Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102523
Name   oriT_pSM144A_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM144A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPA01000007 (180389..180422 [+], 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_pSM144A_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1874 GenBank   WP_130679584
Name   traA_ELI01_RS31365_pSM144A_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   1472 GenBank   WP_130679587
Name   traG_ELI01_RS31350_pSM144A_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.



ID   1473 GenBank   WP_130679568
Name   t4cp2_ELI01_RS31460_pSM144A_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 185561..201284

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI01_RS31370 (ELI01_31375) 183882..184391 + 510 WP_245487465 conjugative transfer signal peptidase TraF -
ELI01_RS31375 (ELI01_31380) 184381..185544 + 1164 WP_130679582 conjugal transfer protein TraB -
ELI01_RS31380 (ELI01_31385) 185561..186181 + 621 WP_130679581 TraH family protein virB1
ELI01_RS31385 (ELI01_31390) 186362..186811 + 450 WP_130679913 GNAT family N-acetyltransferase -
ELI01_RS31390 (ELI01_31395) 186969..187796 - 828 WP_245487467 aminoglycoside phosphotransferase family protein -
ELI01_RS31395 (ELI01_31400) 188087..188461 - 375 WP_087003573 DUF5615 family PIN-like protein -
ELI01_RS31400 (ELI01_31405) 188458..189090 - 633 WP_130679580 DUF433 domain-containing protein -
ELI01_RS31405 (ELI01_31410) 189211..189459 - 249 WP_130679579 helix-turn-helix transcriptional regulator -
ELI01_RS31410 (ELI01_31415) 189751..190041 + 291 WP_130679578 transcriptional repressor TraM -
ELI01_RS31415 (ELI01_31420) 190045..190749 - 705 WP_130679577 autoinducer binding domain-containing protein -
ELI01_RS31420 (ELI01_31425) 190855..191595 - 741 WP_130679576 LuxR family transcriptional regulator -
ELI01_RS31425 (ELI01_31430) 191779..193065 - 1287 WP_130685537 IncP-type conjugal transfer protein TrbI virB10
ELI01_RS31430 (ELI01_31435) 193077..193517 - 441 WP_130679574 conjugal transfer protein TrbH -
ELI01_RS31435 (ELI01_31440) 193521..194333 - 813 WP_130741247 P-type conjugative transfer protein TrbG virB9
ELI01_RS31440 (ELI01_31445) 194351..195013 - 663 WP_130679572 conjugal transfer protein TrbF virB8
ELI01_RS31445 (ELI01_31450) 195034..196215 - 1182 WP_130679571 P-type conjugative transfer protein TrbL virB6
ELI01_RS31450 (ELI01_31455) 196209..196409 - 201 WP_130679570 entry exclusion protein TrbK -
ELI01_RS31455 (ELI01_31460) 196406..197203 - 798 WP_130679569 P-type conjugative transfer protein TrbJ virB5
ELI01_RS31460 (ELI01_31465) 197181..199631 - 2451 WP_130679568 conjugal transfer protein TrbE virb4
ELI01_RS31465 (ELI01_31470) 199642..199941 - 300 WP_130679567 conjugal transfer protein TrbD virB3
ELI01_RS31470 (ELI01_31475) 199934..200317 - 384 WP_130679566 TrbC/VirB2 family protein virB2
ELI01_RS31475 (ELI01_31480) 200307..201284 - 978 WP_130679565 P-type conjugative transfer ATPase TrbB virB11
ELI01_RS31480 (ELI01_31485) 201295..201918 - 624 WP_130679564 acyl-homoserine-lactone synthase -
ELI01_RS31485 (ELI01_31490) 202297..203520 + 1224 WP_130679563 plasmid partitioning protein RepA -
ELI01_RS31490 (ELI01_31495) 203517..204551 + 1035 WP_130679562 plasmid partitioning protein RepB -
ELI01_RS31495 (ELI01_31500) 204743..205957 + 1215 WP_130679561 plasmid replication protein RepC -
ELI01_RS36795 206095..206238 + 144 Protein_213 replication initiation protein RepC -

Host bacterium

ID   2967 GenBank   NZ_SIPA01000007
Plasmid name   pSM144A_Rh08 Incompatibility group   -
Plasmid size   220015 bp Coordinate of oriT [Strand]   180389..180422 [+]
Host baterium   Rhizobium leguminosarum strain SM144A

Cargo genes

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