Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102533
Name   oriT_pSM145B_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM145B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPD01000007 (99854..99887 [-], 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_pSM145B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1884 GenBank   WP_130725757
Name   traA_ELI04_RS32945_pSM145B_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: 123138.20 Da        Isoelectric Point: 9.8201

>WP_130725757.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCARMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAQGMVADWVYHDVLGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGNTDDFNAFRDGWFACQNKHLALAG
LDLRIDGRSFERQGIDLEPTIHLGVGTKAIERKAEQSDHKSETSTPKLERIALQEERRSENARRMQRRPE
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   1484 GenBank   WP_130679568
Name   t4cp2_ELI04_RS32850_pSM145B_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   1485 GenBank   WP_130679587
Name   traG_ELI04_RS32960_pSM145B_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: 78992..94715

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI04_RS36315 74038..74181 - 144 Protein_69 replication initiation protein RepC -
ELI04_RS32815 (ELI04_32815) 74319..75533 - 1215 WP_130679561 plasmid replication protein RepC -
ELI04_RS32820 (ELI04_32820) 75725..76759 - 1035 WP_130679562 plasmid partitioning protein RepB -
ELI04_RS32825 (ELI04_32825) 76756..77979 - 1224 WP_130679563 plasmid partitioning protein RepA -
ELI04_RS32830 (ELI04_32830) 78358..78981 + 624 WP_130679564 acyl-homoserine-lactone synthase -
ELI04_RS32835 (ELI04_32835) 78992..79969 + 978 WP_130679565 P-type conjugative transfer ATPase TrbB virB11
ELI04_RS32840 (ELI04_32840) 79959..80342 + 384 WP_130679566 TrbC/VirB2 family protein virB2
ELI04_RS32845 (ELI04_32845) 80335..80634 + 300 WP_130679567 conjugal transfer protein TrbD virB3
ELI04_RS32850 (ELI04_32850) 80645..83095 + 2451 WP_130679568 conjugal transfer protein TrbE virb4
ELI04_RS32855 (ELI04_32855) 83073..83870 + 798 WP_130679569 P-type conjugative transfer protein TrbJ virB5
ELI04_RS32860 (ELI04_32860) 83867..84067 + 201 WP_130679570 entry exclusion protein TrbK -
ELI04_RS32865 (ELI04_32865) 84061..85242 + 1182 WP_130679571 P-type conjugative transfer protein TrbL virB6
ELI04_RS32870 (ELI04_32870) 85263..85925 + 663 WP_130679572 conjugal transfer protein TrbF virB8
ELI04_RS32875 (ELI04_32875) 85943..86755 + 813 WP_130679573 P-type conjugative transfer protein TrbG virB9
ELI04_RS32880 (ELI04_32880) 86759..87199 + 441 WP_130679574 conjugal transfer protein TrbH -
ELI04_RS32885 (ELI04_32885) 87211..88497 + 1287 WP_130685537 IncP-type conjugal transfer protein TrbI virB10
ELI04_RS32890 (ELI04_32890) 88681..89421 + 741 WP_130679576 LuxR family transcriptional regulator -
ELI04_RS32895 (ELI04_32895) 89527..90231 + 705 WP_130679577 autoinducer binding domain-containing protein -
ELI04_RS32900 (ELI04_32900) 90235..90525 - 291 WP_130679578 transcriptional repressor TraM -
ELI04_RS32905 (ELI04_32905) 90817..91065 + 249 WP_130679579 helix-turn-helix transcriptional regulator -
ELI04_RS32910 (ELI04_32910) 91186..91818 + 633 WP_130679580 DUF433 domain-containing protein -
ELI04_RS32915 (ELI04_32915) 91815..92189 + 375 WP_087003573 DUF5615 family PIN-like protein -
ELI04_RS32920 (ELI04_32920) 92480..93307 + 828 WP_245487467 aminoglycoside phosphotransferase family protein -
ELI04_RS32925 (ELI04_32925) 93465..93914 - 450 WP_130679913 GNAT family N-acetyltransferase -
ELI04_RS32930 (ELI04_32930) 94095..94715 - 621 WP_130679581 TraH family protein virB1
ELI04_RS32935 (ELI04_32935) 94732..95895 - 1164 WP_130679582 conjugal transfer protein TraB -
ELI04_RS32940 (ELI04_32940) 95885..96394 - 510 WP_245487465 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2977 GenBank   NZ_SIPD01000007
Plasmid name   pSM145B_Rh08 Incompatibility group   -
Plasmid size   225373 bp Coordinate of oriT [Strand]   99854..99887 [-]
Host baterium   Rhizobium leguminosarum strain SM145B

Cargo genes

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