 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 695 a.a.        Molecular weight: 79538.91 Da        Isoelectric Point: 4.8317

>WP_004206885.1 MULTISPECIES: conjugal transfer protein TrbC [Enterobacterales]
MQQESVDSKKVLRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15542..42885

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BVU42_RS25625 (BVU42_27245) 10627..10938 + 312 WP_004187333 hypothetical protein -
BVU42_RS25630 (BVU42_27250) 11071..11607 + 537 WP_036970776 hypothetical protein -
BVU42_RS25635 (BVU42_27255) 12108..12473 - 366 WP_015586046 hypothetical protein -
BVU42_RS25640 (BVU42_27260) 12748..13065 + 318 WP_011091068 plasmid mobilization protein MobA -
BVU42_RS25645 (BVU42_27265) 13052..15031 + 1980 WP_004187323 TraI/MobA(P) family conjugative relaxase -
BVU42_RS25650 (BVU42_27270) 15045..15545 + 501 WP_004187320 DotD/TraH family lipoprotein -
BVU42_RS25655 (BVU42_27275) 15542..16321 + 780 WP_004187315 type IV secretory system conjugative DNA transfer family protein traI
BVU42_RS25660 (BVU42_27280) 16332..17495 + 1164 WP_004187313 plasmid transfer ATPase TraJ virB11
BVU42_RS25665 (BVU42_27285) 17485..17745 + 261 WP_004187310 IcmT/TraK family protein traK
BVU42_RS26265 17770..21207 + 3438 WP_015586048 LPD7 domain-containing protein -
BVU42_RS25675 (BVU42_27295) 21173..21685 + 513 WP_011091071 hypothetical protein traL
BVU42_RS25680 (BVU42_27300) 21686..21898 - 213 WP_305953721 Hha/YmoA family nucleoid-associated regulatory protein -
BVU42_RS25685 (BVU42_27305) 21870..22280 - 411 WP_004187465 H-NS family nucleoid-associated regulatory protein -
BVU42_RS25690 (BVU42_27310) 22348..23061 + 714 WP_004187467 DotI/IcmL family type IV secretion protein traM
BVU42_RS25695 (BVU42_27315) 23070..24221 + 1152 WP_004187471 DotH/IcmK family type IV secretion protein traN
BVU42_RS25700 (BVU42_27320) 24233..25582 + 1350 WP_004187474 conjugal transfer protein TraO traO
BVU42_RS25705 (BVU42_27325) 25594..26298 + 705 WP_015060002 conjugal transfer protein TraP traP
BVU42_RS25710 (BVU42_27330) 26322..26852 + 531 WP_004187478 conjugal transfer protein TraQ traQ
BVU42_RS25715 (BVU42_27335) 26869..27258 + 390 WP_004187479 DUF6750 family protein traR
BVU42_RS25720 (BVU42_27340) 27304..27798 + 495 WP_004187480 hypothetical protein -
BVU42_RS25725 (BVU42_27345) 27795..30845 + 3051 WP_004187482 hypothetical protein traU
BVU42_RS25730 (BVU42_27350) 30842..32050 + 1209 WP_011091082 conjugal transfer protein TraW traW
BVU42_RS25735 (BVU42_27355) 32047..32643 + 597 WP_015060003 hypothetical protein -
BVU42_RS25740 (BVU42_27360) 32636..34831 + 2196 WP_015062834 DotA/TraY family protein traY
BVU42_RS25745 (BVU42_27365) 34833..35486 + 654 WP_015060005 hypothetical protein -
BVU42_RS25750 (BVU42_27370) 35555..35797 + 243 WP_023893611 IncL/M type plasmid replication protein RepC -
BVU42_RS25755 (BVU42_27375) 36093..37148 + 1056 WP_015060006 plasmid replication initiator RepA -
BVU42_RS26355 38371..38466 + 96 WP_004206884 DinQ-like type I toxin DqlB -
BVU42_RS25760 (BVU42_27380) 38517..40604 - 2088 WP_004206885 conjugal transfer protein TrbC -
BVU42_RS25765 (BVU42_27385) 40617..41567 - 951 WP_004206886 DsbC family protein trbB
BVU42_RS25770 (BVU42_27390) 41578..42885 - 1308 WP_015059988 hypothetical protein trbA
BVU42_RS25775 (BVU42_27395) 42885..43280 - 396 WP_004187436 lytic transglycosylase domain-containing protein -
BVU42_RS25780 (BVU42_27400) 43385..43768 - 384 WP_019725042 DUF1496 domain-containing protein -
BVU42_RS25785 (BVU42_27405) 43848..44282 + 435 Protein_46 CPBP family intramembrane glutamate endopeptidase -
BVU42_RS25790 (BVU42_27410) 44297..45505 - 1209 WP_001206290 IS4-like element IS10A family transposase -
BVU42_RS25795 (BVU42_27415) 45808..46719 + 912 WP_015586033 LysR family transcriptional regulator -
BVU42_RS25800 (BVU42_27420) 47021..47818 - 798 WP_015059991 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-48 -

Host bacterium

ID   3351 GenBank   NZ_CP019078
Plasmid name   pDT1 Incompatibility group   IncL/M
Plasmid size   70987 bp Coordinate of oriT [Strand]   12641..12746 [+]
Host baterium   Klebsiella pneumoniae strain DT1

Cargo genes

Drug resistance gene   aph(3'')-Ib, aph(3')-VIb, aph(6)-Id, blaOXA-48, blaCTX-M-14b
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -