Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102583
Name   oriT_pSM135B_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM135B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOP01000005 (257955..257988 [-], 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_pSM135B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1931 GenBank   WP_130657460
Name   traA_ELH90_RS36515_pSM135B_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   1560 GenBank   WP_065276635
Name   t4cp2_ELH90_RS36400_pSM135B_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   1561 GenBank   WP_130657461
Name   traG_ELH90_RS36530_pSM135B_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: 233423..252819

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH90_RS36365 (ELH90_36365) 228750..229964 - 1215 WP_065276629 plasmid replication protein RepC -
ELH90_RS36370 (ELH90_36370) 230154..231191 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELH90_RS36375 (ELH90_36375) 231188..232411 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELH90_RS36380 (ELH90_36380) 232788..233426 + 639 WP_130660092 acyl-homoserine-lactone synthase -
ELH90_RS36385 (ELH90_36385) 233423..234400 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELH90_RS36390 (ELH90_36390) 234390..234773 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELH90_RS36395 (ELH90_36395) 234766..235065 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELH90_RS36400 (ELH90_36400) 235076..237526 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELH90_RS36405 (ELH90_36405) 237504..238301 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELH90_RS36410 (ELH90_36410) 238298..238498 + 201 WP_065276637 entry exclusion protein TrbK -
ELH90_RS36415 (ELH90_36415) 238492..239673 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELH90_RS36420 (ELH90_36420) 239694..240356 + 663 WP_065276639 conjugal transfer protein TrbF virB8
ELH90_RS36425 (ELH90_36425) 240374..241186 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELH90_RS36430 (ELH90_36430) 241190..241624 + 435 WP_130657454 conjugal transfer protein TrbH -
ELH90_RS36435 (ELH90_36435) 241636..242934 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELH90_RS36440 (ELH90_36440) 243245..243949 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELH90_RS36445 (ELH90_36445) 243953..244276 - 324 WP_130657456 transcriptional repressor TraM -
ELH90_RS36450 (ELH90_36450) 244499..244741 + 243 WP_130719472 helix-turn-helix transcriptional regulator -
ELH90_RS39835 (ELH90_36455) 244844..245275 + 432 Protein_240 hypothetical protein -
ELH90_RS36460 (ELH90_36460) 245366..245983 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH90_RS36465 (ELH90_36465) 245976..246844 + 869 Protein_242 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH90_RS36470 (ELH90_36470) 247055..247465 + 411 WP_018244910 transposase -
ELH90_RS36475 (ELH90_36475) 247462..247809 + 348 WP_018244911 IS66 family insertion sequence element accessory protein TnpB -
ELH90_RS36480 (ELH90_36480) 247855..249516 + 1662 WP_130719473 IS66 family transposase -
ELH90_RS36485 (ELH90_36485) 249560..249970 + 411 WP_018244910 transposase -
ELH90_RS36490 (ELH90_36490) 249967..250314 + 348 WP_130719474 IS66 family insertion sequence element accessory protein TnpB -
ELH90_RS36495 (ELH90_36495) 250360..252015 + 1656 WP_130719475 IS66 family transposase -
ELH90_RS36500 (ELH90_36500) 252202..252819 - 618 WP_130657457 TraH family protein virB1
ELH90_RS36505 (ELH90_36505) 252836..253999 - 1164 WP_130657458 conjugal transfer protein TraB -
ELH90_RS36510 (ELH90_36510) 253989..254552 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   3027 GenBank   NZ_SIOP01000005
Plasmid name   pSM135B_Rh08 Incompatibility group   -
Plasmid size   290433 bp Coordinate of oriT [Strand]   257955..257988 [-]
Host baterium   Rhizobium leguminosarum strain SM135B

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   -