Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102494
Name   oriT_pCRKP-08_Res in_silico
Organism   Klebsiella pneumoniae strain CRKP-08
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JANPXL010000004 (24500..24581 [+], 82 nt)
oriT length   82 nt
IRs (inverted repeats)      27..32, 35..40  (GCCACC..GGTGGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 82 nt

>oriT_pCRKP-08_Res
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1854 GenBank   WP_032440569
Name   Relaxase_NVV52_RS28780_pCRKP-08_Res insolico UniProt ID   A0A7G3L4G1
Length   642 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 642 a.a.        Molecular weight: 74384.24 Da        Isoelectric Point: 8.3203

>WP_032440569.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDERFQRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVICQHNLMSVETAAMEMNSIAMQNTHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSPRSAEMVKQSVQTSYSDKLHVRDRGA
RAERRQARADARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASDNI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGSFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDDRYYD
DVRHNDDSSYKP

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(52-307)


  Protein structure


Source ID Structure
AlphaFold DB A0A7G3L4G1


T4CP

ID   1447 GenBank   WP_032440593
Name   trbC_NVV52_RS28915_pCRKP-08_Res insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 82679.78 Da        Isoelectric Point: 6.3201

>WP_032440593.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacterales]
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPNTVQRATQLLSLAAAVLTETRGRYRVEYPEP
EKLSVKKDELEKYQHIHQSAVTQQADGFSY

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(439-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 33690..55623

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NVV52_RS28790 (NVV52_28790) 28837..29331 - 495 WP_032440571 molybdopterin-dependent oxidoreductase -
NVV52_RS28795 (NVV52_28795) 29324..30253 - 930 WP_032440581 hypothetical protein -
NVV52_RS28800 (NVV52_28800) 30313..31155 - 843 WP_032440572 helix-turn-helix domain-containing protein -
NVV52_RS28805 (NVV52_28805) 31765..31992 + 228 WP_032440573 hypothetical protein -
NVV52_RS28810 (NVV52_28810) 32724..33203 + 480 WP_032440574 lytic transglycosylase domain-containing protein -
NVV52_RS28815 (NVV52_28815) 33229..33693 + 465 WP_225546581 DotD/TraH family lipoprotein -
NVV52_RS28820 (NVV52_28820) 33690..34508 + 819 WP_032440576 type IV secretory system conjugative DNA transfer family protein traI
NVV52_RS28825 (NVV52_28825) 34486..35673 + 1188 WP_077255878 plasmid transfer ATPase TraJ -
NVV52_RS28830 (NVV52_28830) 35670..35936 + 267 WP_032440577 IcmT/TraK family protein traK
NVV52_RS28835 (NVV52_28835) 35954..39367 + 3414 WP_052145516 LPD7 domain-containing protein -
NVV52_RS28840 (NVV52_28840) 39401..39754 + 354 WP_032440584 hypothetical protein traL
NVV52_RS28845 (NVV52_28845) 39826..40494 + 669 WP_032440585 DotI/IcmL/TraM family protein traM
NVV52_RS28850 (NVV52_28850) 40505..41608 + 1104 WP_077264204 DotH/IcmK family type IV secretion protein traN
NVV52_RS28855 (NVV52_28855) 41612..42952 + 1341 WP_032440586 conjugal transfer protein TraO traO
NVV52_RS28860 (NVV52_28860) 42959..43678 + 720 WP_050597333 conjugal transfer protein TraP traP
NVV52_RS28865 (NVV52_28865) 43688..44221 + 534 WP_032440587 conjugal transfer protein TraQ traQ
NVV52_RS28870 (NVV52_28870) 44277..44678 + 402 WP_032440588 DUF6750 family protein traR
NVV52_RS28875 (NVV52_28875) 44722..45285 + 564 WP_045325070 hypothetical protein traT
NVV52_RS28880 (NVV52_28880) 45295..48342 + 3048 WP_032440589 conjugal transfer protein traU
NVV52_RS28885 (NVV52_28885) 48352..49548 + 1197 WP_032440590 conjugal transfer protein TraW traW
NVV52_RS28890 (NVV52_28890) 49545..50126 + 582 WP_050597335 conjugal transfer protein TraX -
NVV52_RS28895 (NVV52_28895) 50168..52312 + 2145 WP_032440591 DotA/TraY family protein traY
NVV52_RS28900 (NVV52_28900) 52378..53001 + 624 WP_032440592 plasmid IncI1-type surface exclusion protein ExcA -
NVV52_RS28905 (NVV52_28905) 53103..54521 + 1419 WP_063666705 hypothetical protein trbA
NVV52_RS28910 (NVV52_28910) 54532..55623 + 1092 WP_050597336 thioredoxin fold domain-containing protein trbB
NVV52_RS28915 (NVV52_28915) 55625..57817 + 2193 WP_032440593 F-type conjugative transfer protein TrbC -
NVV52_RS28920 (NVV52_28920) 57863..58396 + 534 WP_032440594 phospholipase D family protein -
NVV52_RS28925 (NVV52_28925) 58408..58659 + 252 WP_113394424 hypothetical protein -
NVV52_RS28930 (NVV52_28930) 59165..59860 + 696 WP_254910806 RepA family replication protein -

Host bacterium

ID   2938 GenBank   NZ_JANPXL010000004
Plasmid name   pCRKP-08_Res Incompatibility group   IncFII
Plasmid size   85665 bp Coordinate of oriT [Strand]   24500..24581 [+]
Host baterium   Klebsiella pneumoniae strain CRKP-08

Cargo genes

Drug resistance gene   blaLAP-2, qnrS1, dfrA14, sul2, catA2, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -