Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101142
Name   oriT_pSM157C_Rh03_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM157C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQI01000004 (34193..34226 [-], 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_pSM157C_Rh03_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1141 GenBank   WP_130680553
Name   traA_ELI35_RS30210_pSM157C_Rh03_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: 122693.44 Da        Isoelectric Point: 9.6904

>WP_130680553.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKFVYQLWAGSTEDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQGPEALRLERERINFATGSRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWEIRWNQSRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDAALDLARGNVGKA
VDAYRGYGHVRGLDLKAQAVESLIADWNHGYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLGKVVEASRNRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYD
KASFYGQALRFAEARGFHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSFPDTI
KEAKPMVSGITTFPQTLDQAVEDKLAADPGLKKQWEDVSTRFQLVYATPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPESFGAIKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTGG
KTFETVTAGMTAGQKAEVQSAWNAMRTVQQLGSHERTTEAHKQAETLQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-572)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(686-740)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   703 GenBank   WP_130680549
Name   t4cp2_ELI35_RS30095_pSM157C_Rh03_Rh08 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91492.16 Da        Isoelectric Point: 5.6886

>WP_130680549.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREVLQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAANSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGNSLLPLTLAASGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVAITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRTLKSEHGHDWPIHWLETRGVHDAASLFK

  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   704 GenBank   WP_130657461
Name   traG_ELI35_RS30225_pSM157C_Rh03_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: 69518.76 Da        Isoelectric Point: 8.9386

>WP_130657461.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALAVMPAALMILVVIGMTGIEQWLSGFGKTEAARLAWGRTGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTETLNADKSVLAYLDPATAIGAGVALMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRIDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGHTDG
HDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFATNDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKVRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPKPA

  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: 8837..18343

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI35_RS30060 (ELI35_30070) 4164..5378 - 1215 WP_130666985 plasmid replication protein RepC -
ELI35_RS30065 (ELI35_30075) 5568..6605 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI35_RS30070 (ELI35_30080) 6602..7825 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI35_RS30075 (ELI35_30085) 8202..8840 + 639 WP_130657452 acyl-homoserine-lactone synthase -
ELI35_RS30080 (ELI35_30090) 8837..9814 + 978 WP_130680548 P-type conjugative transfer ATPase TrbB virB11
ELI35_RS30085 (ELI35_30095) 9804..10187 + 384 WP_130680522 TrbC/VirB2 family protein virB2
ELI35_RS30090 (ELI35_30100) 10180..10479 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI35_RS30095 (ELI35_30105) 10490..12940 + 2451 WP_130680549 conjugal transfer protein TrbE virb4
ELI35_RS30100 (ELI35_30110) 12918..13715 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI35_RS30105 (ELI35_30115) 13712..13912 + 201 WP_065276637 entry exclusion protein TrbK -
ELI35_RS30110 (ELI35_30120) 13906..15087 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI35_RS30115 (ELI35_30125) 15108..15765 + 658 Protein_15 conjugal transfer protein TrbF -
ELI35_RS30120 (ELI35_30130) 15783..16595 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI35_RS30125 (ELI35_30135) 16599..17033 + 435 WP_130657454 conjugal transfer protein TrbH -
ELI35_RS30130 (ELI35_30140) 17045..18343 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELI35_RS30135 (ELI35_30145) 18654..19358 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI35_RS30140 (ELI35_30150) 19362..19685 - 324 WP_130657456 transcriptional repressor TraM -
ELI35_RS30145 (ELI35_30155) 19908..20150 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI35_RS40230 (ELI35_30160) 20253..20690 + 438 Protein_22 hypothetical protein -
ELI35_RS30155 (ELI35_30165) 20781..21398 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI35_RS30160 (ELI35_30170) 21391..22260 + 870 Protein_24 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI35_RS30165 (ELI35_30175) 22471..22881 + 411 WP_018244910 transposase -
ELI35_RS30170 (ELI35_30180) 22878..23123 + 246 WP_130660511 IS66 family insertion sequence element accessory protein TnpB -

Host bacterium

ID   1586 GenBank   NZ_SIQI01000004
Plasmid name   pSM157C_Rh03_Rh08 Incompatibility group   -
Plasmid size   280831 bp Coordinate of oriT [Strand]   34193..34226 [-]
Host baterium   Rhizobium ruizarguesonis strain SM157C

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD, fixG, fixQ, fixO, fixN, nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifT, nodJ, nodI, nodC, nodA, nodF, nodE, nodM
Anti-CRISPR   -