Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102532
Name   oriT_pSM160_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM160
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQL01000005 (93845..93882 [-], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 38 nt

>oriT_pSM160_Rh08
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1883 GenBank   WP_130729904
Name   traA_ELI38_RS35340_pSM160_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: 122848.14 Da        Isoelectric Point: 9.8768

>WP_130729904.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLIEDGFGSKKVAILGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSARASHGVREAVLHATFARHSRLSDEQRTAIEHVAGATRIAAIIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNRLDDKTVIVLDEAGMVSSRQM
ALLVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLARVLEAASGRIVAEIGDGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLAYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYQ
KSALYRQALRFAEARGLQLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSIRDTI
KEAKPMVSGITTFPKSLDQAVEGKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDAMLTDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   1482 GenBank   WP_130729901
Name   t4cp2_ELI38_RS35255_pSM160_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: 91439.18 Da        Isoelectric Point: 5.8944

>WP_130729901.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKPFRVTGPSFADLVPYAGLIDDGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSKDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANSLSIRRMETRETFERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLESTRKKWQQKVRPFFEQIFQTQSRSVDQDAMTMVVETQDAIAQASSRLVAYGYYTPVVVL
FDIDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
HRNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATATPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSENGHDWPIHWLETRGVHDAAPLLK

  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   1483 GenBank   WP_130729905
Name   traG_ELI38_RS35355_pSM160_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: 69418.64 Da        Isoelectric Point: 9.3575

>WP_130729905.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTINRIALVIVPAALMIPVVIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYGASAAIGILFLFASAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTKALNADKSVLAYLDPATAIGAGVALMCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLLPDAGGIVIGERYRVDKDNVGSQAFRADSAETWGASG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTEE
KEQTLRRVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGQMKGRALFLLDEVARLGY
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: 74574..88709

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI38_RS35220 (ELI38_35210) 69901..71115 - 1215 WP_130729900 plasmid replication protein RepC -
ELI38_RS35225 (ELI38_35215) 71305..72342 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI38_RS35230 (ELI38_35220) 72339..73562 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI38_RS35235 (ELI38_35225) 73939..74577 + 639 WP_130654277 acyl-homoserine-lactone synthase -
ELI38_RS35240 (ELI38_35230) 74574..75551 + 978 WP_130654278 P-type conjugative transfer ATPase TrbB virB11
ELI38_RS35245 (ELI38_35235) 75541..75924 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI38_RS35250 (ELI38_35240) 75917..76216 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI38_RS35255 (ELI38_35245) 76227..78677 + 2451 WP_130729901 conjugal transfer protein TrbE virb4
ELI38_RS35260 (ELI38_35250) 78655..79452 + 798 WP_130654281 P-type conjugative transfer protein TrbJ virB5
ELI38_RS35265 (ELI38_35255) 79446..79622 + 177 WP_130654282 entry exclusion protein TrbK -
ELI38_RS35270 (ELI38_35260) 79627..80814 + 1188 WP_130654283 P-type conjugative transfer protein TrbL virB6
ELI38_RS35275 (ELI38_35265) 80835..81497 + 663 WP_130654284 conjugal transfer protein TrbF virB8
ELI38_RS35280 (ELI38_35270) 81515..82327 + 813 WP_130729902 P-type conjugative transfer protein TrbG virB9
ELI38_RS35285 (ELI38_35275) 82331..82771 + 441 WP_130654286 conjugal transfer protein TrbH -
ELI38_RS35290 (ELI38_35280) 82783..84081 + 1299 WP_130654287 IncP-type conjugal transfer protein TrbI virB10
ELI38_RS35295 (ELI38_35285) 84393..85097 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI38_RS35300 (ELI38_35290) 85101..85424 - 324 WP_130654289 transcriptional repressor TraM -
ELI38_RS35305 (ELI38_35295) 85646..85888 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI38_RS37265 (ELI38_35300) 85991..86422 + 432 Protein_89 hypothetical protein -
ELI38_RS35315 (ELI38_35305) 86513..87130 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI38_RS35320 (ELI38_35310) 87123..87989 + 867 Protein_91 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI38_RS35325 (ELI38_35315) 88092..88709 - 618 WP_130654292 TraH family protein virB1
ELI38_RS35330 (ELI38_35320) 88726..89889 - 1164 WP_130729903 conjugal transfer protein TraB -
ELI38_RS35335 (ELI38_35325) 89879..90442 - 564 WP_130714114 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2976 GenBank   NZ_SIQL01000005
Plasmid name   pSM160_Rh08 Incompatibility group   -
Plasmid size   107263 bp Coordinate of oriT [Strand]   93845..93882 [-]
Host baterium   Rhizobium leguminosarum strain SM160

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -