Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102573
Name   oriT_pSM136A_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM136A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOQ01000007 (97187..97220 [-], 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_pSM136A_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1921 GenBank   WP_130705007
Name   traA_ELH91_RS30885_pSM136A_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: 123178.21 Da        Isoelectric Point: 9.7792

>WP_130705007.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCARMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAQGMVADWVYHDVLGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGNTDDFNAFRDGWFACQNKHLALAG
LDLRIDGRSFERQGIDLEPTIHLGVGTKAIERKAEQSDHKSETSTPKLERIALQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSREALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVAGGERIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEREAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRKLNDMARAKLVERSVIADGSAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEATPGRVVAELGEGEHRRLVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGFHLVNVARTIADDRLQWAVRQKQKLADLGARLAAIAAALGLVRGSNKHSIPNTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYANPEAAFKAINVDTMLKDQSVAQS
TLARVAGEPESFGALKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLSLAAKDTSG
KTFETVTADMTAGQKAEVQSAWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-740)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   1545 GenBank   WP_130679568
Name   t4cp2_ELH91_RS30790_pSM136A_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   1546 GenBank   WP_130679587
Name   traG_ELH91_RS30900_pSM136A_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: 76325..92048

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH91_RS36275 71371..71514 - 144 Protein_71 replication initiation protein RepC -
ELH91_RS30755 (ELH91_30750) 71652..72866 - 1215 WP_130679561 plasmid replication protein RepC -
ELH91_RS30760 (ELH91_30755) 73058..74092 - 1035 WP_130679562 plasmid partitioning protein RepB -
ELH91_RS30765 (ELH91_30760) 74089..75312 - 1224 WP_130679563 plasmid partitioning protein RepA -
ELH91_RS30770 (ELH91_30765) 75691..76314 + 624 WP_130679564 acyl-homoserine-lactone synthase -
ELH91_RS30775 (ELH91_30770) 76325..77302 + 978 WP_130679565 P-type conjugative transfer ATPase TrbB virB11
ELH91_RS30780 (ELH91_30775) 77292..77675 + 384 WP_130679566 TrbC/VirB2 family protein virB2
ELH91_RS30785 (ELH91_30780) 77668..77967 + 300 WP_130679567 conjugal transfer protein TrbD virB3
ELH91_RS30790 (ELH91_30785) 77978..80428 + 2451 WP_130679568 conjugal transfer protein TrbE virb4
ELH91_RS30795 (ELH91_30790) 80406..81203 + 798 WP_130679569 P-type conjugative transfer protein TrbJ virB5
ELH91_RS30800 (ELH91_30795) 81200..81400 + 201 WP_130679570 entry exclusion protein TrbK -
ELH91_RS30805 (ELH91_30800) 81394..82575 + 1182 WP_130679571 P-type conjugative transfer protein TrbL virB6
ELH91_RS30810 (ELH91_30805) 82596..83258 + 663 WP_130679572 conjugal transfer protein TrbF virB8
ELH91_RS30815 (ELH91_30810) 83276..84088 + 813 WP_130679573 P-type conjugative transfer protein TrbG virB9
ELH91_RS30820 (ELH91_30815) 84092..84532 + 441 WP_130679574 conjugal transfer protein TrbH -
ELH91_RS30825 (ELH91_30820) 84544..85830 + 1287 WP_130685537 IncP-type conjugal transfer protein TrbI virB10
ELH91_RS30830 (ELH91_30825) 86014..86754 + 741 WP_130679576 LuxR family transcriptional regulator -
ELH91_RS30835 (ELH91_30830) 86860..87564 + 705 WP_130679577 autoinducer binding domain-containing protein -
ELH91_RS30840 (ELH91_30835) 87568..87858 - 291 WP_130679578 transcriptional repressor TraM -
ELH91_RS30845 (ELH91_30840) 88150..88398 + 249 WP_130679579 helix-turn-helix transcriptional regulator -
ELH91_RS30850 (ELH91_30845) 88519..89151 + 633 WP_130679580 DUF433 domain-containing protein -
ELH91_RS30855 (ELH91_30850) 89148..89522 + 375 WP_087003573 DUF5615 family PIN-like protein -
ELH91_RS30860 (ELH91_30855) 89813..90640 + 828 WP_245487467 aminoglycoside phosphotransferase family protein -
ELH91_RS30865 (ELH91_30860) 90798..91247 - 450 WP_130679913 GNAT family N-acetyltransferase -
ELH91_RS30870 (ELH91_30865) 91428..92048 - 621 WP_130679581 TraH family protein virB1
ELH91_RS30875 (ELH91_30870) 92065..93228 - 1164 WP_130679582 conjugal transfer protein TraB -
ELH91_RS30880 (ELH91_30875) 93218..93727 - 510 WP_245487465 conjugative transfer signal peptidase TraF -

Host bacterium

ID   3017 GenBank   NZ_SIOQ01000007
Plasmid name   pSM136A_Rh08 Incompatibility group   -
Plasmid size   203039 bp Coordinate of oriT [Strand]   97187..97220 [-]
Host baterium   Rhizobium leguminosarum strain SM136A

Cargo genes

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