Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102535
Name   oriT_pSM146B_Rh08 in_silico
Organism   Rhizobium leguminosarum strain SM146B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPG01000007 (105577..105610 [-], 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_pSM146B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1886 GenBank   WP_130679584
Name   traA_ELI07_RS33030_pSM146B_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   1488 GenBank   WP_130679568
Name   t4cp2_ELI07_RS32935_pSM146B_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   1489 GenBank   WP_130679587
Name   traG_ELI07_RS33045_pSM146B_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: 84715..100438

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI07_RS36790 79761..79904 - 144 Protein_61 replication initiation protein RepC -
ELI07_RS32900 (ELI07_32910) 80042..81256 - 1215 WP_130679561 plasmid replication protein RepC -
ELI07_RS32905 (ELI07_32915) 81448..82482 - 1035 WP_130679562 plasmid partitioning protein RepB -
ELI07_RS32910 (ELI07_32920) 82479..83702 - 1224 WP_130679563 plasmid partitioning protein RepA -
ELI07_RS32915 (ELI07_32925) 84081..84704 + 624 WP_130679564 acyl-homoserine-lactone synthase -
ELI07_RS32920 (ELI07_32930) 84715..85692 + 978 WP_130679565 P-type conjugative transfer ATPase TrbB virB11
ELI07_RS32925 (ELI07_32935) 85682..86065 + 384 WP_130679566 TrbC/VirB2 family protein virB2
ELI07_RS32930 (ELI07_32940) 86058..86357 + 300 WP_130679567 conjugal transfer protein TrbD virB3
ELI07_RS32935 (ELI07_32945) 86368..88818 + 2451 WP_130679568 conjugal transfer protein TrbE virb4
ELI07_RS32940 (ELI07_32950) 88796..89593 + 798 WP_130679569 P-type conjugative transfer protein TrbJ virB5
ELI07_RS32945 (ELI07_32955) 89590..89790 + 201 WP_130679570 entry exclusion protein TrbK -
ELI07_RS32950 (ELI07_32960) 89784..90965 + 1182 WP_130679571 P-type conjugative transfer protein TrbL virB6
ELI07_RS32955 (ELI07_32965) 90986..91648 + 663 WP_130679572 conjugal transfer protein TrbF virB8
ELI07_RS32960 (ELI07_32970) 91666..92478 + 813 WP_130679573 P-type conjugative transfer protein TrbG virB9
ELI07_RS32965 (ELI07_32975) 92482..92922 + 441 WP_130742952 conjugal transfer protein TrbH -
ELI07_RS32970 (ELI07_32980) 92934..94220 + 1287 WP_130685537 IncP-type conjugal transfer protein TrbI virB10
ELI07_RS32975 (ELI07_32985) 94404..95144 + 741 WP_130679576 LuxR family transcriptional regulator -
ELI07_RS32980 (ELI07_32990) 95250..95954 + 705 WP_130679577 autoinducer binding domain-containing protein -
ELI07_RS32985 (ELI07_32995) 95958..96248 - 291 WP_130679578 transcriptional repressor TraM -
ELI07_RS32990 (ELI07_33000) 96540..96788 + 249 WP_130679579 helix-turn-helix transcriptional regulator -
ELI07_RS32995 (ELI07_33005) 96909..97541 + 633 WP_130679580 DUF433 domain-containing protein -
ELI07_RS33000 (ELI07_33010) 97538..97912 + 375 WP_087003573 DUF5615 family PIN-like protein -
ELI07_RS33005 (ELI07_33015) 98203..99030 + 828 WP_245487467 aminoglycoside phosphotransferase family protein -
ELI07_RS33010 (ELI07_33020) 99188..99637 - 450 WP_130679913 GNAT family N-acetyltransferase -
ELI07_RS33015 (ELI07_33025) 99818..100438 - 621 WP_130679581 TraH family protein virB1
ELI07_RS33020 (ELI07_33030) 100455..101618 - 1164 WP_130679582 conjugal transfer protein TraB -
ELI07_RS33025 (ELI07_33035) 101608..102117 - 510 WP_245487465 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2979 GenBank   NZ_SIPG01000007
Plasmid name   pSM146B_Rh08 Incompatibility group   -
Plasmid size   213357 bp Coordinate of oriT [Strand]   105577..105610 [-]
Host baterium   Rhizobium leguminosarum strain SM146B

Cargo genes

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