Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106082
Name   oriT_pXH1508-3 in_silico
Organism   Klebsiella pneumoniae strain XH1508
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP092789 (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_pXH1508-3
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4081 GenBank   WP_032440569
Name   Relaxase_ML259_RS29215_pXH1508-3 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   4093 GenBank   WP_032440593
Name   trbC_ML259_RS29350_pXH1508-3 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
ML259_RS29225 (ML259_29225) 28837..29331 - 495 WP_032440571 molybdopterin-dependent oxidoreductase -
ML259_RS29230 (ML259_29230) 29324..30253 - 930 WP_032440581 hypothetical protein -
ML259_RS29235 (ML259_29235) 30313..31155 - 843 WP_032440572 helix-turn-helix domain-containing protein -
ML259_RS29240 (ML259_29240) 31765..31992 + 228 WP_032440573 hypothetical protein -
ML259_RS29245 (ML259_29245) 32724..33203 + 480 WP_032440574 lytic transglycosylase domain-containing protein -
ML259_RS29250 (ML259_29250) 33229..33693 + 465 WP_225546581 DotD/TraH family lipoprotein -
ML259_RS29255 (ML259_29255) 33690..34508 + 819 WP_032440576 type IV secretory system conjugative DNA transfer family protein traI
ML259_RS29260 (ML259_29260) 34486..35673 + 1188 WP_077255878 plasmid transfer ATPase TraJ -
ML259_RS29265 (ML259_29265) 35670..35936 + 267 WP_032440577 IcmT/TraK family protein traK
ML259_RS29270 (ML259_29270) 35954..39367 + 3414 WP_052145516 LPD7 domain-containing protein -
ML259_RS29275 (ML259_29275) 39401..39754 + 354 WP_032440584 hypothetical protein traL
ML259_RS29280 (ML259_29280) 39826..40494 + 669 WP_032440585 DotI/IcmL/TraM family protein traM
ML259_RS29285 (ML259_29285) 40505..41608 + 1104 WP_077264204 DotH/IcmK family type IV secretion protein traN
ML259_RS29290 (ML259_29290) 41612..42952 + 1341 WP_032440586 conjugal transfer protein TraO traO
ML259_RS29295 (ML259_29295) 42959..43678 + 720 WP_050597333 conjugal transfer protein TraP traP
ML259_RS29300 (ML259_29300) 43688..44221 + 534 WP_032440587 conjugal transfer protein TraQ traQ
ML259_RS29305 (ML259_29305) 44277..44678 + 402 WP_032440588 DUF6750 family protein traR
ML259_RS29310 (ML259_29310) 44722..45285 + 564 WP_045325070 hypothetical protein traT
ML259_RS29315 (ML259_29315) 45295..48342 + 3048 WP_032440589 conjugal transfer protein traU
ML259_RS29320 (ML259_29320) 48352..49548 + 1197 WP_032440590 conjugal transfer protein TraW traW
ML259_RS29325 (ML259_29325) 49545..50126 + 582 WP_050597335 conjugal transfer protein TraX -
ML259_RS29330 (ML259_29330) 50168..52312 + 2145 WP_032440591 DotA/TraY family protein traY
ML259_RS29335 (ML259_29335) 52378..53001 + 624 WP_032440592 plasmid IncI1-type surface exclusion protein ExcA -
ML259_RS29340 (ML259_29340) 53103..54521 + 1419 WP_063666705 hypothetical protein trbA
ML259_RS29345 (ML259_29345) 54532..55623 + 1092 WP_050597336 thioredoxin fold domain-containing protein trbB
ML259_RS29350 (ML259_29350) 55625..57817 + 2193 WP_032440593 F-type conjugative transfer protein TrbC -
ML259_RS29355 (ML259_29355) 57863..58396 + 534 WP_032440594 phospholipase D family protein -
ML259_RS29360 (ML259_29360) 58408..58659 + 252 WP_113394424 hypothetical protein -
ML259_RS29365 (ML259_29365) 59165..59860 + 696 WP_254910806 RepA family replication protein -

Host bacterium

ID   6519 GenBank   NZ_CP092789
Plasmid name   pXH1508-3 Incompatibility group   IncFII
Plasmid size   87095 bp Coordinate of oriT [Strand]   24500..24581 [+]
Host baterium   Klebsiella pneumoniae strain XH1508

Cargo genes

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