Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102524
Name   oriT_pSM144B_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM144B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPB01000007 (45630..45663 [-], 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_pSM144B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1875 GenBank   WP_130679584
Name   traA_ELI02_RS28190_pSM144B_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   1474 GenBank   WP_130679568
Name   t4cp2_ELI02_RS28095_pSM144B_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   1475 GenBank   WP_130679587
Name   traG_ELI02_RS28205_pSM144B_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: 24768..40491

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI02_RS37145 19814..19957 - 144 Protein_17 replication initiation protein RepC -
ELI02_RS28060 (ELI02_28060) 20095..21309 - 1215 WP_130679561 plasmid replication protein RepC -
ELI02_RS28065 (ELI02_28065) 21501..22535 - 1035 WP_130679562 plasmid partitioning protein RepB -
ELI02_RS28070 (ELI02_28070) 22532..23755 - 1224 WP_130679563 plasmid partitioning protein RepA -
ELI02_RS28075 (ELI02_28075) 24134..24757 + 624 WP_130679564 acyl-homoserine-lactone synthase -
ELI02_RS28080 (ELI02_28080) 24768..25745 + 978 WP_130679565 P-type conjugative transfer ATPase TrbB virB11
ELI02_RS28085 (ELI02_28085) 25735..26118 + 384 WP_130679566 TrbC/VirB2 family protein virB2
ELI02_RS28090 (ELI02_28090) 26111..26410 + 300 WP_130679567 conjugal transfer protein TrbD virB3
ELI02_RS28095 (ELI02_28095) 26421..28871 + 2451 WP_130679568 conjugal transfer protein TrbE virb4
ELI02_RS28100 (ELI02_28100) 28849..29646 + 798 WP_130679569 P-type conjugative transfer protein TrbJ virB5
ELI02_RS28105 (ELI02_28105) 29643..29843 + 201 WP_130679570 entry exclusion protein TrbK -
ELI02_RS28110 (ELI02_28110) 29837..31018 + 1182 WP_130679571 P-type conjugative transfer protein TrbL virB6
ELI02_RS28115 (ELI02_28115) 31039..31701 + 663 WP_130679572 conjugal transfer protein TrbF virB8
ELI02_RS28120 (ELI02_28120) 31719..32531 + 813 WP_130679573 P-type conjugative transfer protein TrbG virB9
ELI02_RS28125 (ELI02_28125) 32535..32975 + 441 WP_130679574 conjugal transfer protein TrbH -
ELI02_RS28130 (ELI02_28130) 32987..34273 + 1287 WP_130679575 IncP-type conjugal transfer protein TrbI virB10
ELI02_RS28135 (ELI02_28135) 34457..35197 + 741 WP_130679576 LuxR family transcriptional regulator -
ELI02_RS28140 (ELI02_28140) 35303..36007 + 705 WP_130679577 autoinducer binding domain-containing protein -
ELI02_RS28145 (ELI02_28145) 36011..36301 - 291 WP_130679578 transcriptional repressor TraM -
ELI02_RS28150 (ELI02_28150) 36593..36841 + 249 WP_130679579 helix-turn-helix transcriptional regulator -
ELI02_RS28155 (ELI02_28155) 36962..37594 + 633 WP_130679580 DUF433 domain-containing protein -
ELI02_RS28160 (ELI02_28160) 37591..37965 + 375 WP_087003573 DUF5615 family PIN-like protein -
ELI02_RS28165 (ELI02_28165) 38256..39083 + 828 WP_245487467 aminoglycoside phosphotransferase family protein -
ELI02_RS28170 (ELI02_28170) 39241..39690 - 450 WP_130679913 GNAT family N-acetyltransferase -
ELI02_RS28175 (ELI02_28175) 39871..40491 - 621 WP_130679581 TraH family protein virB1
ELI02_RS28180 (ELI02_28180) 40508..41671 - 1164 WP_130679582 conjugal transfer protein TraB -
ELI02_RS28185 (ELI02_28185) 41661..42170 - 510 WP_245487465 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2968 GenBank   NZ_SIPB01000007
Plasmid name   pSM144B_Rh08 Incompatibility group   -
Plasmid size   577387 bp Coordinate of oriT [Strand]   45630..45663 [-]
Host baterium   Rhizobium leguminosarum strain SM144B

Cargo genes

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