Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102575
Name   oriT_pSM138B_Rh13 in_silico
Organism   Rhizobium leguminosarum strain SM138B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOU01000007 (131510..131543 [+], 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_pSM138B_Rh13
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1923 GenBank   WP_130747837
Name   traA_ELH95_RS31510_pSM138B_Rh13 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: 122627.81 Da        Isoelectric Point: 9.9195

>WP_130747837.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLAEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSPPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDNVALFQSLMVRILQSPEALRLERERINFAIGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLQATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIGSRTLSSWELRWNQGRNQLDHKTVFVLDEAGMVSSRQM
ALLVETVTKAGAKLVLVGDPEQLQPIAAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRKLNDMARAKLVERSVIADGSAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEATPGRVVAELGEGEHRRLVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGFHLVNVARTIADDRLQWAVRQKQKLADLGARLAAIAAALGLVRGSNKHSIPNTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYANPEAAFKAINVDTMLKDQSVAQS
TLARVAGEPESFGALKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLDYALADKMVKAELEGFAKAVSERFGERTFLSLAAKDTSG
KTFETVTAGMTAGQKAEVQSAWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-740)

AAA domain (AAA_30)

(387-570)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   1548 GenBank   WP_130747834
Name   traG_ELH95_RS31495_pSM138B_Rh13 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: 69379.45 Da        Isoelectric Point: 9.3498

>WP_130747834.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTINRIALVIVPAALMIPVVIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYVAGAVIGVLLLFASAGSI
NIKQAGWGVVAGSSGTILVAAVRETVRLSSFMKTVPADKTVLAFLDPATSIGASAALLCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAQLFPDAGGIVIGERYRVDKDNVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGGAGRDVFILD
PRKPDVGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGSRGVRDDFFRASALQLLTALIADVCLSGHTDE
KEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKASVG
PNRFHMIGDTPKPA

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(163-634)

  Protein structure



No available structure.



ID   1549 GenBank   WP_130747842
Name   t4cp2_ELH95_RS31605_pSM138B_Rh13 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: 91606.33 Da        Isoelectric Point: 5.7770

>WP_130747842.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVIAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSSLLPLTLAADGDHYEIGGDNAEEGRALAFCPLSDLKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
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: 136682..152411

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH95_RS31515 (ELH95_31520) 135003..135512 + 510 WP_245487465 conjugative transfer signal peptidase TraF -
ELH95_RS31520 (ELH95_31525) 135502..136665 + 1164 WP_130679582 conjugal transfer protein TraB -
ELH95_RS31525 (ELH95_31530) 136682..137302 + 621 WP_130679581 TraH family protein virB1
ELH95_RS31530 (ELH95_31535) 137483..137932 + 450 WP_130679913 GNAT family N-acetyltransferase -
ELH95_RS31535 (ELH95_31540) 138090..138917 - 828 WP_245487467 aminoglycoside phosphotransferase family protein -
ELH95_RS31540 (ELH95_31545) 139208..139582 - 375 WP_087003573 DUF5615 family PIN-like protein -
ELH95_RS31545 (ELH95_31550) 139579..140211 - 633 WP_130679580 DUF433 domain-containing protein -
ELH95_RS31550 (ELH95_31555) 140332..140580 - 249 WP_130679579 helix-turn-helix transcriptional regulator -
ELH95_RS31555 (ELH95_31560) 140872..141162 + 291 WP_130679578 transcriptional repressor TraM -
ELH95_RS31560 (ELH95_31565) 141166..141870 - 705 WP_130679577 autoinducer binding domain-containing protein -
ELH95_RS31565 (ELH95_31570) 141976..142716 - 741 WP_130747838 LuxR family transcriptional regulator -
ELH95_RS31570 (ELH95_31575) 142900..144195 - 1296 WP_130747839 IncP-type conjugal transfer protein TrbI virB10
ELH95_RS31575 (ELH95_31580) 144207..144647 - 441 WP_130747840 conjugal transfer protein TrbH -
ELH95_RS31580 (ELH95_31585) 144651..145463 - 813 WP_130747841 P-type conjugative transfer protein TrbG virB9
ELH95_RS31585 (ELH95_31590) 145481..146143 - 663 WP_130679572 conjugal transfer protein TrbF virB8
ELH95_RS31590 (ELH95_31595) 146164..147345 - 1182 WP_130679571 P-type conjugative transfer protein TrbL virB6
ELH95_RS31595 (ELH95_31600) 147339..147539 - 201 WP_130679570 entry exclusion protein TrbK -
ELH95_RS31600 (ELH95_31605) 147536..148333 - 798 WP_130679569 P-type conjugative transfer protein TrbJ virB5
ELH95_RS31605 (ELH95_31610) 148311..150761 - 2451 WP_130747842 conjugal transfer protein TrbE virb4
ELH95_RS31610 (ELH95_31615) 150772..151071 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELH95_RS31615 (ELH95_31620) 151064..151444 - 381 WP_130747843 TrbC/VirB2 family protein virB2
ELH95_RS31620 (ELH95_31625) 151434..152411 - 978 WP_130747844 P-type conjugative transfer ATPase TrbB virB11
ELH95_RS31625 (ELH95_31630) 152422..153042 - 621 WP_130747845 acyl-homoserine-lactone synthase -
ELH95_RS31630 (ELH95_31635) 153422..154618 + 1197 WP_130747846 plasmid partitioning protein RepA -
ELH95_RS31635 (ELH95_31640) 154742..155701 + 960 WP_130747847 plasmid partitioning protein RepB -
ELH95_RS31640 (ELH95_31645) 155874..157091 + 1218 WP_130747848 plasmid replication protein RepC -

Host bacterium

ID   3019 GenBank   NZ_SIOU01000007
Plasmid name   pSM138B_Rh13 Incompatibility group   -
Plasmid size   183277 bp Coordinate of oriT [Strand]   131510..131543 [+]
Host baterium   Rhizobium leguminosarum strain SM138B

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7