Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101160
Name   oriT_pSM165A_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM165A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQS01000006 (84779..84812 [-], 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_pSM165A_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1157 GenBank   WP_130657460
Name   traA_ELI45_RS31830_pSM165A_Rh08 insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 122987.83 Da        Isoelectric Point: 9.6219

>WP_130657460.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKFVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKVEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQGPEALRLERERINFATGSRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWEIRWNQSRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDAALDLARGNVGKA
VDAYRGYGHVRGLDLKAQAVESLIADWNHGYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLGKVVEASRNRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYD
KASFYGQALRFAEARGFHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSFPDTI
KEAKPMVSGITTFPQTLDQAVEDKLAADPGLKKQWEDVSTRFQLVYATPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPESFGAIKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSSAAKQTLERVRDVIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTDGQKAEVQSTWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(686-740)

AAA domain (AAA_30)

(387-572)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   735 GenBank   WP_065276635
Name   t4cp2_ELI45_RS31725_pSM165A_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: 91588.38 Da        Isoelectric Point: 5.9977

>WP_065276635.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKPFRVTGPSFADLVPYAGLIDDGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSKDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNALRELEQYFANSLSIRRMETRETFERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETQDAIAQASSRLVAYGYYTPVVVL
FDIDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
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   736 GenBank   WP_130657461
Name   traG_ELI45_RS31845_pSM165A_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: 62705..79643

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI45_RS31690 (ELI45_31685) 58032..59246 - 1215 WP_130657450 plasmid replication protein RepC -
ELI45_RS31695 (ELI45_31690) 59436..60473 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI45_RS31700 (ELI45_31695) 60470..61693 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI45_RS31705 (ELI45_31700) 62070..62708 + 639 WP_130657452 acyl-homoserine-lactone synthase -
ELI45_RS31710 (ELI45_31705) 62705..63682 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELI45_RS31715 (ELI45_31710) 63672..64055 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI45_RS31720 (ELI45_31715) 64048..64347 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI45_RS31725 (ELI45_31720) 64358..66808 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELI45_RS31730 (ELI45_31725) 66786..67583 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI45_RS31735 (ELI45_31730) 67580..67780 + 201 WP_065276637 entry exclusion protein TrbK -
ELI45_RS31740 (ELI45_31735) 67774..68955 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI45_RS31745 (ELI45_31740) 68976..69638 + 663 WP_065276639 conjugal transfer protein TrbF virB8
ELI45_RS31750 (ELI45_31745) 69656..70468 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI45_RS31755 (ELI45_31750) 70472..70906 + 435 WP_130657454 conjugal transfer protein TrbH -
ELI45_RS31760 (ELI45_31755) 70918..72216 + 1299 WP_130657455 IncP-type conjugal transfer protein TrbI virB10
ELI45_RS31765 (ELI45_31760) 72527..73231 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI45_RS31770 (ELI45_31765) 73235..73558 - 324 WP_130657456 transcriptional repressor TraM -
ELI45_RS31775 (ELI45_31770) 73781..74023 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI45_RS40130 (ELI45_31775) 74126..74563 + 438 Protein_81 hypothetical protein -
ELI45_RS31785 (ELI45_31780) 74654..75271 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI45_RS31790 (ELI45_31785) 75264..76133 + 870 Protein_83 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI45_RS31795 (ELI45_31790) 76344..76754 + 411 WP_018244910 transposase -
ELI45_RS31800 (ELI45_31795) 76751..76956 + 206 WP_130657493 IS66 family insertion sequence element accessory protein TnpB -
ELI45_RS31805 (ELI45_31800) 77057..77200 + 144 WP_165411116 IS66 family insertion sequence element accessory protein TnpB -
ELI45_RS31810 (ELI45_31805) 77246..78901 + 1656 WP_065276572 IS66 family transposase -
ELI45_RS31815 (ELI45_31810) 79026..79643 - 618 WP_130657457 TraH family protein virB1
ELI45_RS31820 (ELI45_31815) 79660..80823 - 1164 WP_130657458 conjugal transfer protein TraB -
ELI45_RS31825 (ELI45_31820) 80813..81376 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1604 GenBank   NZ_SIQS01000006
Plasmid name   pSM165A_Rh08 Incompatibility group   -
Plasmid size   273673 bp Coordinate of oriT [Strand]   84779..84812 [-]
Host baterium   Rhizobium ruizarguesonis strain SM165A

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   -