Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101948
Name   oriT_pUTK21 in_silico
Organism   Pseudomonas fluorescens HK44
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AFOY02000029 (71226..71653 [+], 428 nt)
oriT length   428 nt
IRs (inverted repeats)      162..168, 176..182  (AAGCCGC..GCGGCTT)
 137..142, 144..149  (CATGAA..TTCATG)
 80..86, 92..98  (ATAAAAT..ATTTTAT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 428 nt

>oriT_pUTK21
GGTGGTCCTCTCTGAGCCAAATATGGGACTAATTCAGGATAACGATAACTTCCGAAATAGCGTATAGCAAATGCAATACATAAAATGCTTGATTTTATTGGTCTAAATGATAATTTTGTAATACATATGTATAGCGCATGAAATTCATGAATTTGCTCTGTAAGCCGCTCCCAGCGCGGCTTTAACCTACCGCTAGGGGGGTGCGTGTTGTGTATTGAGACTTTGACCCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGTCAGGCCGCAGGCCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCAGGAAGGGTGCTAAGAGAGTGCAAGAGGGGTGCAACTTGACTACAGGTAGGGGGCGATTAAGATGCACCTAGAGTGCAATAGGGGTGCAGATAGGGTGCAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   1241 GenBank   WP_011117449
Name   t4cp2_HK44_RS28710_pUTK21 insolico UniProt ID   _
Length   518 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 518 a.a.        Molecular weight: 58356.75 Da        Isoelectric Point: 8.8904

>WP_011117449.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Pseudomonas]
MHKREVDSAVMTAGFGLPIAGWAAGVYLAQMPLTPFPAAFKETLHNGWQNPIVLGATIATSAVAASLVYY
LYEYCDDGFRGEQYQEFLRGSEIKNWHTVKAKVRRRNEKTNRERKKRGLAKSEPVMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALKRGDRMAVVDPNGTFYSKFSFKGDYILNPFDARSAGWTIFNEIRGIH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLKETNNPNQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMSKGDFSIYQWVNDPNAGNLFITWREDMRDTMKPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNAGMASEILGSHDVKRWRKSYTAGKLTRTEEVTRDEPVVQASEISNLPDLVAYVKFGE
DFPITKVKTPYIDYKERAQAIMITGQAA

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(125-499)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 23874..44724

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HK44_RS28440 (HK44_029140) 19839..20585 + 747 WP_080690697 hypothetical protein -
HK44_RS28445 (HK44_029145) 20776..20913 + 138 WP_206756135 hypothetical protein -
HK44_RS28450 (HK44_029150) 21058..21474 + 417 WP_011117398 hypothetical protein -
HK44_RS28455 (HK44_029155) 21575..22834 - 1260 WP_011117397 site-specific integrase -
HK44_RS28460 (HK44_029160) 22831..23238 - 408 WP_011117396 hypothetical protein -
HK44_RS28465 (HK44_029170) 23874..25484 + 1611 WP_228409389 Y-family DNA polymerase traN
HK44_RS28470 (HK44_029175) 25481..25876 - 396 WP_011117394 hypothetical protein -
HK44_RS30050 25920..27188 - 1269 Protein_29 DUF1173 family protein -
HK44_RS30335 27347..27535 - 189 WP_052014790 hypothetical protein -
HK44_RS28490 (HK44_029200) 27988..28749 - 762 WP_011117390 hypothetical protein -
HK44_RS28495 (HK44_029205) 28789..29358 - 570 WP_011117389 replication protein -
HK44_RS28500 (HK44_029210) 29806..30435 - 630 WP_011117388 recombinase family protein -
HK44_RS28505 (HK44_029215) 30703..31023 - 321 WP_012727769 hypothetical protein -
HK44_RS28510 (HK44_029225) 31124..31429 - 306 WP_011117387 hypothetical protein -
HK44_RS28515 (HK44_029230) 31434..31775 - 342 WP_011117386 TrfB-related DNA-binding protein -
HK44_RS28520 (HK44_029235) 31772..32698 - 927 WP_011117385 ParB/RepB/Spo0J family partition protein -
HK44_RS28525 (HK44_029240) 32712..33485 - 774 WP_019694514 ParA family protein -
HK44_RS28530 (HK44_029250) 34423..34884 + 462 WP_011117467 TrbC/VirB2 family protein virB2
HK44_RS28535 34888..35181 + 294 WP_011117466 VirB3 family type IV secretion system protein virB3
HK44_RS28540 (HK44_029255) 35210..37852 + 2643 WP_019694561 hypothetical protein virb4
HK44_RS28545 (HK44_029260) 37849..38538 + 690 WP_011117464 type IV secretion system protein virB5
HK44_RS28550 (HK44_029265) 38566..38778 + 213 WP_011117463 hypothetical protein -
HK44_RS28555 (HK44_029270) 38771..39175 + 405 WP_011117462 hypothetical protein -
HK44_RS28560 (HK44_029275) 39163..40026 + 864 WP_011117461 type IV secretion system protein virB6
HK44_RS28565 (HK44_029280) 40030..40695 + 666 WP_011117460 type IV secretion system protein virB8
HK44_RS28570 (HK44_029285) 40720..41511 + 792 WP_011117459 TrbG/VirB9 family P-type conjugative transfer protein virB9
HK44_RS28575 (HK44_029290) 41514..42797 + 1284 WP_011117458 TrbI/VirB10 family protein virB10
HK44_RS28580 (HK44_029295) 42807..43835 + 1029 WP_011117457 P-type DNA transfer ATPase VirB11 virB11
HK44_RS28585 (HK44_029300) 43819..44724 + 906 WP_011117456 lytic transglycosylase domain-containing protein virB1
HK44_RS28590 (HK44_029305) 44754..45083 + 330 WP_011117455 TrbM/KikA/MpfK family conjugal transfer protein -
HK44_RS28595 (HK44_029310) 45073..45678 + 606 WP_011117454 phospholipase D family protein -
HK44_RS28600 (HK44_029315) 45693..46175 + 483 WP_011117453 hypothetical protein -
HK44_RS28605 (HK44_029320) 46223..46861 + 639 WP_011117452 hypothetical protein -
HK44_RS28610 (HK44_029325) 47190..47771 - 582 WP_011117451 hypothetical protein -

Host bacterium

ID   2392 GenBank   NZ_AFOY02000029
Plasmid name   pUTK21 Incompatibility group   -
Plasmid size   116775 bp Coordinate of oriT [Strand]   71226..71653 [+]
Host baterium   Pseudomonas fluorescens HK44

Cargo genes

Drug resistance gene   tet(A)
Virulence gene   cheY, fleN
Metal resistance gene   -
Degradation gene   nagJ, nahD, nahE, nahC, nahF, nahB, nahAc, nahA2, nahAa, nahAb, nahH, nahI, nahN, nahL, nahO, nahM, nahK, nahJ
Symbiosis gene   -
Anti-CRISPR   -