Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101156
Name   oriT_pSM149C_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM149C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPP01000006 (236790..236823 [+], 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_pSM149C_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1153 GenBank   WP_130657460
Name   traA_ELI16_RS33380_pSM149C_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: 122987.83 Da        Isoelectric Point: 9.6219

>WP_130657460.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKFVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKVEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQGPEALRLERERINFATGSRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWEIRWNQSRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDAALDLARGNVGKA
VDAYRGYGHVRGLDLKAQAVESLIADWNHGYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLGKVVEASRNRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYD
KASFYGQALRFAEARGFHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSFPDTI
KEAKPMVSGITTFPQTLDQAVEDKLAADPGLKKQWEDVSTRFQLVYATPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPESFGAIKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSSAAKQTLERVRDVIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTDGQKAEVQSTWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(686-740)

AAA domain (AAA_30)

(387-572)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   727 GenBank   WP_130657461
Name   traG_ELI16_RS33365_pSM149C_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: 69518.76 Da        Isoelectric Point: 8.9386

>WP_130657461.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALAVMPAALMILVVIGMTGIEQWLSGFGKTEAARLAWGRTGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTETLNADKSVLAYLDPATAIGAGVALMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRIDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGHTDG
HDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFATNDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKVRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   728 GenBank   WP_065276635
Name   t4cp2_ELI16_RS33480_pSM149C_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: 91588.38 Da        Isoelectric Point: 5.9977

>WP_065276635.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKPFRVTGPSFADLVPYAGLIDDGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSKDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNALRELEQYFANSLSIRRMETRETFERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETQDAIAQASSRLVAYGYYTPVVVL
FDIDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRTLKSEHGHDWPIHWLETRGVHDAASLFK

  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: 241959..258795

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI16_RS33385 (ELI16_33385) 240226..240789 + 564 WP_130657459 conjugative transfer signal peptidase TraF -
ELI16_RS33390 (ELI16_33390) 240779..241942 + 1164 WP_130657458 conjugal transfer protein TraB -
ELI16_RS33395 (ELI16_33395) 241959..242576 + 618 WP_130657457 TraH family protein virB1
ELI16_RS33400 (ELI16_33400) 242701..244356 - 1656 WP_065276572 IS66 family transposase -
ELI16_RS33405 (ELI16_33405) 244402..244749 - 348 WP_018244911 IS66 family insertion sequence element accessory protein TnpB -
ELI16_RS33410 (ELI16_33410) 244746..245156 - 411 WP_018244910 transposase -
ELI16_RS33415 (ELI16_33415) 245367..246236 - 870 Protein_239 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI16_RS33420 (ELI16_33420) 246229..246846 - 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI16_RS39970 (ELI16_33425) 246937..247374 - 438 Protein_241 hypothetical protein -
ELI16_RS33430 (ELI16_33430) 247477..247719 - 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI16_RS33435 (ELI16_33435) 247942..248265 + 324 WP_130657456 transcriptional repressor TraM -
ELI16_RS33440 (ELI16_33440) 248269..248973 - 705 WP_130654288 autoinducer binding domain-containing protein -
ELI16_RS33445 (ELI16_33445) 249284..250582 - 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELI16_RS33450 (ELI16_33450) 250594..251028 - 435 WP_130657454 conjugal transfer protein TrbH -
ELI16_RS33455 (ELI16_33455) 251032..251844 - 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI16_RS33460 (ELI16_33460) 251862..252524 - 663 WP_065276639 conjugal transfer protein TrbF virB8
ELI16_RS33465 (ELI16_33465) 252545..253726 - 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI16_RS33470 (ELI16_33470) 253720..253920 - 201 WP_065276637 entry exclusion protein TrbK -
ELI16_RS33475 (ELI16_33475) 253917..254714 - 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI16_RS33480 (ELI16_33480) 254692..257142 - 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELI16_RS33485 (ELI16_33485) 257153..257452 - 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI16_RS33490 (ELI16_33490) 257445..257828 - 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI16_RS33495 (ELI16_33495) 257818..258795 - 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELI16_RS33500 (ELI16_33500) 258792..259430 - 639 WP_130657452 acyl-homoserine-lactone synthase -
ELI16_RS33505 (ELI16_33505) 259807..261030 + 1224 WP_065276670 plasmid partitioning protein RepA -
ELI16_RS33510 (ELI16_33510) 261027..262064 + 1038 WP_130657451 plasmid partitioning protein RepB -
ELI16_RS33515 (ELI16_33515) 262254..263468 + 1215 WP_130666985 plasmid replication protein RepC -

Host bacterium

ID   1600 GenBank   NZ_SIPP01000006
Plasmid name   pSM149C_Rh08 Incompatibility group   -
Plasmid size   275747 bp Coordinate of oriT [Strand]   236790..236823 [+]
Host baterium   Rhizobium ruizarguesonis strain SM149C

Cargo genes

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