Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106402
Name   oriT_XJ20|p2 in_silico
Organism   Shinella zoogloeoides strain XJ20
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP093530 (17326..17365 [+], 40 nt)
oriT length   40 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 40 nt

>oriT_XJ20|p2
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4284 GenBank   WP_064334768
Name   traA_MOE34_RS23490_XJ20|p2 insolico UniProt ID   A0A1A9GEW8
Length   1193 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  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


T4CP

ID   4305 GenBank   WP_064334765
Name   traG_MOE34_RS23475_XJ20|p2 insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 69129.18 Da        Isoelectric Point: 9.7542

>WP_064334765.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Shinella]
MKANRVALVVAPIALMILVTISMVGIEHWLSAFGKTDAARLTLGRAGITFPYVAAAAIGILFLFAAAGSA
DIKFAGGGVTAGNVVTIMIAFVREAIRLAAISADVTQGKSVLSYLDPATMLGAGAATIAAGFGLRVMLKG
NAAFARAMPRRIRGKRALHGEAEWMKMPDAQKLFPDVGGIVIGERYRVDTDTVAAQAFRADRQETWGSGG
KSPLLCFDGSFGSSHGIVFAGSGGYKTTSVTIPTALKWGSTLIVLDPSNEVAPMVLDHRARSGRDVHILD
PKRPEIGVNVLDWIGRHGGTKEEDIASVASWIMSDSGRASGVRDDFFRASGLQLLTALIADVCLSGHTEE
KDQTLRQVRKNLAEPEPRLRERLQTIHENSKSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSSFTTDDLAAGTVDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGNVGGRALFLLDEVARLGY
MRILETARDAGRKYGVTLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGTTT
VEIDQMSRSSAAKGTSRTRSKQLAARALIQPHEVLRMRGDEQIVFTAGNPPLRCGRAIWFRRADMKTCVG
QNRFHGAAKP

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(163-636)

  Protein structure



No available structure.



ID   4306 GenBank   WP_064334782
Name   t4cp2_MOE34_RS23610_XJ20|p2 insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91445.07 Da        Isoelectric Point: 5.8231

>WP_064334782.1 MULTISPECIES: conjugal transfer protein TrbE [Shinella]
MVALRRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDAESATDLERNELSRQINAILSRLG
TGWMIQVEAVRIPTVDYPSQTRCFFPDPVTRAIDAERRAHFEREQGHFESRHALVLTYRPLESKKSALSK
YVYSDEESRKKSYADTVLFIFKNAIREIEQYLGNTLSIRRMETRETVERGGERVARYDELLQFVRFCITG
ENHPIRLPDVPMYLDWIATAELQHGLTPKVENTFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDALTMVAETEDAIAQASSQLVAYGYYTPVVIL
FDHDREALQEKAEAIRRLVQAEGFGARIEGLNATDAYLGSLPGNWFCNVREPLINTSNLADLVPLNSVWS
GSPVAPCPFYQEGSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLYPLTLAAGGDHYEIGGDAEEGRALAFCPLSDLATDGDRAWASEWIETLVALQGVTITPDHRNA
ISRQIGLMANAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAERDGLTLGGFQCFEIEQLMNMGE
RSLVPVLTYLFRRIEKRLDGAPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAERS
GIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSTAIPKREYYVATPDGRRLFDMSLGPV
ALSFVGASGKDDLKRIRALKSEHGQEWPAHWLQSRGVSDAIDVPSKT

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 34435..43955

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MOE34_RS23550 30563..30901 - 339 WP_080579326 IS66 family insertion sequence element accessory protein TnpB -
MOE34_RS23555 30913..31284 - 372 WP_242220772 transposase -
MOE34_RS23560 31844..32989 - 1146 WP_064334957 IS110 family transposase -
MOE34_RS23565 33212..33526 + 315 WP_145926151 transcriptional repressor TraM -
MOE34_RS23570 33530..34231 - 702 WP_084438747 autoinducer binding domain-containing protein -
MOE34_RS23575 34435..35739 - 1305 WP_064334775 IncP-type conjugal transfer protein TrbI virB10
MOE34_RS23580 35750..36187 - 438 WP_064334776 conjugal transfer protein TrbH -
MOE34_RS23585 36190..37002 - 813 WP_064334777 P-type conjugative transfer protein TrbG virB9
MOE34_RS23590 37019..37681 - 663 WP_064334778 conjugal transfer protein TrbF virB8
MOE34_RS23595 37699..38880 - 1182 WP_064334779 P-type conjugative transfer protein TrbL virB6
MOE34_RS23600 38874..39062 - 189 WP_242225018 entry exclusion protein TrbK -
MOE34_RS23605 39077..39880 - 804 WP_064334781 P-type conjugative transfer protein TrbJ virB5
MOE34_RS23610 39852..42305 - 2454 WP_064334782 conjugal transfer protein TrbE virb4
MOE34_RS23615 42316..42615 - 300 WP_064334783 conjugal transfer protein TrbD virB3
MOE34_RS23620 42608..42940 - 333 WP_242225020 TrbC/VirB2 family protein virB2
MOE34_RS23625 42984..43955 - 972 WP_064334785 P-type conjugative transfer ATPase TrbB virB11
MOE34_RS23630 43959..44585 - 627 WP_064334786 acyl-homoserine-lactone synthase TraI -
MOE34_RS23635 45043..46161 + 1119 WP_242225022 plasmid partitioning protein RepA -
MOE34_RS23640 46240..47226 + 987 WP_064334788 plasmid partitioning protein RepB -
MOE34_RS23645 47398..48615 + 1218 WP_064334789 plasmid replication protein RepC -

Host bacterium

ID   6839 GenBank   NZ_CP093530
Plasmid name   XJ20|p2 Incompatibility group   -
Plasmid size   145386 bp Coordinate of oriT [Strand]   17326..17365 [+]
Host baterium   Shinella zoogloeoides strain XJ20

Cargo genes

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