Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100077
Name   oriT_pRi1724 in_silico
Organism   Rhizobium rhizogenes
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_002575 (140057..140088 [+], 32 nt)
oriT length   32 nt
IRs (inverted repeats)      15..20, 25..30  (CGTCGC..GCGACG)
Location of nic site      4..5
Conserved sequence flanking the
  nic site    		  AGGG|CGCA
Note   Ri plasmid

  oriT sequence  


Download         Length: 32 nt

>oriT_pRi1724
AGGGCGCAATTATACGTCGCTGATGCGACGCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Wetzel ME et al. (2015) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. Genome Biol Evol. 7(12):3337-57. [PMID:26590210]


Relaxase

ID   72 GenBank   NP_066693
Name   TraA_pRi1724 insolico UniProt ID   Q9F5E0
Length   1108 a.a. PDB ID   
Note   Dtr system oriT relaxase; Provisional

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 123281.78 Da        Isoelectric Point: 9.9183

>NP_066693.1 riorf112 (plasmid) [Agrobacterium rhizogenes]
MAVPHFSVSIVARGSGRSVVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADSPEWLRSMIADR
SVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTSEQNIALMRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFETQGIDLEPTIHLGVGTKAIERKAGQTDRTSETSAPKLERIEIQEARRSENARRIQRRPE
IVLELITREKSVFDERDVAKVLYRYIDDARLFQSLMVRILQSPEALRLERERLNFATGIRTPAKYTTREM
IRLEAEMANRAIWLSARASHGVREAVLQATFERHARLSGEQRTAIEHVVGGERIAAIIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDNKTIIVLDEAGMVSSRQM
ALLVETVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRVGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNEMARAKLVERGVVAAGFAF
KTEQGIRMFAAGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEIGDAEHRRQVTIEQRFYDNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKAGGLIPILSRRNAKETTLDYD
KASFYGQALRFAEARGMHLMNVARTVARDRLEWTIRQSSRLVDLGVRLAAIATKLGFVGSFKNSPIQNPI
KEAKPMVSGITTFPKSFEQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDAMIKDQSVAQS
TLTRIADAPESFGALKGKTGLLASRAEKQDREKAVANVPALARNLERYLRERAEAELKHEMEERAVRLKV
SVDIPALSPAARQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTSG
KTFETVTAGMTAGQKAEVQSAWNSMRTIQQLAAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

AAA domain (AAA_30)

(387-570)


  Protein structure


Source ID Structure
AlphaFold DB Q9F5E0


Auxiliary protein

ID   104 GenBank   NP_066692
Name   TraC_pRi1724 insolico UniProt ID   Q9F5E1
Length   97 a.a. PDB ID   _
Note   conjugal transfer protein TraC; Provisional

  Auxiliary protein sequence


Download         Length: 97 a.a.        Molecular weight: 10095.29 Da        Isoelectric Point: 8.6348

>NP_066692.1 riorf111 (plasmid) [Agrobacterium rhizogenes]
MKKPSSKIRDEIAKLQEQLKIAETKEAERIGRVALKAGLGEIEVEEGELQAAFEEVAKRFRGGKGASNGK
ERGGPGAVTQQTTPNSTGAGAGSTGEA

  Protein domains


Predicted by InterproScan.

TraC-like protein (TraC)

(2-96)


  Protein structure


Source ID Structure
AlphaFold DB Q9F5E1

ID   105 GenBank   NP_066691
Name   TraD_pRi1724 insolico UniProt ID   Q9F5E2
Length   71 a.a. PDB ID   _
Note   conjugal transfer protein TraD; Provisional

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 7769.88 Da        Isoelectric Point: 9.8617

>NP_066691.1 riorf110 (plasmid) [Agrobacterium rhizogenes]
MARTITSDARKKDTREKIELGGLIVKAGMRYEKRALLLGALIDAAHRIKGDEGERSRLTAIGAEAFGNDD
Q

  Protein domains


Predicted by InterproScan.

Conjugal transfer protein TraD (TraD)

(8-67)


  Protein structure


Source ID Structure
AlphaFold DB Q9F5E2


T4CP

ID   72 GenBank   NP_066690
Name   TraG_pRi1724 insolico UniProt ID   Q9F5E3
Length   667 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG

  T4CP protein sequence


Download         Length: 667 a.a.        Molecular weight: 71613.60 Da        Isoelectric Point: 8.4471

>NP_066690.1 riorf109 (plasmid) [Agrobacterium rhizogenes]
MTINRIALVVGPAALMILVIIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYIASAAIGVLFLFASAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTKALPADKTIFAYLDPATSIGAGAAFMCACFAFRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDSGGIVVGERYLVDKDSVGSQAFRADNAETWGAGG
KSTLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDMFVLD
PRKSDIGFNVLDWVGGYGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGKLEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQDSRSSQARGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRADMRVCVG
ENRFHSTGGGEKKASNSTPSVKADETTPTVRSAGEEG

  Protein domains


Predicted by InterproScan.

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

(163-637)

  Protein structure


Source ID Structure
AlphaFold DB Q9F5E3


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 145220..159011

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXG32_RS00630 (pRi1724_p114) 143489..144055 + 567 WP_010900302 conjugative transfer signal peptidase TraF -
HXG32_RS00635 (pRi1724_p115) 144045..145208 + 1164 WP_010900303 carbon-nitrogen hydrolase family protein -
HXG32_RS00640 (pRi1724_p116) 145220..145831 + 612 WP_010900304 TraH family protein virB1
HXG32_RS00645 (pRi1724_p117) 146035..147600 + 1566 WP_010900305 Fic family protein -
HXG32_RS00650 (pRi1724_p118) 147691..147897 - 207 WP_142845039 helix-turn-helix transcriptional regulator -
HXG32_RS00655 (pRi1724_p119) 148115..148438 + 324 WP_010900307 transcriptional repressor TraM -
HXG32_RS00660 (pRi1724_p120) 148442..149146 - 705 WP_142845038 autoinducer binding domain-containing protein -
HXG32_RS00665 (pRi1724_p121) 149495..150793 - 1299 WP_010900309 IncP-type conjugal transfer protein TrbI virB10
HXG32_RS00670 (pRi1724_p122) 150805..151245 - 441 WP_010900310 conjugal transfer protein TrbH -
HXG32_RS00675 (pRi1724_p123) 151249..152061 - 813 WP_010900311 P-type conjugative transfer protein TrbG virB9
HXG32_RS00680 (pRi1724_p124) 152078..152740 - 663 WP_010900312 conjugal transfer protein TrbF virB8
HXG32_RS00685 (pRi1724_p125) 152761..153942 - 1182 WP_010900313 P-type conjugative transfer protein TrbL virB6
HXG32_RS01045 153936..153983 - 48 Protein_140 entry exclusion protein TrbK -
HXG32_RS01050 154020..154136 - 117 WP_010900314 DUF2749 domain-containing protein -
HXG32_RS00695 (pRi1724_p127) 154133..154930 - 798 WP_010900315 P-type conjugative transfer protein TrbJ virB5
HXG32_RS00700 (pRi1724_p128) 154908..157358 - 2451 WP_010900316 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXG32_RS00705 (pRi1724_p129) 157369..157668 - 300 WP_010900317 conjugal transfer protein TrbD virB3
HXG32_RS00710 (pRi1724_p130) 157661..158044 - 384 WP_010900318 TrbC/VirB2 family protein virB2
HXG32_RS00715 (pRi1724_p131) 158034..159011 - 978 WP_010900319 P-type conjugative transfer ATPase TrbB virB11
HXG32_RS00720 (pRi1724_p132) 159021..159644 - 624 WP_010900320 acyl-homoserine-lactone synthase -
HXG32_RS00725 (pRi1724_p133) 160027..161235 + 1209 WP_234886500 plasmid partitioning protein RepA -
HXG32_RS00730 (pRi1724_p134) 161329..162336 + 1008 WP_010900322 plasmid partitioning protein RepB -
HXG32_RS00735 (pRi1724_p135) 162503..163714 + 1212 WP_010900323 plasmid replication protein RepC -

Region 2: 192879..202265

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXG32_RS00855 (pRi1724_p152) 188092..189348 + 1257 WP_234886495 cytochrome P450 -
HXG32_RS00860 (pRi1724_p153) 189552..192107 + 2556 WP_010900341 two-component system VirA-like sensor kinase -
HXG32_RS00865 192180..192422 - 243 WP_077768110 hypothetical protein -
HXG32_RS00870 (pRi1724_p154) 192879..193601 + 723 WP_010900342 type IV secretion system lytic transglycosylase VirB1 virB1
HXG32_RS00875 (pRi1724_p155) 193601..193966 + 366 WP_010900343 pilin major subunit VirB2 virB2
HXG32_RS00880 (pRi1724_p156) 193963..194289 + 327 WP_010900344 type IV secretion system protein VirB3 virB3
HXG32_RS00885 (pRi1724_p157) 194289..196658 + 2370 WP_010900345 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXG32_RS00890 (pRi1724_p158) 196675..197343 + 669 WP_010900346 pilin minor subunit VirB5 -
HXG32_RS00895 (pRi1724_p159) 197410..198297 + 888 WP_010900347 type IV secretion system protein virB6
HXG32_RS00900 (pRi1724_p160) 198325..198492 + 168 WP_010900348 type IV secretion system lipoprotein VirB7 -
HXG32_RS00905 (pRi1724_p161) 198479..199192 + 714 WP_010900349 type IV secretion system protein VirB8 virB8
HXG32_RS00910 (pRi1724_p162) 199189..200067 + 879 WP_010900350 P-type conjugative transfer protein VirB9 virB9
HXG32_RS00915 (pRi1724_p163) 200067..201197 + 1131 WP_010900351 type IV secretion system protein VirB10 virB10
HXG32_RS00920 (pRi1724_p164) 201231..202265 + 1035 WP_010900352 P-type DNA transfer ATPase VirB11 virB11
HXG32_RS00925 (pRi1724_p165) 202537..203226 + 690 WP_010900353 winged helix-turn-helix domain-containing protein -
HXG32_RS01005 203202..203750 - 549 WP_234886501 IS5 family transposase -
HXG32_RS01010 203666..204031 - 366 WP_012476038 IS5 family transposase -
HXG32_RS00935 (pRi1724_p166) 204195..204800 - 606 WP_010900354 conjugal transfer protein VirC2 -
HXG32_RS00940 (pRi1724_p167) 204803..205498 - 696 WP_010900355 conjugal transfer ATPase VirC1 -
HXG32_RS00945 (pRi1724_p168) 205753..206199 + 447 WP_010900356 T-DNA border endonuclease subunit VirD1 -

Host bacterium

ID   72 GenBank   NC_002575
Plasmid name   pRi1724 Incompatibility group   -
Plasmid size   217594 bp Coordinate of oriT [Strand]   140057..140088 [+]
Host baterium   Rhizobium rhizogenes

Cargo genes

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