Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101152
Name   oriT_pSM132_Rh08_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM132
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOJ01000005 (33094..33134 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pSM132_Rh08_Rh04
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1149 GenBank   WP_130714113
Name   traA_ELH84_RS31020_pSM132_Rh08_Rh04 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: 123097.40 Da        Isoelectric Point: 9.7427

>WP_130714113.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADS
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTVEQNIALMRDFVAGHITAQGMIADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
VRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRVGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAAGGIIAEIGEGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYE
KSALYRQAFRFAEARGLHLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGKAIGLVRGSNKQTAPNTI
KEAKPMVSGITTFPKSLDQAVEDKLAGDPGLKKQWEDVSTRFQLVYAQPEAAFKAINVDAMVKDQSVAQS
TLARIAGEPESFGALKGKAGVLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-740)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   719 GenBank   WP_130714111
Name   traG_ELH84_RS31005_pSM132_Rh08_Rh04 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: 69549.58 Da        Isoelectric Point: 9.5666

>WP_130714111.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVIVPTALMIPVVIGMTGIEQWLSGFGKTESARLAWGRTGIALPYVASAAIGVLWLFSSAGSI
NIKQAGWGVVAGSSGTILVAAVRETVRLSGFMKTVPADKTVLAYLDPATSIGASTALLGACFALRVALIG
KAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSEHRGGAGRDVFILD
PRKPDTGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTEE
NGQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGRKFSTSDIAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQARGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMIGDAPKPA

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(163-634)

  Protein structure



No available structure.



ID   720 GenBank   WP_130714128
Name   t4cp2_ELH84_RS31100_pSM132_Rh08_Rh04 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: 91778.44 Da        Isoelectric Point: 5.5823

>WP_130714128.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLLAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVIAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSSLLPLTLAADGDHYEIGGDNAEEGRALAFCPLSDLKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIMDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRGLKSEHGHDWPMHWLETRGVHDAASLLRFE

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 38262..52044

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH84_RS31025 (ELH84_31025) 36529..37092 + 564 WP_130714114 conjugative transfer signal peptidase TraF -
ELH84_RS31030 (ELH84_31030) 37082..38245 + 1164 WP_130714115 conjugal transfer protein TraB -
ELH84_RS31035 (ELH84_31035) 38262..38879 + 618 WP_130746547 TraH family protein virB1
ELH84_RS31040 (ELH84_31040) 38986..39851 - 866 Protein_42 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH84_RS31045 (ELH84_31045) 39844..40461 - 618 WP_130714117 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH84_RS31050 (ELH84_31050) 40703..40951 - 249 WP_130714118 helix-turn-helix transcriptional regulator -
ELH84_RS31055 (ELH84_31055) 41211..41501 + 291 WP_130714119 transcriptional repressor TraM -
ELH84_RS31060 (ELH84_31060) 41505..42209 - 705 WP_130714120 autoinducer binding domain-containing protein -
ELH84_RS31065 (ELH84_31065) 42521..43819 - 1299 WP_130746548 IncP-type conjugal transfer protein TrbI virB10
ELH84_RS31070 (ELH84_31070) 43831..44271 - 441 WP_130714122 conjugal transfer protein TrbH -
ELH84_RS31075 (ELH84_31075) 44275..45087 - 813 WP_130746549 P-type conjugative transfer protein TrbG virB9
ELH84_RS31080 (ELH84_31080) 45105..45767 - 663 WP_130714124 conjugal transfer protein TrbF virB8
ELH84_RS31085 (ELH84_31085) 45788..46969 - 1182 WP_130714125 P-type conjugative transfer protein TrbL virB6
ELH84_RS31090 (ELH84_31090) 46963..47163 - 201 WP_130714126 entry exclusion protein TrbK -
ELH84_RS31095 (ELH84_31095) 47160..47963 - 804 WP_130714127 P-type conjugative transfer protein TrbJ virB5
ELH84_RS31100 (ELH84_31100) 47935..50391 - 2457 WP_130714128 conjugal transfer protein TrbE virb4
ELH84_RS31105 (ELH84_31105) 50402..50701 - 300 WP_130714129 conjugal transfer protein TrbD virB3
ELH84_RS31110 (ELH84_31110) 50694..51077 - 384 WP_130714130 TrbC/VirB2 family protein virB2
ELH84_RS31115 (ELH84_31115) 51067..52044 - 978 WP_130746550 P-type conjugative transfer ATPase TrbB virB11
ELH84_RS31120 (ELH84_31120) 52041..52679 - 639 WP_130714132 acyl-homoserine-lactone synthase -
ELH84_RS31125 (ELH84_31125) 53056..54279 + 1224 WP_165411169 plasmid partitioning protein RepA -
ELH84_RS31130 (ELH84_31130) 54276..55313 + 1038 WP_130714134 plasmid partitioning protein RepB -
ELH84_RS31135 (ELH84_31135) 55503..56717 + 1215 WP_130714135 plasmid replication protein RepC -

Host bacterium

ID   1596 GenBank   NZ_SIOJ01000005
Plasmid name   pSM132_Rh08_Rh04 Incompatibility group   -
Plasmid size   74032 bp Coordinate of oriT [Strand]   33094..33134 [+]
Host baterium   Rhizobium ruizarguesonis strain SM132

Cargo genes

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