Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100932
Name   oriT_pRi2659 in_silico
Organism   Rhizobium rhizogenes strain K599 (NCPPB2659)
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NZ_CP019703 (116298..116329 [+], 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   predicted by the oriTfinder

  oriT sequence  


Download         Length: 32 nt

>oriT_pRi2659
AGGGCGCAATTATACGTCGCTCACGCGACGCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1003 GenBank   WP_012475990
Name   TraA_pRi2659 insolico UniProt ID   A8W094
Length   1108 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


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

>WP_012475990.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium/Agrobacterium group]
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


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56197..68385

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
B0909_RS25685 (B0909_24050) 54466..55032 + 567 WP_012475991 conjugative transfer signal peptidase TraF -
B0909_RS25690 (B0909_24045) 55022..56185 + 1164 WP_012475992 conjugal transfer protein TraB -
B0909_RS25695 (B0909_24040) 56197..56811 + 615 WP_012475993 TraH family protein virB1
B0909_RS25700 (B0909_24035) 57067..57273 - 207 WP_077768126 helix-turn-helix transcriptional regulator -
B0909_RS25705 (B0909_24030) 57491..57814 + 324 WP_012475995 transcriptional repressor TraM -
B0909_RS25710 (B0909_24025) 57819..58523 - 705 WP_077768125 autoinducer binding domain-containing protein -
B0909_RS25715 (B0909_24020) 58869..60161 - 1293 WP_012475997 IncP-type conjugal transfer protein TrbI virB10
B0909_RS25720 (B0909_24015) 60173..60613 - 441 WP_012475998 conjugal transfer protein TrbH -
B0909_RS25725 (B0909_24010) 60617..61429 - 813 WP_012475999 P-type conjugative transfer protein TrbG virB9
B0909_RS25730 (B0909_24005) 61446..62108 - 663 WP_012476000 conjugal transfer protein TrbF virB8
B0909_RS25735 (B0909_24000) 62129..63310 - 1182 WP_012476001 P-type conjugative transfer protein TrbL virB6
B0909_RS25740 (B0909_23995) 63304..63504 - 201 WP_012476002 entry exclusion protein TrbK -
B0909_RS25745 (B0909_23990) 63501..64304 - 804 WP_077768124 P-type conjugative transfer protein TrbJ virB5
B0909_RS25750 (B0909_23985) 64276..66732 - 2457 WP_012476004 conjugal transfer protein TrbE virb4
B0909_RS25755 (B0909_23980) 66743..67042 - 300 WP_012476005 conjugal transfer protein TrbD virB3
B0909_RS25760 (B0909_23975) 67035..67418 - 384 WP_012476006 TrbC/VirB2 family protein virB2
B0909_RS25765 (B0909_23970) 67408..68385 - 978 WP_077768123 P-type conjugative transfer ATPase TrbB virB11
B0909_RS25770 (B0909_23965) 68395..69018 - 624 WP_012476008 acyl-homoserine-lactone synthase -
B0909_RS25775 (B0909_23960) 69401..70609 + 1209 WP_234888145 plasmid partitioning protein RepA -
B0909_RS25780 (B0909_23955) 70703..71710 + 1008 WP_012476010 plasmid partitioning protein RepB -
B0909_RS25785 (B0909_23950) 71877..73088 + 1212 WP_012476011 plasmid replication protein RepC -

Region 2: 102351..111737

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
B0909_RS25905 (B0909_23830) 97564..98820 + 1257 WP_234886495 cytochrome P450 -
B0909_RS25910 (B0909_23825) 99024..101579 + 2556 WP_010900341 two-component system VirA-like sensor kinase -
B0909_RS25915 (B0909_23820) 101652..101894 - 243 WP_077768110 hypothetical protein -
B0909_RS25920 (B0909_23815) 102351..103073 + 723 WP_010900342 type IV secretion system lytic transglycosylase VirB1 virB1
B0909_RS25925 (B0909_23810) 103073..103438 + 366 WP_010900343 pilin major subunit VirB2 virB2
B0909_RS25930 (B0909_23805) 103435..103761 + 327 WP_010900344 type IV secretion system protein VirB3 virB3
B0909_RS25935 (B0909_23800) 103761..106130 + 2370 WP_077768109 VirB4 family type IV secretion/conjugal transfer ATPase virb4
B0909_RS25940 (B0909_23795) 106147..106815 + 669 WP_012476031 pilin minor subunit VirB5 traI
B0909_RS25945 (B0909_23790) 106882..107769 + 888 WP_010900347 type IV secretion system protein virB6
B0909_RS25950 (B0909_23785) 107797..107964 + 168 WP_010900348 type IV secretion system lipoprotein VirB7 -
B0909_RS25955 (B0909_23780) 107951..108664 + 714 WP_012476032 type IV secretion system protein VirB8 virB8
B0909_RS25960 (B0909_23775) 108661..109539 + 879 WP_012476033 P-type conjugative transfer protein VirB9 virB9
B0909_RS25965 (B0909_23770) 109539..110669 + 1131 WP_012476034 type IV secretion system protein VirB10 virB10
B0909_RS25970 (B0909_23765) 110703..111737 + 1035 WP_012476035 P-type DNA transfer ATPase VirB11 virB11
B0909_RS25975 (B0909_23760) 111973..112698 + 726 WP_012476036 response regulator -
B0909_RS25980 (B0909_26680) 112732..113508 - 777 Protein_110 IS5 family transposase -
B0909_RS25985 (B0909_23745) 113666..114271 - 606 WP_010900354 conjugal transfer protein VirC2 -
B0909_RS25990 (B0909_23740) 114274..114969 - 696 WP_012476039 conjugal transfer ATPase VirC1 -
B0909_RS25995 (B0909_23735) 115224..115670 + 447 WP_012476040 T-DNA border endonuclease subunit VirD1 -

Host bacterium

ID   1391 GenBank   NZ_CP019703
Plasmid name   pRi2659 Incompatibility group   _
Plasmid size   202302 bp Coordinate of oriT [Strand]   116298..116329 [+]
Host baterium   Rhizobium rhizogenes strain K599 (NCPPB2659)

Cargo genes

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