Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102552
Name   oriT_pSM52_Rh21 in_silico
Organism   Rhizobium leguminosarum strain SM52
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SILH01000006 (193955..193988 [+], 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_pSM52_Rh21
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1903 GenBank   WP_130657460
Name   traA_ELH04_RS36835_pSM52_Rh21 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   1515 GenBank   WP_130657461
Name   traG_ELH04_RS36820_pSM52_Rh21 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.



ID   1516 GenBank   WP_065276635
Name   t4cp2_ELH04_RS36935_pSM52_Rh21 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 199124..215953

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH04_RS36840 (ELH04_36840) 197391..197954 + 564 WP_130657459 conjugative transfer signal peptidase TraF -
ELH04_RS36845 (ELH04_36845) 197944..199107 + 1164 WP_130657458 conjugal transfer protein TraB -
ELH04_RS36850 (ELH04_36850) 199124..199741 + 618 WP_130657457 TraH family protein virB1
ELH04_RS36855 (ELH04_36855) 199866..201521 - 1656 WP_130813594 IS66 family transposase -
ELH04_RS36860 (ELH04_36860) 201567..201914 - 348 WP_018244911 IS66 family insertion sequence element accessory protein TnpB -
ELH04_RS36865 (ELH04_36865) 201911..202321 - 411 WP_018244910 transposase -
ELH04_RS36870 (ELH04_36870) 202532..203400 - 869 Protein_190 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH04_RS36875 (ELH04_36875) 203393..204010 - 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH04_RS38320 (ELH04_36880) 204101..204532 - 432 Protein_192 hypothetical protein -
ELH04_RS36885 (ELH04_36885) 204635..204877 - 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELH04_RS36890 (ELH04_36890) 205100..205423 + 324 WP_130657456 transcriptional repressor TraM -
ELH04_RS36895 (ELH04_36895) 205427..206131 - 705 WP_130654288 autoinducer binding domain-containing protein -
ELH04_RS36900 (ELH04_36900) 206442..207740 - 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELH04_RS36905 (ELH04_36905) 207752..208186 - 435 WP_130657454 conjugal transfer protein TrbH -
ELH04_RS36910 (ELH04_36910) 208190..209002 - 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELH04_RS36915 (ELH04_36915) 209020..209682 - 663 WP_065276639 conjugal transfer protein TrbF virB8
ELH04_RS36920 (ELH04_36920) 209703..210884 - 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELH04_RS36925 (ELH04_36925) 210878..211078 - 201 WP_130813595 entry exclusion protein TrbK -
ELH04_RS36930 (ELH04_36930) 211075..211872 - 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELH04_RS36935 (ELH04_36935) 211850..214300 - 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELH04_RS36940 (ELH04_36940) 214311..214610 - 300 WP_130654279 conjugal transfer protein TrbD virB3
ELH04_RS36945 (ELH04_36945) 214603..214986 - 384 WP_130813596 TrbC/VirB2 family protein virB2
ELH04_RS36950 (ELH04_36950) 214976..215953 - 978 WP_130813597 P-type conjugative transfer ATPase TrbB virB11
ELH04_RS36955 (ELH04_36955) 215950..216588 - 639 WP_130813598 acyl-homoserine-lactone synthase -
ELH04_RS36960 (ELH04_36960) 216977..218167 + 1191 WP_097595931 plasmid partitioning protein RepA -
ELH04_RS36965 (ELH04_36965) 218252..219244 + 993 WP_130813599 plasmid partitioning protein RepB -
ELH04_RS36970 (ELH04_36970) 219402..220643 + 1242 WP_130813600 plasmid replication protein RepC -

Host bacterium

ID   2996 GenBank   NZ_SILH01000006
Plasmid name   pSM52_Rh21 Incompatibility group   -
Plasmid size   281137 bp Coordinate of oriT [Strand]   193955..193988 [+]
Host baterium   Rhizobium leguminosarum strain SM52

Cargo genes

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