Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102300
Name   oriT_PEC-VIM|punnamed3 in_silico
Organism   Klebsiella pneumoniae strain PEC-VIM
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_QHMM01000023 (4122..4227 [+], 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_PEC-VIM|punnamed3
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1761 GenBank   WP_004187323
Name   Relaxase_DL507_RS24640_PEC-VIM|punnamed3 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   1349 GenBank   WP_004206885
Name   t4cp2_DL507_RS24760_PEC-VIM|punnamed3 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: 7023..34186

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DL507_RS24620 (DL507_24610) 2107..2418 + 312 WP_004187333 hypothetical protein -
DL507_RS24625 (DL507_24615) 2551..3087 + 537 WP_004187332 hypothetical protein -
DL507_RS24630 (DL507_24620) 3589..3984 - 396 WP_019725163 hypothetical protein -
DL507_RS31600 4019..4546 + 528 WP_172740549 plasmid mobilization protein MobA -
DL507_RS24640 (DL507_24630) 4533..6512 + 1980 WP_004187323 TraI/MobA(P) family conjugative relaxase -
DL507_RS24645 (DL507_24635) 6526..7026 + 501 WP_004187320 DotD/TraH family lipoprotein -
DL507_RS24650 (DL507_24640) 7023..7802 + 780 WP_004187315 type IV secretory system conjugative DNA transfer family protein traI
DL507_RS24655 (DL507_24645) 7813..8976 + 1164 WP_004187313 plasmid transfer ATPase TraJ virB11
DL507_RS24660 (DL507_24650) 8966..9226 + 261 WP_004187310 IcmT/TraK family protein traK
DL507_RS31605 9251..12553 + 3303 WP_242449189 LPD7 domain-containing protein -
DL507_RS24670 (DL507_24660) 12519..13031 + 513 WP_011091071 hypothetical protein traL
DL507_RS24675 (DL507_24665) 13032..13244 - 213 WP_305953721 Hha/YmoA family nucleoid-associated regulatory protein -
DL507_RS24680 (DL507_24670) 13216..13626 - 411 WP_004187465 H-NS family nucleoid-associated regulatory protein -
DL507_RS24685 (DL507_24675) 13694..14407 + 714 WP_004187467 DotI/IcmL family type IV secretion protein traM
DL507_RS24695 (DL507_24685) 14416..15567 + 1152 WP_004187471 DotH/IcmK family type IV secretion protein traN
DL507_RS24700 (DL507_24690) 15579..16928 + 1350 WP_004187474 conjugal transfer protein TraO traO
DL507_RS24705 (DL507_24695) 16940..17644 + 705 WP_015060002 conjugal transfer protein TraP traP
DL507_RS24710 (DL507_24700) 17668..18198 + 531 WP_004187478 conjugal transfer protein TraQ traQ
DL507_RS24715 (DL507_24705) 18215..18604 + 390 WP_004187479 DUF6750 family protein traR
DL507_RS24720 (DL507_24710) 18650..19144 + 495 WP_004187480 hypothetical protein -
DL507_RS24725 (DL507_24715) 19141..22191 + 3051 WP_004187482 hypothetical protein traU
DL507_RS24730 (DL507_24720) 22188..23396 + 1209 WP_011091082 conjugal transfer protein TraW traW
DL507_RS24735 (DL507_24725) 23393..23989 + 597 WP_015060003 hypothetical protein -
DL507_RS24740 (DL507_24730) 23982..26177 + 2196 WP_015062834 DotA/TraY family protein traY
DL507_RS24745 (DL507_24735) 26179..26832 + 654 WP_015060005 hypothetical protein -
DL507_RS24750 (DL507_24740) 26901..27143 + 243 WP_023893611 IncL/M type plasmid replication protein RepC -
DL507_RS24755 (DL507_24745) 27439..28494 + 1056 WP_015060006 plasmid replication initiator RepA -
DL507_RS31910 29717..29812 + 96 WP_004206884 DinQ-like type I toxin DqlB -
DL507_RS24760 (DL507_24750) 29863..31950 - 2088 WP_004206885 conjugal transfer protein TrbC -
DL507_RS24765 (DL507_24755) 31963..32913 - 951 WP_004206886 DsbC family protein trbB
DL507_RS24770 (DL507_24760) 32924..34186 - 1263 WP_004206887 hypothetical protein trbA
DL507_RS24775 (DL507_24765) 34231..34626 - 396 WP_004187436 lytic transglycosylase domain-containing protein -
DL507_RS24780 (DL507_24770) 34731..35114 - 384 WP_019725042 DUF1496 domain-containing protein -
DL507_RS24785 (DL507_24775) 35194..35847 + 654 WP_004206890 type II CAAX endopeptidase family protein -
DL507_RS30645 35939..36196 + 258 WP_004187429 type II toxin-antitoxin system antitoxin PemI -
DL507_RS24790 (DL507_24780) 36198..36530 + 333 WP_004187427 type II toxin-antitoxin system toxin endoribonuclease PemK-mt -
DL507_RS24795 (DL507_24785) 36623..37057 + 435 WP_004187425 translesion error-prone DNA polymerase V autoproteolytic subunit -
DL507_RS24800 (DL507_24790) 37045..38310 + 1266 WP_021242902 translesion error-prone DNA polymerase V subunit UmuC -
DL507_RS24805 (DL507_24795) 38433..38642 - 210 WP_004187413 hypothetical protein -
DL507_RS24810 (DL507_24800) 38645..38863 - 219 WP_004187411 hypothetical protein -

Host bacterium

ID   2744 GenBank   NZ_QHMM01000023
Plasmid name   PEC-VIM|punnamed3 Incompatibility group   IncL/M
Plasmid size   56539 bp Coordinate of oriT [Strand]   4122..4227 [+]
Host baterium   Klebsiella pneumoniae strain PEC-VIM

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -