Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102546
Name   oriT_pSM7_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIJU01000006 (35648..35685 [-], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 38 nt

>oriT_pSM7_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1897 GenBank   WP_130790745
Name   traA_ELG65_RS32145_pSM7_Rh07 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: 123282.59 Da        Isoelectric Point: 10.0651

>WP_130790745.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCANMEFEREARTIDYTRKQGLLHEEFVVPADAPEWLRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKSIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
RDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRRENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLAGRTSHGVREAMLRATFARHVRLSDEQRTAIEHIARATRIAAVIGRAGAGKTTMLK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIGSRTLSSWELRWNQGRNKFDHKTVFVLDEAGMVSSRQM
ALFVEAVSRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VEAYTVHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRKLNDMARAKLVERGVIADGSAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRVVAELGEGEHRRLVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYE
KRALYRQALRFAEARGLHLMDVARTVAHDRLQWAVRQSSRLADLGARLAAIGAALGLVRGGNKQSIPNTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPKAAFKAINVDSMLKDQSVAQS
TLARIAGEPESFGALKGKTGLFASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTADQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-740)


  Protein structure



No available structure.




T4CP

ID   1505 GenBank   WP_130790739
Name   t4cp2_ELG65_RS32060_pSM7_Rh07 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91814.32 Da        Isoelectric Point: 5.5010

>WP_130790739.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNEQSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLIPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPSNSPPLVQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRVLAFCPLSDLNSDVDRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEELMNMG
ERNLVPVLTYLFRRIERRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLRFE

  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   1506 GenBank   WP_130790746
Name   traG_ELG65_RS32160_pSM7_Rh07 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: 69472.74 Da        Isoelectric Point: 9.2484

>WP_130790746.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVIVPAALMIPVVIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYLASAAVGILFLFATAGAI
SIKQAGWGVVAGCSGTILIAALRETIRLSAFMKTVPADKTVLAFLDPATSIGANAALLCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGGAGRDVFLLD
PRKPDIGFNVLDWVGRFGGTKEEDIASIASWIMSDSGGVRGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPRPA

  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: 16218..38261

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG65_RS32020 (ELG65_32020) 11748..12770 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG65_RS32025 (ELG65_32025) 12767..13981 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELG65_RS39500 14893..15105 - 213 WP_245458276 hypothetical protein -
ELG65_RS32040 (ELG65_32040) 15583..16221 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG65_RS32045 (ELG65_32045) 16218..17195 + 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG65_RS32050 (ELG65_32050) 17185..17568 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG65_RS32055 (ELG65_32055) 17561..17860 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG65_RS32060 (ELG65_32060) 17871..20327 + 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG65_RS32065 (ELG65_32065) 20299..21102 + 804 WP_130876046 P-type conjugative transfer protein TrbJ virB5
ELG65_RS32070 (ELG65_32070) 21099..21299 + 201 WP_130759154 entry exclusion protein TrbK -
ELG65_RS32075 (ELG65_32075) 21293..22474 + 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELG65_RS32080 (ELG65_32080) 22495..23157 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG65_RS32085 (ELG65_32085) 23175..23987 + 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG65_RS32090 (ELG65_32090) 23991..24431 + 441 WP_130692284 conjugal transfer protein TrbH -
ELG65_RS32095 (ELG65_32095) 24443..25741 + 1299 WP_130876047 IncP-type conjugal transfer protein TrbI virB10
ELG65_RS32100 (ELG65_32100) 26050..26754 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG65_RS32105 (ELG65_32105) 26739..27080 - 342 WP_128408807 transcriptional repressor TraM -
ELG65_RS32110 (ELG65_32110) 27306..27548 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG65_RS32115 (ELG65_32115) 27662..28294 + 633 WP_128408809 DUF433 domain-containing protein -
ELG65_RS32120 (ELG65_32120) 28291..28665 + 375 WP_130790741 DUF5615 family PIN-like protein -
ELG65_RS32125 (ELG65_32125) 29022..29744 + 723 Protein_28 Crp/Fnr family transcriptional regulator -
ELG65_RS32130 (ELG65_32130) 29889..30509 - 621 WP_130790742 TraH family protein virB1
ELG65_RS32135 (ELG65_32135) 30527..31693 - 1167 WP_130817194 conjugal transfer protein TraB -
ELG65_RS32140 (ELG65_32140) 31683..32246 - 564 WP_130790744 conjugative transfer signal peptidase TraF -
ELG65_RS32145 (ELG65_32145) 32243..35569 - 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG65_RS32150 (ELG65_32150) 35824..36120 + 297 WP_063473650 conjugal transfer protein TraC -
ELG65_RS32155 (ELG65_32155) 36125..36340 + 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG65_RS32160 (ELG65_32160) 36327..38261 + 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG65_RS32165 (ELG65_32165) 38699..39147 + 449 Protein_36 thermonuclease family protein -
ELG65_RS32170 (ELG65_32170) 39390..39704 - 315 WP_064251367 hypothetical protein -
ELG65_RS39860 (ELG65_32175) 40148..40456 + 309 WP_130790747 WGR domain-containing protein -
ELG65_RS39510 40625..40768 + 144 WP_245488070 hypothetical protein -
ELG65_RS38865 40989..41150 - 162 WP_018516739 hypothetical protein -
ELG65_RS32185 (ELG65_32185) 41451..41762 - 312 WP_127431460 DUF736 domain-containing protein -
ELG65_RS38870 42213..42389 + 177 WP_018482051 hypothetical protein -

Host bacterium

ID   2990 GenBank   NZ_SIJU01000006
Plasmid name   pSM7_Rh07 Incompatibility group   -
Plasmid size   113956 bp Coordinate of oriT [Strand]   35648..35685 [-]
Host baterium   Rhizobium leguminosarum strain SM7

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD, fixG, fixQ, fixO, fixN
Anti-CRISPR   -