Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100805
Name   oriT_pShin-05 in_silico
Organism   Shinella sp. HZN7
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NZ_CP015741 (90914..90944 [-], 31 nt)
oriT length   31 nt
IRs (inverted repeats)      15..20, 25..30  (CGTCGC..GCGACG)
Location of nic site      4..5
Conserved sequence flanking the
  nic site    		  AGGG|CGCA
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 31 nt

>oriT_pShin-05
AGGGCGCAATTATACGTCGCTGATGCGACGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   877 GenBank   WP_064334296
Name   TraA_pShin-05 insolico UniProt ID   A0A1A9GDD3
Length   1102 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 121760.54 Da        Isoelectric Point: 9.5111

>WP_064334296.1 Ti-type conjugative transfer relaxase TraA [Shinella sp. HZN7]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQDLLHEEFVIPVDAPEWLQSMIADR
SVSGASEAFWNKVEKFEKRSDAQLAKDVTIALPIELSADKNIELVRDFVARHITAEGMVADWVFHDAPGN
PHIHLMTTLRPLTEDGFGSKKVAVVGPDGKALRNDSGKIVYELWAGGLDDFNAFRDGWFACQNRHLALAC
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKAEGAEEKAALERLELQEERRAENARRIQRDPEIVLDL
IMREKSVFDERDVAKILHRNIDDAGLFQNLMARILQSPDTLRLDCERLDFVTGMRAPAKYTTRELIRLEA
EMANRAIWLSQRSSYGVRKTVLEATFARHERLSDEQRAAIEHVASGERIAAVIGLAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRGKLNDKTVFVLDEAGMVSSRQMALFVE
TVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYVELETIYRQREQWMRDASLDLARGNVGKAVSAYQ
SNGKMIGSELKADAVTNLIADWNRDYDPAKSTLILAHLRRDVRMLNELARKKLIERGIIEHGSPFKTADG
VRSFAAGDQIVFLKNEGSIGVKNGMLGKVVEAASGRIVAVIGEGEHLRQVSVEQRFYTNVDHGYATTVHK
SQGATVDRVKVLASVSLDRHLTYVAMTRHREDLGVYYGSRSFAKAGGLVEILSRRNSKETTLDYAGGSIY
GQALRFAEARGMHVVNVARTVARDRLEWTARQKQKLVDLAGRLAVLGARLGFATSAASTIQTSAKEANPM
VAGITTFPKSIDQAVEDKLASDPALKKQWEEVSMRFHHVYARPEAAFKAVDVAAMLRDQAAAAKTIARIA
SEPETFGALKGKTGVFASRADKSERDRALKNVTPLADSISDYLRQRGDAERRNHAEELAVRRQVALEIPA
LSSNAKSVLERVRDSIDRNDLPSGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDANGEAFQRV
TSGMNAAQKSEVQQGWTTMRTVQQLSAHERSVTALKQTEALRQTRSQGLTLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-565)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(691-735)

MobA/MobL family (MobA_MobL)

(17-243)

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

(858-954)


  Protein structure


Source ID Structure
AlphaFold DB A0A1A9GDD3


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 72941..85798

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
shn_RS30450 (shn_30450) 68224..69462 - 1239 WP_064334275 plasmid replication protein RepC -
shn_RS30455 (shn_30455) 69615..70637 - 1023 WP_064334276 plasmid partitioning protein RepB -
shn_RS30460 (shn_30460) 70731..71930 - 1200 WP_084438685 plasmid partitioning protein RepA -
shn_RS30465 (shn_30465) 72312..72938 + 627 WP_064334278 acyl-homoserine-lactone synthase TraI -
shn_RS30470 (shn_30470) 72941..73912 + 972 WP_064334279 P-type conjugative transfer ATPase TrbB virB11
shn_RS30475 (shn_30475) 73902..74279 + 378 WP_064334280 TrbC/VirB2 family protein virB2
shn_RS30480 (shn_30480) 74276..74560 + 285 WP_064334281 conjugal transfer protein TrbD virB3
shn_RS30485 (shn_30485) 74571..77027 + 2457 WP_064334282 conjugal transfer protein TrbE virb4
shn_RS30490 (shn_30490) 76999..77802 + 804 WP_064334283 P-type conjugative transfer protein TrbJ virB5
shn_RS30495 (shn_30495) 77799..78002 + 204 WP_064334284 entry exclusion protein TrbK -
shn_RS30500 (shn_30500) 77996..79174 + 1179 WP_064334285 P-type conjugative transfer protein TrbL virB6
shn_RS30505 (shn_30505) 79197..79859 + 663 WP_062428114 conjugal transfer protein TrbF virB8
shn_RS30510 (shn_30510) 79876..80688 + 813 WP_064334286 P-type conjugative transfer protein TrbG virB9
shn_RS30515 (shn_30515) 80692..81129 + 438 WP_064334287 conjugal transfer protein TrbH -
shn_RS30520 (shn_30520) 81144..82442 + 1299 WP_064334288 IncP-type conjugal transfer protein TrbI virB10
shn_RS30525 (shn_30525) 82659..83360 + 702 WP_168168999 autoinducer binding domain-containing protein -
shn_RS30530 (shn_30530) 83362..83682 - 321 WP_084438680 transcriptional repressor TraM -
shn_RS30535 (shn_30535) 83822..84040 + 219 WP_064334290 helix-turn-helix transcriptional regulator -
shn_RS30540 (shn_30540) 84139..84759 + 621 WP_064334291 DUF433 domain-containing protein -
shn_RS30545 (shn_30545) 84764..85141 + 378 WP_064334292 DUF5615 family PIN-like protein -
shn_RS30550 (shn_30550) 85190..85798 - 609 WP_064334293 TraH family protein virB1
shn_RS30555 (shn_30555) 85813..86973 - 1161 WP_064334294 conjugal transfer protein TraB -
shn_RS30560 (shn_30560) 86963..87493 - 531 WP_245337521 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1265 GenBank   NZ_CP015741
Plasmid name   pShin-05 Incompatibility group   _
Plasmid size   155026 bp Coordinate of oriT [Strand]   90914..90944 [-]
Host baterium   Shinella sp. HZN7

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixB, fixA
Anti-CRISPR   -