Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102527
Name   oriT_pSM154C_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM154C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQC01000007 (56284..56317 [-], 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_pSM154C_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1878 GenBank   WP_130679584
Name   traA_ELI29_RS33780_pSM154C_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: 123120.17 Da        Isoelectric Point: 9.8201

>WP_130679584.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCARMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAQGMVADWVYHDVLGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGNTDDFNAFRDGWFACQNKHLALAG
LDLRIDGRSFERQGIDLEPTIHLGVGTKAIERKAEQSDHKSETSTPKLERIALQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSREALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVAGGERIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEREAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRKLNDMARAKLVERSVIADGSAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEATPGRVVAELGEGEHRRLVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGFHLVNVARTIADDRLQWAVRQKQKLADLGARLAAIAAALGLVRGSNKHSIPNTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYANPEAAFKAINVDTMLKDQSVAQS
TLARVAGEPESFGALKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLSLAAKDTSG
KTFETVTAGMTAGQKAEVQSAWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-740)

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   1477 GenBank   WP_130679568
Name   t4cp2_ELI29_RS33685_pSM154C_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: 91622.37 Da        Isoelectric Point: 5.9765

>WP_130679568.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPTEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFSNTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDSVEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPALTYLFRRIEKRLEGSPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREFGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGRHWPIHWLETRGVHDAASLFK

  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   1478 GenBank   WP_130679587
Name   traG_ELI29_RS33795_pSM154C_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: 69275.44 Da        Isoelectric Point: 9.3423

>WP_130679587.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTINRIALVVVPAALMILAVIGMTGIEHGLSGIGKTETARLAWGRAGIALPYLASAAVGILFLFATAGSI
SIKQAGWGVVAGCSGTILIAALRESMRLATFTKALPADKTVFAYLDPATSIGMVAAFMCACFAVRVAFIG
NAAFASAAPKRIRGKRALHGEADWMKLTEAAKLFAEAGGIVIGERYRVDKDSAAAQAFSADSADTWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDNGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRNFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKASVG
PNRFHMIGDTPKPA

  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: 35422..51145

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI29_RS37575 30468..30611 - 144 Protein_30 replication initiation protein RepC -
ELI29_RS33650 (ELI29_33640) 30749..31963 - 1215 WP_130679561 plasmid replication protein RepC -
ELI29_RS33655 (ELI29_33645) 32155..33189 - 1035 WP_130679562 plasmid partitioning protein RepB -
ELI29_RS33660 (ELI29_33650) 33186..34409 - 1224 WP_130679563 plasmid partitioning protein RepA -
ELI29_RS33665 (ELI29_33655) 34788..35411 + 624 WP_130679564 acyl-homoserine-lactone synthase -
ELI29_RS33670 (ELI29_33660) 35422..36399 + 978 WP_130679565 P-type conjugative transfer ATPase TrbB virB11
ELI29_RS33675 (ELI29_33665) 36389..36772 + 384 WP_130679566 TrbC/VirB2 family protein virB2
ELI29_RS33680 (ELI29_33670) 36765..37064 + 300 WP_130679567 conjugal transfer protein TrbD virB3
ELI29_RS33685 (ELI29_33675) 37075..39525 + 2451 WP_130679568 conjugal transfer protein TrbE virb4
ELI29_RS33690 (ELI29_33680) 39503..40300 + 798 WP_130679569 P-type conjugative transfer protein TrbJ virB5
ELI29_RS33695 (ELI29_33685) 40297..40497 + 201 WP_130679570 entry exclusion protein TrbK -
ELI29_RS33700 (ELI29_33690) 40491..41672 + 1182 WP_130679571 P-type conjugative transfer protein TrbL virB6
ELI29_RS33705 (ELI29_33695) 41693..42355 + 663 WP_130679572 conjugal transfer protein TrbF virB8
ELI29_RS33710 (ELI29_33700) 42373..43185 + 813 WP_130679573 P-type conjugative transfer protein TrbG virB9
ELI29_RS33715 (ELI29_33705) 43189..43629 + 441 WP_130679574 conjugal transfer protein TrbH -
ELI29_RS33720 (ELI29_33710) 43641..44927 + 1287 WP_130685537 IncP-type conjugal transfer protein TrbI virB10
ELI29_RS33725 (ELI29_33715) 45111..45851 + 741 WP_130679576 LuxR family transcriptional regulator -
ELI29_RS33730 (ELI29_33720) 45957..46661 + 705 WP_130679577 autoinducer binding domain-containing protein -
ELI29_RS33735 (ELI29_33725) 46665..46955 - 291 WP_130679578 transcriptional repressor TraM -
ELI29_RS33740 (ELI29_33730) 47247..47495 + 249 WP_130679579 helix-turn-helix transcriptional regulator -
ELI29_RS33745 (ELI29_33735) 47616..48248 + 633 WP_130679580 DUF433 domain-containing protein -
ELI29_RS33750 (ELI29_33740) 48245..48619 + 375 WP_087003573 DUF5615 family PIN-like protein -
ELI29_RS33755 (ELI29_33745) 48910..49737 + 828 WP_245487467 aminoglycoside phosphotransferase family protein -
ELI29_RS33760 (ELI29_33750) 49895..50344 - 450 WP_130679913 GNAT family N-acetyltransferase -
ELI29_RS33765 (ELI29_33755) 50525..51145 - 621 WP_130679581 TraH family protein virB1
ELI29_RS33770 (ELI29_33760) 51162..52325 - 1164 WP_130679582 conjugal transfer protein TraB -
ELI29_RS33775 (ELI29_33765) 52315..52824 - 510 WP_245487465 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2971 GenBank   NZ_SIQC01000007
Plasmid name   pSM154C_Rh08 Incompatibility group   -
Plasmid size   177216 bp Coordinate of oriT [Strand]   56284..56317 [-]
Host baterium   Rhizobium leguminosarum strain SM154C

Cargo genes

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