Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102540
Name   oriT_pSM13_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIJZ01000006 (219785..219822 [-], 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_pSM13_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1891 GenBank   WP_130790745
Name   traA_ELG70_RS35005_pSM13_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   1495 GenBank   WP_130790739
Name   t4cp2_ELG70_RS34920_pSM13_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   1496 GenBank   WP_130790746
Name   traG_ELG70_RS35020_pSM13_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: 200355..222398

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG70_RS34880 (ELG70_34880) 195885..196907 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG70_RS34885 (ELG70_34885) 196904..198118 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELG70_RS40290 199030..199242 - 213 WP_245458276 hypothetical protein -
ELG70_RS34900 (ELG70_34900) 199720..200358 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG70_RS34905 (ELG70_34905) 200355..201332 + 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG70_RS34910 (ELG70_34910) 201322..201705 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG70_RS34915 (ELG70_34915) 201698..201997 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG70_RS34920 (ELG70_34920) 202008..204464 + 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG70_RS34925 (ELG70_34925) 204436..205239 + 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
ELG70_RS34930 (ELG70_34930) 205236..205436 + 201 WP_130759154 entry exclusion protein TrbK -
ELG70_RS34935 (ELG70_34935) 205430..206611 + 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELG70_RS34940 (ELG70_34940) 206632..207294 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG70_RS34945 (ELG70_34945) 207312..208124 + 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG70_RS34950 (ELG70_34950) 208128..208568 + 441 WP_130692284 conjugal transfer protein TrbH -
ELG70_RS34955 (ELG70_34955) 208580..209878 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELG70_RS34960 (ELG70_34960) 210187..210891 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG70_RS34965 (ELG70_34965) 210876..211217 - 342 WP_128408807 transcriptional repressor TraM -
ELG70_RS34970 (ELG70_34970) 211443..211685 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG70_RS34975 (ELG70_34975) 211799..212431 + 633 WP_128408809 DUF433 domain-containing protein -
ELG70_RS34980 (ELG70_34980) 212428..212802 + 375 WP_130790741 DUF5615 family PIN-like protein -
ELG70_RS34985 (ELG70_34985) 213159..213881 + 723 Protein_204 Crp/Fnr family transcriptional regulator -
ELG70_RS34990 (ELG70_34990) 214026..214646 - 621 WP_130790742 TraH family protein virB1
ELG70_RS34995 (ELG70_34995) 214664..215830 - 1167 WP_130817194 conjugal transfer protein TraB -
ELG70_RS35000 (ELG70_35000) 215820..216383 - 564 WP_130790744 conjugative transfer signal peptidase TraF -
ELG70_RS35005 (ELG70_35005) 216380..219706 - 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG70_RS35010 (ELG70_35010) 219961..220257 + 297 WP_063473650 conjugal transfer protein TraC -
ELG70_RS35015 (ELG70_35015) 220262..220477 + 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG70_RS35020 (ELG70_35020) 220464..222398 + 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG70_RS35025 (ELG70_35025) 222836..223284 + 449 Protein_212 thermonuclease family protein -
ELG70_RS35030 (ELG70_35030) 223527..223841 - 315 WP_064251367 hypothetical protein -
ELG70_RS40615 (ELG70_35035) 224285..224593 + 309 WP_130790747 WGR domain-containing protein -
ELG70_RS40300 224762..224905 + 144 WP_245488070 hypothetical protein -
ELG70_RS39705 225126..225287 - 162 WP_018516739 hypothetical protein -
ELG70_RS35045 (ELG70_35045) 225588..225899 - 312 WP_127431460 DUF736 domain-containing protein -
ELG70_RS39710 226350..226526 + 177 WP_018482051 hypothetical protein -

Host bacterium

ID   2984 GenBank   NZ_SIJZ01000006
Plasmid name   pSM13_Rh07 Incompatibility group   -
Plasmid size   301227 bp Coordinate of oriT [Strand]   219785..219822 [-]
Host baterium   Rhizobium leguminosarum strain SM13

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifT, nodJ, nodI, nodC, nodA, nodD, nodF, nodE, nodM, fixG, fixQ, fixO, fixN
Anti-CRISPR   -