Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102528
Name   oriT_pSM168A_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM168A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQX01000004 (95211..95248 [-], 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_pSM168A_Rh08
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1879 GenBank   WP_130654295
Name   traA_ELI50_RS32605_pSM168A_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: 122889.15 Da        Isoelectric Point: 9.8379

>WP_130654295.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLIEDGFGSKKVAILGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPTKYTTREM
IRIEAEMANHAIWLSARASHGVREAVLHATFARHSRLSDEQRTAIEHVAGATRIAAIIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNRLDDKTVIVLDEAGMVSSRQM
ALLVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLARVLEAASGRIVAEIGDGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYQ
KSALYRQALRFAEARGLQLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSIRDTI
KEAKPMVSGITTFPKSLDQAVEGKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDAMLTDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   1479 GenBank   WP_130654280
Name   t4cp2_ELI50_RS32520_pSM168A_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: 91543.33 Da        Isoelectric Point: 5.5133

>WP_130654280.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKPFRVTGPSFADLVPYAGLIDDGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSKDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANSLSIRRMETRETFERGGERIARYDELLQFARFCTTG
ESHPIRLPDIPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLESTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDRDREGLLEKAEAIRRLIQVEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGNSLLSLTLAAGADYYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMAIASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
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   1480 GenBank   WP_130654298
Name   traG_ELI50_RS32620_pSM168A_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: 69354.56 Da        Isoelectric Point: 9.2319

>WP_130654298.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTINRIALVIVPAALMILVVIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYGASAAIGILFLFASAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTKALNADKSVLAYLDPATAIGAGVALMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLLPDAGGIVIGERYRVDKDNVGSQAFRADSAETWGASG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDG
HDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFATNDIAAGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGQMKGRALFLLDEVARLGY
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: 75939..90075

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI50_RS32485 (ELI50_32485) 71265..72479 - 1215 WP_130654329 plasmid replication protein RepC -
ELI50_RS32490 (ELI50_32490) 72670..73707 - 1038 WP_130654275 plasmid partitioning protein RepB -
ELI50_RS32495 (ELI50_32495) 73704..74927 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI50_RS32500 (ELI50_32500) 75304..75942 + 639 WP_130654277 acyl-homoserine-lactone synthase -
ELI50_RS32505 (ELI50_32505) 75939..76916 + 978 WP_130654278 P-type conjugative transfer ATPase TrbB virB11
ELI50_RS32510 (ELI50_32510) 76906..77289 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI50_RS32515 (ELI50_32515) 77282..77581 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI50_RS32520 (ELI50_32520) 77592..80042 + 2451 WP_130654280 conjugal transfer protein TrbE virb4
ELI50_RS32525 (ELI50_32525) 80020..80817 + 798 WP_130654281 P-type conjugative transfer protein TrbJ virB5
ELI50_RS32530 (ELI50_32530) 80811..80987 + 177 WP_130654282 entry exclusion protein TrbK -
ELI50_RS32535 (ELI50_32535) 80992..82179 + 1188 WP_130654283 P-type conjugative transfer protein TrbL virB6
ELI50_RS32540 (ELI50_32540) 82200..82862 + 663 WP_130654284 conjugal transfer protein TrbF virB8
ELI50_RS32545 (ELI50_32545) 82880..83692 + 813 WP_130654285 P-type conjugative transfer protein TrbG virB9
ELI50_RS32550 (ELI50_32550) 83696..84136 + 441 WP_130654286 conjugal transfer protein TrbH -
ELI50_RS32555 (ELI50_32555) 84148..85446 + 1299 WP_130654287 IncP-type conjugal transfer protein TrbI virB10
ELI50_RS32560 (ELI50_32560) 85758..86462 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI50_RS32565 (ELI50_32565) 86466..86789 - 324 WP_130654289 transcriptional repressor TraM -
ELI50_RS32570 (ELI50_32570) 87012..87254 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI50_RS37880 (ELI50_32575) 87357..87788 + 432 Protein_92 hypothetical protein -
ELI50_RS32580 (ELI50_32580) 87879..88496 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI50_RS32585 (ELI50_32585) 88489..89355 + 867 Protein_94 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI50_RS32590 (ELI50_32590) 89458..90075 - 618 WP_130654292 TraH family protein virB1
ELI50_RS32595 (ELI50_32595) 90092..91255 - 1164 WP_130654293 conjugal transfer protein TraB -
ELI50_RS32600 (ELI50_32600) 91245..91808 - 564 WP_130654294 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2972 GenBank   NZ_SIQX01000004
Plasmid name   pSM168A_Rh08 Incompatibility group   -
Plasmid size   153113 bp Coordinate of oriT [Strand]   95211..95248 [-]
Host baterium   Rhizobium leguminosarum strain SM168A

Cargo genes

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