Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101162
Name   oriT_pSM148B_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM148B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPL01000006 (78982..79015 [-], 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_pSM148B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1159 GenBank   WP_130657460
Name   traA_ELI12_RS30910_pSM148B_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   739 GenBank   WP_065276635
Name   t4cp2_ELI12_RS30820_pSM148B_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   740 GenBank   WP_130657461
Name   traG_ELI12_RS30925_pSM148B_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: 58710..73846

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI12_RS30785 (ELI12_30785) 54037..55251 - 1215 WP_065276629 plasmid replication protein RepC -
ELI12_RS30790 (ELI12_30790) 55441..56478 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI12_RS30795 (ELI12_30795) 56475..57698 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI12_RS30800 (ELI12_30800) 58075..58713 + 639 WP_130660092 acyl-homoserine-lactone synthase -
ELI12_RS30805 (ELI12_30805) 58710..59687 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELI12_RS30810 (ELI12_30810) 59677..60060 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI12_RS30815 (ELI12_30815) 60053..60352 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI12_RS30820 (ELI12_30820) 60363..62813 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELI12_RS30825 (ELI12_30825) 62791..63588 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI12_RS30830 (ELI12_30830) 63585..63785 + 201 WP_130676499 entry exclusion protein TrbK -
ELI12_RS30835 (ELI12_30835) 63779..64960 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI12_RS30840 (ELI12_30840) 64981..65643 + 663 WP_130676500 conjugal transfer protein TrbF virB8
ELI12_RS30845 (ELI12_30845) 65661..66473 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI12_RS30850 (ELI12_30850) 66477..66911 + 435 WP_130657454 conjugal transfer protein TrbH -
ELI12_RS30855 (ELI12_30855) 66923..68221 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELI12_RS30860 (ELI12_30860) 68532..69236 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI12_RS30865 (ELI12_30865) 69240..69563 - 324 WP_130654289 transcriptional repressor TraM -
ELI12_RS30870 (ELI12_30870) 69787..70029 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI12_RS40545 (ELI12_30875) 70132..70563 + 432 Protein_72 hypothetical protein -
ELI12_RS30880 (ELI12_30880) 70654..71271 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI12_RS30885 (ELI12_30885) 71264..71743 + 480 Protein_74 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI12_RS30890 (ELI12_30890) 71740..73104 + 1365 Protein_75 IS66 family transposase -
ELI12_RS30895 (ELI12_30895) 73229..73846 - 618 WP_130657457 TraH family protein virB1
ELI12_RS30900 (ELI12_30900) 73863..75026 - 1164 WP_130685430 conjugal transfer protein TraB -
ELI12_RS30905 (ELI12_30905) 75016..75579 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1606 GenBank   NZ_SIPL01000006
Plasmid name   pSM148B_Rh08 Incompatibility group   -
Plasmid size   267071 bp Coordinate of oriT [Strand]   78982..79015 [-]
Host baterium   Rhizobium ruizarguesonis strain SM148B

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   -