Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100878
Name   oriT_pVaf-108-3 in_silico
Organism   Rhizobium leguminosarum strain Vaf-108
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NZ_CP018231 (38985..39027 [-], 43 nt)
oriT length   43 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      11..12
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 43 nt

>oriT_pVaf-108-3
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   949 GenBank   WP_065284726
Name   TraA_pVaf-108-3 insolico UniProt ID   A0A1B1CP89
Length   1193 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1193 a.a.        Molecular weight: 131490.11 Da        Isoelectric Point: 8.8551

>WP_065284726.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPEDAPDWLRSMLADR
SVSGASEAFWNKVEAFEKRSDAQLAKDVTIALPIELSADQNIALVRDFVERHITAKGVVADWVFHDAPGN
PHIHLMTTLRPLTEDGFGAKKVAVLGPDGNPVRNDAGKIVYELWAGSADDFNAFRDGWFACQNRHLALAG
FDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKGDSGEEKVALERLELQEERRAENARRIQRNPEIVVDL
ITREKSVFDERDIAKVLYRYIDDAALFQNLMARLLQSPQTLRLDRERMDLVTGVRAPAKYTTRELIRLEA
QMANQAIWLSQRSSHRVNRTVLSGIVSRHDRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAADGLEKEAGIASRTLSAWELRWDQERDRLDEKSVFVLDEAGMVSSRQMARFVE
AVTLSGAKLVLVGDPEQLQPIEAGAAFRAIAERIGYAELETIYRQREQWMRDASLDLARGNVSAALDAYA
QRDLVRTGWTRDEAITALIAEWDHEYDPAKSTLILAHRRVDVRLLNEMARSKLVERGLIEAGHAFKTEDG
TRQFAAGDQIVFLKNEGSLGVKNGMLALVVDAQPGRIVAEIGNGEDRRRVVVEQRFYANVDHGYATTVHK
SQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPGNRDSYYV
TLGFANGQERTVWGVDLARAMDASDSRIGDRIGLKHVGSQRVTLPNGTEVDRNSWKVVPIQELAMARLHE
RLSRAGSKETTLDYQDASHYRAALRFAEARGLHLMNVARTIAHDQLQWTVRQSSKLAELGARLVAVAAKL
GLGGAKSTVSTTSVIKEAKPMVFGTTTFPRSIGQAVEDKLSADPGLKASWQEVSARFHHVFADPQAAFKA
VNVDAMLANGTVAATTIVRIAEQPESFGALKGKTGLFAGSAEKQARDTALVNAPALARDLQGFIAKRAAA
ARRYEDEERAVRAQLSLDIPALSASGKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAVSERF
GERTFLPLAAKTADGKAFEVASAGMQPAQKNELRSAWDTIRTVQQLAAHERTAVALKQAEAIRQTQTKGL
SLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-568)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(949-1043)


  Protein structure


Source ID Structure
AlphaFold DB A0A1B1CP89


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 18373..27920

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BMW22_RS34555 (BMW22_34500) 14327..15571 - 1245 WP_072642062 plasmid replication protein RepC -
BMW22_RS34560 (BMW22_34505) 15729..16721 - 993 WP_028744193 plasmid partitioning protein RepB -
BMW22_RS34565 (BMW22_34510) 16803..17993 - 1191 WP_072642063 plasmid partitioning protein RepA -
BMW22_RS34570 (BMW22_34515) 18373..19338 + 966 WP_065284717 P-type conjugative transfer ATPase TrbB virB11
BMW22_RS34575 (BMW22_34520) 19328..19720 + 393 WP_011654762 TrbC/VirB2 family protein virB2
BMW22_RS34580 (BMW22_34525) 19713..20012 + 300 WP_011654761 conjugal transfer protein TrbD virB3
BMW22_RS34585 (BMW22_34530) 20023..22458 + 2436 WP_028744195 conjugal transfer protein TrbE virb4
BMW22_RS34590 (BMW22_34535) 22451..23260 + 810 WP_011654759 P-type conjugative transfer protein TrbJ virB5
BMW22_RS34595 (BMW22_34540) 23257..23457 + 201 WP_028744197 entry exclusion protein TrbK -
BMW22_RS34600 (BMW22_34545) 23451..24632 + 1182 WP_072642064 P-type conjugative transfer protein TrbL virB6
BMW22_RS34605 (BMW22_34550) 24654..25307 + 654 WP_018010287 conjugal transfer protein TrbF virB8
BMW22_RS34610 (BMW22_34555) 25323..26153 + 831 WP_072642065 P-type conjugative transfer protein TrbG virB9
BMW22_RS34615 (BMW22_34560) 26157..26603 + 447 WP_028744199 conjugal transfer protein TrbH -
BMW22_RS34620 (BMW22_34565) 26619..27920 + 1302 WP_072642066 IncP-type conjugal transfer protein TrbI virB10
BMW22_RS34625 (BMW22_34570) 28121..28420 + 300 WP_027690597 transcriptional repressor TraM -
BMW22_RS34630 (BMW22_34575) 28421..29125 - 705 WP_072642131 autoinducer binding domain-containing protein -
BMW22_RS34635 (BMW22_34580) 29408..31024 + 1617 WP_065284721 hypothetical protein -
BMW22_RS34640 (BMW22_34585) 31014..32009 + 996 WP_065284722 dienelactone hydrolase-related enzyme -
BMW22_RS34645 (BMW22_34590) 32158..32337 + 180 WP_018010295 hypothetical protein -

Region 2: 285939..295539

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BMW22_RS42295 282602..282807 - 206 Protein_288 ISAs1 family transposase -
BMW22_RS43275 (BMW22_35910) 282810..283064 - 255 WP_072642120 hypothetical protein -
BMW22_RS35990 (BMW22_35915) 283564..285942 - 2379 WP_072642121 type IV secretory system conjugative DNA transfer family protein -
BMW22_RS35995 (BMW22_35920) 285939..286967 - 1029 WP_064697762 P-type DNA transfer ATPase VirB11 virB11
BMW22_RS36000 (BMW22_35925) 286981..288648 - 1668 WP_072642139 type IV secretion system protein VirB10 virB9
BMW22_RS36005 (BMW22_35930) 288708..289439 - 732 WP_064697760 type IV secretion system protein virB8
BMW22_RS36010 (BMW22_35935) 289468..290514 - 1047 WP_245294490 type IV secretion system protein virB6
BMW22_RS36020 (BMW22_35945) 290803..291555 - 753 WP_072642122 type IV secretion system protein -
BMW22_RS36025 (BMW22_35950) 291552..291695 - 144 WP_155773515 hypothetical protein -
BMW22_RS36030 (BMW22_35955) 291757..292431 - 675 WP_245372399 hypothetical protein -
BMW22_RS36035 (BMW22_35960) 292428..294863 - 2436 WP_065284684 VirB4 family type IV secretion/conjugal transfer ATPase virb4
BMW22_RS36040 (BMW22_35965) 294890..295186 - 297 WP_064697755 VirB3 family type IV secretion system protein virB3
BMW22_RS36045 (BMW22_35970) 295186..295539 - 354 WP_064697754 TrbC/VirB2 family protein virB2
BMW22_RS36050 (BMW22_35975) 295558..296349 - 792 WP_245294491 lytic transglycosylase domain-containing protein -
BMW22_RS36055 (BMW22_35980) 296508..296822 + 315 WP_237352876 hypothetical protein -
BMW22_RS36060 (BMW22_35985) 296866..297327 + 462 WP_064697751 hypothetical protein -
BMW22_RS36065 (BMW22_35990) 297335..297784 + 450 WP_065284685 hypothetical protein -
BMW22_RS36070 (BMW22_35995) 297781..298467 + 687 WP_065284686 acyltransferase -
BMW22_RS36075 (BMW22_36000) 298464..299063 + 600 WP_064697748 hypothetical protein -
BMW22_RS36080 (BMW22_36005) 299109..299444 + 336 WP_064697747 DUF736 family protein -
BMW22_RS36085 (BMW22_36010) 299450..299938 + 489 WP_064697746 hypothetical protein -

Host bacterium

ID   1337 GenBank   NZ_CP018231
Plasmid name   pVaf-108-3 Incompatibility group   _
Plasmid size   339300 bp Coordinate of oriT [Strand]   38985..39027 [-]
Host baterium   Rhizobium leguminosarum strain Vaf-108

Cargo genes

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