Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100806
Name   oriT_pShin-10 in_silico
Organism   Shinella sp. HZN7
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NZ_CP015746 (24514..24553 [+], 40 nt)
oriT length   40 nt
IRs (inverted repeats)      16..24, 29..37  (ATACGTCGC..GCGACGCCT)
Location of nic site      8..9
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 40 nt

>oriT_pShin-10
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   878 GenBank   WP_064334768
Name   TraA_pShin-10 insolico UniProt ID   A0A1A9GEW8
Length   1193 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1193 a.a.        Molecular weight: 131501.12 Da        Isoelectric Point: 8.8122

>WP_064334768.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Shinella]
MAVPHFSVSVVARGSGRSAVLSAAYRHCVKMEFEREARTIDYTRKQGLLHEEFVIPEDAPDWLRSMIADR
SVAAASEAFWNAVEGFEKRSDAQLAKDVTMALPIELSADQNIALVREFVASHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTDDGFGAKKVAVLGADGKSLRNDSGKIVYELWAGGVGDFNAFRDGWFVCQNRHLALAG
LDIRVDGRSYEKQGIALEPTIHLGVGANAIKQKSAEASEPITLERIELQEERRAENARRIEDRPAVVIDM
IAREKSVFDERDVAKILHRYVDDAGLFQSLMARVLQSPDVVRLEREHVDFASGARVPAKLTTRDLIRTEA
EMASRAVFLAGRSSHRVENAILQETFARYSRLSKEQKTAIAHVAGSHRIAAVVGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLETEAGIVSRTLSSWELRWNDGRSQLDDKTVFVLDEAGMVSSRQLALFVE
AVTKAGAKLVLVGDPDQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGNVAAALSAYD
AADLVQTGWTRQDAIEGLIDNWNYDFDPTKTTLILAHRRRDVRELNELARAKLVERGIVGEGSVFRTEDG
ARRFAAGDQIVFLKNEGSLGVKNGMLAKVVEAAPGRIVAEIGEGDSRRQVTVEQRFYSNVDHGYATTIHK
SQGATVDRVKVLASNTLDRHLTYVAMTRHREAAELYVGMEEFTNRRGGVLVDHGEAPYEHKPGNRDSYFV
TLTYGDGQERTIWGVDLARAIDEADAHVGDRIGLRHEGSESVRLPDGTMAKRNTWKIVPVKELAMERLKE
RLSRDASKETTLDYEGASSYRAALRFAEARGMHLMNVARTISRDRLAWTVRQKQKLVDLAARLKAVGAAL
GLARGSDKQSVPTIVKEARPMVAGITTFAKSLEQSVEDKLSNDPALKQQWKDVSTRFQMVYAQPEAAFAA
INVDAMIKDQARATATIAKISAEPETFGTLKGKTGMFASRADKQERDTALVNAPALARNLERYLRGRAEA
ERKHETEERAARIKVSVDIPALSPNAKQTLERIRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVTERF
GERTFLGVSAKEAGGEAFKTVTRGMTDPQKAEVQTAWNSMRAVQQLAAHERVVVGIKQAEALRQTQAKGL
SLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(949-1045)

AAA domain (AAA_30)

(382-567)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)


  Protein structure


Source ID Structure
AlphaFold DB A0A1A9GEW8


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29939..46709

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
shn_RS33605 (shn_33605) 28253..28771 + 519 WP_245337565 conjugative transfer signal peptidase TraF -
shn_RS33610 (shn_33610) 28761..29924 + 1164 WP_064334770 conjugal transfer protein TraB -
shn_RS33615 (shn_33615) 29939..30577 + 639 WP_064334771 TraH family protein virB1
shn_RS33620 (shn_33620) 30666..31769 - 1104 WP_245337566 SEC-C domain-containing protein -
shn_RS33625 (shn_33625) 32020..32796 + 777 WP_242224988 hypothetical protein -
shn_RS33630 (shn_33630) 33288..34211 + 924 WP_168168934 IS110 family transposase -
shn_RS33635 (shn_33635) 34296..34730 + 435 WP_064334772 hypothetical protein -
shn_RS33640 (shn_33640) 34922..35320 - 399 WP_064334773 type II toxin-antitoxin system VapC family toxin -
shn_RS33645 (shn_33645) 35317..35673 - 357 WP_242224990 type II toxin-antitoxin system VapB family antitoxin -
shn_RS33650 (shn_33650) 35966..36280 + 315 WP_145926151 transcriptional repressor TraM -
shn_RS33655 (shn_33655) 36284..36985 - 702 WP_084438747 autoinducer binding domain-containing protein -
shn_RS33660 (shn_33660) 37189..38493 - 1305 WP_064334775 IncP-type conjugal transfer protein TrbI virB10
shn_RS33665 (shn_33665) 38504..38941 - 438 WP_064334776 conjugal transfer protein TrbH -
shn_RS33670 (shn_33670) 38944..39756 - 813 WP_064334777 P-type conjugative transfer protein TrbG virB9
shn_RS33675 (shn_33675) 39773..40435 - 663 WP_064334778 conjugal transfer protein TrbF virB8
shn_RS33680 (shn_33680) 40453..41634 - 1182 WP_064334779 P-type conjugative transfer protein TrbL virB6
shn_RS33685 (shn_33685) 41628..41834 - 207 WP_064334780 entry exclusion protein TrbK -
shn_RS33690 (shn_33690) 41831..42634 - 804 WP_064334781 P-type conjugative transfer protein TrbJ virB5
shn_RS33695 (shn_33695) 42606..45059 - 2454 WP_064334782 conjugal transfer protein TrbE virb4
shn_RS33700 (shn_33700) 45070..45369 - 300 WP_064334783 conjugal transfer protein TrbD virB3
shn_RS33705 (shn_33705) 45362..45694 - 333 WP_242225020 TrbC/VirB2 family protein virB2
shn_RS33710 (shn_33710) 45738..46709 - 972 WP_064334785 P-type conjugative transfer ATPase TrbB virB11
shn_RS33715 (shn_33715) 46713..47339 - 627 WP_064334786 acyl-homoserine-lactone synthase TraI -
shn_RS33720 (shn_33720) 47734..48915 + 1182 WP_256388555 plasmid partitioning protein RepA -
shn_RS33725 (shn_33725) 48994..49980 + 987 WP_064334788 plasmid partitioning protein RepB -
shn_RS33730 (shn_33730) 50152..51369 + 1218 WP_064334789 plasmid replication protein RepC -

Host bacterium

ID   1266 GenBank   NZ_CP015746
Plasmid name   pShin-10 Incompatibility group   _
Plasmid size   112708 bp Coordinate of oriT [Strand]   24514..24553 [+]
Host baterium   Shinella sp. HZN7

Cargo genes

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