Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101172
Name   oriT_pSM165B_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM165B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQT01000006 (29602..29635 [-], 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_pSM165B_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1169 GenBank   WP_130738440
Name   traA_ELI46_RS29635_pSM165B_Rh07 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   759 GenBank   WP_130738437
Name   t4cp2_ELI46_RS29550_pSM165B_Rh07 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: 91757.43 Da        Isoelectric Point: 5.8099

>WP_130738437.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNEQSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLIPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMSMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNAPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATSEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLETRGVHDAASLLKYV

  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.



ID   760 GenBank   WP_130738441
Name   traG_ELI46_RS29650_pSM165B_Rh07 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 10288..24464

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI46_RS29510 (ELI46_29510) 5819..6841 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELI46_RS29515 (ELI46_29515) 6838..8052 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELI46_RS29520 (ELI46_29520) 8669..8923 - 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELI46_RS41450 8964..9176 - 213 WP_245458276 hypothetical protein -
ELI46_RS29530 (ELI46_29530) 9654..10277 + 624 WP_130738434 acyl-homoserine-lactone synthase -
ELI46_RS29535 (ELI46_29535) 10288..11265 + 978 WP_130738435 P-type conjugative transfer ATPase TrbB virB11
ELI46_RS29540 (ELI46_29540) 11255..11638 + 384 WP_130738436 TrbC/VirB2 family protein virB2
ELI46_RS29545 (ELI46_29545) 11631..11930 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI46_RS29550 (ELI46_29550) 11941..14397 + 2457 WP_130738437 conjugal transfer protein TrbE virb4
ELI46_RS29555 (ELI46_29555) 14369..15172 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELI46_RS29560 (ELI46_29560) 15169..15369 + 201 WP_130680525 entry exclusion protein TrbK -
ELI46_RS29565 (ELI46_29565) 15363..16544 + 1182 WP_130738438 P-type conjugative transfer protein TrbL virB6
ELI46_RS29570 (ELI46_29570) 16565..17227 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELI46_RS29575 (ELI46_29575) 17245..18057 + 813 WP_130680527 P-type conjugative transfer protein TrbG virB9
ELI46_RS29580 (ELI46_29580) 18061..18501 + 441 WP_130680528 conjugal transfer protein TrbH -
ELI46_RS29585 (ELI46_29585) 18513..19808 + 1296 WP_130680529 IncP-type conjugal transfer protein TrbI virB10
ELI46_RS29590 (ELI46_29590) 19993..20733 + 741 WP_130680530 LuxR family transcriptional regulator -
ELI46_RS29595 (ELI46_29595) 20840..21544 + 705 WP_130680531 autoinducer binding domain-containing protein -
ELI46_RS29600 (ELI46_29600) 21548..21838 - 291 WP_130680532 transcriptional repressor TraM -
ELI46_RS29605 (ELI46_29605) 22130..22378 + 249 WP_130680533 helix-turn-helix transcriptional regulator -
ELI46_RS29610 (ELI46_29610) 22499..23131 + 633 WP_130680534 DUF433 domain-containing protein -
ELI46_RS29615 (ELI46_29615) 23128..23502 + 375 WP_130680535 DUF5615 family PIN-like protein -
ELI46_RS29620 (ELI46_29620) 23844..24464 - 621 WP_130738439 TraH family protein virB1
ELI46_RS29625 (ELI46_29625) 24481..25647 - 1167 WP_130680551 conjugal transfer protein TraB -
ELI46_RS29630 (ELI46_29630) 25637..26134 - 498 WP_245484661 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1616 GenBank   NZ_SIQT01000006
Plasmid name   pSM165B_Rh07 Incompatibility group   -
Plasmid size   44270 bp Coordinate of oriT [Strand]   29602..29635 [-]
Host baterium   Rhizobium ruizarguesonis strain SM165B

Cargo genes

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