Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100029
Name   oriT_pRi2659 in_silico
Organism   Rhizobium rhizogenes
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_010841 (106646..106677 [+], 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_pRi2659
AGGGCGCAATTATACGTCGCTCACGCGACGCC

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   28 GenBank   YP_001961052
Name   TraA_pRi2659 insolico UniProt ID   A8W094
Length   1108 a.a. PDB ID   
Note   Dtr system oriT relaxase

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 123233.95 Da        Isoelectric Point: 10.0584

>YP_001961052.1 rcorf77 (plasmid) [Agrobacterium rhizogenes]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKLGLLHEEFVIPADSPEWVRSMIADR
SVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTSEQNIALMRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGRDGKPIRNDAGKIVYDLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDGKQETAPPKLERIELQEARRSENARRIQRRPE
IVLELITREKSVFDERDVAKVLYRYIDDARLFQSLMVRILQSPEALRLERERMNLATGVRELAKYTTREM
IRLEAEMANRAIWLSARASHGVREAVLQATFARHSRLSDEQRTAIEHVAGGERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGIALAGKAAEGLEKEAGIPSRTLSSWELRWNQGRNQLDNKTVIVLDEAGMVSSRQM
ALLVETVTKAGAKLVLVGDPEQLQPIEAGAAFRAIAARIGYAELETIYRQRQQWMRDASLDLARGNIRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVAEGFAF
KTEDGHRKFAPGDQIVFLKNEGSLGVKNGMLAKVLKAAPGRVVAEVGEGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
QASFYRQALRFAEARGLHLMNVARAVARDRLEWTIRQKQKLVGLGARLAAIATKLGFVGNFKNSPIQNPI
KEAKPMVSGITTFPKSFEQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDAMVKDQSVAKS
TLAKVADAPESFGTLKGKPGLLASRAEKQDREKAIANVPALGRNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSPAAKQMLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTNG
KAFETVTAGMTAGQKAEVQSAWNSMRTVQQLAAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-740)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)


  Protein structure


Source ID Structure
AlphaFold DB A8W094


Auxiliary protein

ID   42 GenBank   YP_001961051
Name   TraC_pRi2659 insolico UniProt ID   A8W092
Length   102 a.a. PDB ID   _
Note   probable traC gene, Ti plasmid conjugal DNA processing; similar to riorf111 in pRi1724

  Auxiliary protein sequence


Download         Length: 102 a.a.        Molecular weight: 10259.32 Da        Isoelectric Point: 5.2518

>YP_001961051.1 rcorf76 (plasmid) [Agrobacterium rhizogenes]
MKKPASKIRDEIAKLQEQLKVAETREAERIGRIALKAGLGEIEIEEGELQAAFEEVATRFRGGQGGGKGA
TNGGKKGAGDSSGATSTPADSSGAGAGSTGEA

  Protein domains


Predicted by InterproScan.

TraC-like protein (TraC)

(2-101)


  Protein structure


Source ID Structure
AlphaFold DB A8W092

ID   43 GenBank   YP_001961050
Name   TraD_pRi2659 insolico UniProt ID   A8W090
Length   71 a.a. PDB ID   _
Note   probable traD gene, conjugal transfer protein similar to riorf110 in pRi1724

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 7831.01 Da        Isoelectric Point: 10.2652

>YP_001961050.1 rcorf75 (plasmid) [Agrobacterium rhizogenes]
MARTMTSDARKKETREKIELGGLIVKAGLRYEKRALLLGALIDVARRIKGDEGERSRLTAIGAEAFGNDD
Q

  Protein domains


Predicted by InterproScan.

Conjugal transfer protein TraD (TraD)

(8-67)


  Protein structure


Source ID Structure
AlphaFold DB A8W090


T4CP

ID   28 GenBank   YP_001961049
Name   TraG_pRi2659 insolico UniProt ID   A8W087
Length   667 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG

  T4CP protein sequence


Download         Length: 667 a.a.        Molecular weight: 71753.90 Da        Isoelectric Point: 8.9260

>YP_001961049.1 rcorf74 (plasmid) [Agrobacterium rhizogenes]
MTINRIALVVGPAALMILVVIGMTGIEQWISGFGKTEAARLAWGRAGIALPYVASAAIGIVFLFASAGAI
SIKQAGWGVVAGCSGTILIAATRETIRLAAFTKTLPTGKTVFAYLDPATSIGVGAAFMCACFALRVAFIG
NAAFARAEPKRIQGKRALHGEADWMKPPEAAKLFSDSGGIVIGERYRVDKDSVAALAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKSDMGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHMDE
KDQTLRRVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGRKFSTSDIAAGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGKLEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSSQARGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRNDMRACVG
ENRFHSMGGREKEGSNSASAVNAYETKPAVTSAAEEE

  Protein domains


Predicted by InterproScan.

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

(164-636)

  Protein structure


Source ID Structure
AlphaFold DB A8W087


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 111802..123023

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS649_RS00500 (pRi2659_p079) 110071..110637 + 567 WP_012475991 conjugative transfer signal peptidase TraF -
HS649_RS00505 (pRi2659_p080) 110627..111790 + 1164 WP_012475992 conjugal transfer protein TraB -
HS649_RS00510 (pRi2659_p081) 111802..112416 + 615 WP_012475993 TraH family protein virB1
HS649_RS00515 (pRi2659_p082) 112672..112878 - 207 WP_077768126 helix-turn-helix transcriptional regulator -
HS649_RS00520 (pRi2659_p083) 113096..113419 + 324 WP_012475995 transcriptional repressor TraM -
HS649_RS00525 (pRi2659_p084) 113424..114128 - 705 WP_172684625 autoinducer binding domain-containing protein -
HS649_RS00530 (pRi2659_p085) 114474..115766 - 1293 WP_012475997 IncP-type conjugal transfer protein TrbI virB10
HS649_RS00535 (pRi2659_p086) 115778..116218 - 441 WP_012475998 conjugal transfer protein TrbH -
HS649_RS00540 (pRi2659_p087) 116222..117034 - 813 WP_012475999 P-type conjugative transfer protein TrbG virB9
HS649_RS00545 (pRi2659_p088) 117051..117713 - 663 WP_012476000 conjugal transfer protein TrbF virB8
HS649_RS00550 (pRi2659_p089) 117734..118915 - 1182 WP_012476001 P-type conjugative transfer protein TrbL virB6
HS649_RS00555 (pRi2659_p090) 118909..119109 - 201 WP_012476002 entry exclusion protein TrbK -
HS649_RS00560 (pRi2659_p091) 119106..119909 - 804 WP_077768124 P-type conjugative transfer protein TrbJ virB5
HS649_RS00565 (pRi2659_p092) 119881..122337 - 2457 WP_012476004 conjugal transfer protein TrbE virb4
HS649_RS00570 (pRi2659_p093) 122348..122647 - 300 WP_012476005 conjugal transfer protein TrbD virB3
HS649_RS00575 (pRi2659_p094) 122640..123023 - 384 WP_012476006 TrbC/VirB2 family protein virB2
HS649_RS00580 123013..123989 - 977 Protein_116 P-type conjugative transfer ATPase TrbB -
HS649_RS00585 (pRi2659_p096) 123999..124622 - 624 WP_012476008 acyl-homoserine-lactone synthase -
HS649_RS00590 (pRi2659_p097) 125005..126213 + 1209 WP_234888145 plasmid partitioning protein RepA -
HS649_RS00595 (pRi2659_p098) 126307..127314 + 1008 WP_012476010 plasmid partitioning protein RepB -

Region 2: 157955..167341

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS649_RS00725 (pRi2659_p120) 153168..154424 + 1257 WP_234886495 cytochrome P450 -
HS649_RS00730 (pRi2659_p121) 154628..157183 + 2556 WP_012476029 two-component system VirA-like sensor kinase -
HS649_RS00735 157256..157498 - 243 WP_077768110 hypothetical protein -
HS649_RS00740 (pRi2659_p122) 157955..158677 + 723 WP_010900342 type IV secretion system lytic transglycosylase VirB1 virB1
HS649_RS00745 (pRi2659_p123) 158677..159042 + 366 WP_010900343 pilin major subunit VirB2 virB2
HS649_RS00750 (pRi2659_p124) 159039..159365 + 327 WP_010900344 type IV secretion system protein VirB3 virB3
HS649_RS00755 (pRi2659_p125) 159365..161734 + 2370 WP_012476030 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS649_RS00760 (pRi2659_p126) 161751..162419 + 669 WP_012476031 pilin minor subunit VirB5 traI
HS649_RS00765 (pRi2659_p127) 162486..163373 + 888 WP_010900347 type IV secretion system protein virB6
HS649_RS00770 (pRi2659_p128) 163401..163568 + 168 WP_010900348 type IV secretion system lipoprotein VirB7 -
HS649_RS00775 (pRi2659_p129) 163555..164268 + 714 WP_012476032 type IV secretion system protein VirB8 virB8
HS649_RS00780 (pRi2659_p130) 164265..165143 + 879 WP_012476033 P-type conjugative transfer protein VirB9 virB9
HS649_RS00785 (pRi2659_p131) 165143..166273 + 1131 WP_012476034 type IV secretion system protein VirB10 virB10
HS649_RS00790 (pRi2659_p132) 166307..167341 + 1035 WP_012476035 P-type DNA transfer ATPase VirB11 virB11
HS649_RS00795 (pRi2659_p133) 167613..168302 + 690 WP_234888146 winged helix-turn-helix domain-containing protein -
HS649_RS00800 168336..169112 - 777 Protein_161 IS5 family transposase -
HS649_RS00805 (pRi2659_p136) 169270..169875 - 606 WP_010900354 conjugal transfer protein VirC2 -
HS649_RS00810 (pRi2659_p137) 169878..170573 - 696 WP_012476039 conjugal transfer ATPase VirC1 -
HS649_RS00815 (pRi2659_p138) 170828..171274 + 447 WP_012476040 T-DNA border endonuclease subunit VirD1 -

Host bacterium

ID   28 GenBank   NC_010841
Plasmid name   pRi2659 Incompatibility group   _
Plasmid size   185462 bp Coordinate of oriT [Strand]   106646..106677 [+]
Host baterium   Rhizobium rhizogenes

Cargo genes

Drug resistance gene   -
Virulence gene   virulence-rhizogenic
  T-DNA processing virulence virA/G regulated protein
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -