Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101163
Name   oriT_pSM126B_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM126B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOB01000005 (29544..29584 [+], 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_pSM126B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1160 GenBank   WP_130714113
Name   traA_ELH76_RS32870_pSM126B_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: 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   741 GenBank   WP_130714111
Name   traG_ELH76_RS32855_pSM126B_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: 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   742 GenBank   WP_130714128
Name   t4cp2_ELH76_RS32950_pSM126B_Rh08 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: 34712..48494

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH76_RS32875 (ELH76_32880) 32979..33542 + 564 WP_130714114 conjugative transfer signal peptidase TraF -
ELH76_RS32880 (ELH76_32885) 33532..34695 + 1164 WP_130714115 conjugal transfer protein TraB -
ELH76_RS32885 (ELH76_32890) 34712..35329 + 618 WP_130714116 TraH family protein virB1
ELH76_RS32890 (ELH76_32895) 35436..36301 - 866 Protein_38 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH76_RS32895 (ELH76_32900) 36294..36911 - 618 WP_130714117 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH76_RS32900 (ELH76_32905) 37153..37401 - 249 WP_130714118 helix-turn-helix transcriptional regulator -
ELH76_RS32905 (ELH76_32910) 37661..37951 + 291 WP_130714119 transcriptional repressor TraM -
ELH76_RS32910 (ELH76_32915) 37955..38659 - 705 WP_130714120 autoinducer binding domain-containing protein -
ELH76_RS32915 (ELH76_32920) 38971..40269 - 1299 WP_130714121 IncP-type conjugal transfer protein TrbI virB10
ELH76_RS32920 (ELH76_32925) 40281..40721 - 441 WP_130714122 conjugal transfer protein TrbH -
ELH76_RS32925 (ELH76_32930) 40725..41537 - 813 WP_130714123 P-type conjugative transfer protein TrbG virB9
ELH76_RS32930 (ELH76_32935) 41555..42217 - 663 WP_130714124 conjugal transfer protein TrbF virB8
ELH76_RS32935 (ELH76_32940) 42238..43419 - 1182 WP_130714125 P-type conjugative transfer protein TrbL virB6
ELH76_RS32940 (ELH76_32945) 43413..43613 - 201 WP_130714126 entry exclusion protein TrbK -
ELH76_RS32945 (ELH76_32950) 43610..44413 - 804 WP_130714127 P-type conjugative transfer protein TrbJ virB5
ELH76_RS32950 (ELH76_32955) 44385..46841 - 2457 WP_130714128 conjugal transfer protein TrbE virb4
ELH76_RS32955 (ELH76_32960) 46852..47151 - 300 WP_130714129 conjugal transfer protein TrbD virB3
ELH76_RS32960 (ELH76_32965) 47144..47527 - 384 WP_130714130 TrbC/VirB2 family protein virB2
ELH76_RS32965 (ELH76_32970) 47517..48494 - 978 WP_130714131 P-type conjugative transfer ATPase TrbB virB11
ELH76_RS32970 (ELH76_32975) 48491..49129 - 639 WP_130714132 acyl-homoserine-lactone synthase -
ELH76_RS32975 (ELH76_32980) 49506..50729 + 1224 WP_165411169 plasmid partitioning protein RepA -
ELH76_RS32980 (ELH76_32985) 50726..51763 + 1038 WP_130714134 plasmid partitioning protein RepB -
ELH76_RS32985 (ELH76_32990) 51953..53167 + 1215 WP_130714135 plasmid replication protein RepC -

Host bacterium

ID   1607 GenBank   NZ_SIOB01000005
Plasmid name   pSM126B_Rh08 Incompatibility group   -
Plasmid size   56753 bp Coordinate of oriT [Strand]   29544..29584 [+]
Host baterium   Rhizobium ruizarguesonis strain SM126B

Cargo genes

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