Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101176
Name   oriT_pSM141A_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM141A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOX01000007 (16801..16834 [-], 34 nt)
oriT length   34 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: 34 nt

>oriT_pSM141A_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1173 GenBank   WP_130738440
Name   traA_ELH98_RS29175_pSM141A_Rh08 insolico UniProt ID   _
Length   1107 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1107 a.a.        Molecular weight: 122984.17 Da        Isoelectric Point: 9.7988

>WP_130738440.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSVVARGSGHSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNISLMRDFVERHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGGTEDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRALWLSGRASHGVRDAVLQATFARHSRLSDEQRTAIEHVAGATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDRCVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVFVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEIGEGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETSLDYE
KSALYRQALRFAEARGLHLMNVARTIARDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKVINVDTMLKDQSVAQA
TLARIAGEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTGG
KTFETVTAGMTAGQKAEVQSAWNAMRTVQQLGSHERTTEAHKQAETLQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-740)

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(18-243)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   765 GenBank   WP_130738441
Name   traG_ELH98_RS29190_pSM141A_Rh08 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 69609.91 Da        Isoelectric Point: 8.9733

>WP_130738441.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTVNRIALAVVPTVLMILVVVGMTGIEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGVLLLFATAGAI
NIKQAGWGVLAGCCGTILIAVTRETMRLATFTKTLHADKSFLAYLDPATAIGASVALMCACFALRVVLVG
NAAFARPEPKRINGKRALHGEADWMKLTEAAKLFPDRGGIVIGERYRVDKDSVGARAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDVGFNVLDWVGCFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVSLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNIDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETAEYISKRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPEPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   766 GenBank   WP_130763005
Name   t4cp2_ELH98_RS29710_pSM141A_Rh08 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91668.39 Da        Isoelectric Point: 5.6886

>WP_130763005.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMSMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNAPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATSEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLKYV

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1568..11663

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH98_RS29090 (ELH98_29085) 1..1596 + 1596 Protein_0 conjugal transfer protein TrbE -
ELH98_RS29095 (ELH98_29090) 1568..2371 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELH98_RS29100 (ELH98_29095) 2368..2568 + 201 WP_130680525 entry exclusion protein TrbK -
ELH98_RS29105 (ELH98_29100) 2562..3743 + 1182 WP_130738438 P-type conjugative transfer protein TrbL virB6
ELH98_RS29110 (ELH98_29105) 3764..4426 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELH98_RS29115 (ELH98_29110) 4444..5256 + 813 WP_130680527 P-type conjugative transfer protein TrbG virB9
ELH98_RS29120 (ELH98_29115) 5260..5700 + 441 WP_130680528 conjugal transfer protein TrbH -
ELH98_RS29125 (ELH98_29120) 5712..7007 + 1296 WP_130680529 IncP-type conjugal transfer protein TrbI virB10
ELH98_RS29130 (ELH98_29125) 7192..7932 + 741 WP_130680530 LuxR family transcriptional regulator -
ELH98_RS29135 (ELH98_29130) 8039..8743 + 705 WP_130680531 autoinducer binding domain-containing protein -
ELH98_RS29140 (ELH98_29135) 8747..9037 - 291 WP_130680532 transcriptional repressor TraM -
ELH98_RS29145 (ELH98_29140) 9329..9577 + 249 WP_130680533 helix-turn-helix transcriptional regulator -
ELH98_RS29150 (ELH98_29145) 9698..10330 + 633 WP_130680534 DUF433 domain-containing protein -
ELH98_RS29155 (ELH98_29150) 10327..10701 + 375 WP_130680535 DUF5615 family PIN-like protein -
ELH98_RS29160 (ELH98_29155) 11043..11663 - 621 WP_130738439 TraH family protein virB1
ELH98_RS29165 (ELH98_29160) 11680..12846 - 1167 WP_130680551 conjugal transfer protein TraB -
ELH98_RS29170 (ELH98_29165) 12836..13333 - 498 WP_245484661 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1620 GenBank   NZ_SIOX01000007
Plasmid name   pSM141A_Rh08 Incompatibility group   -
Plasmid size   139343 bp Coordinate of oriT [Strand]   16801..16834 [-]
Host baterium   Rhizobium ruizarguesonis strain SM141A

Cargo genes

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