Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102797
Name   oriT_Vaf10|unnamed4 in_silico
Organism   Rhizobium leguminosarum strain Vaf10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP016292 (111666..111708 [-], 43 nt)
oriT length   43 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 43 nt

>oriT_Vaf10|unnamed4
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2071 GenBank   WP_065284726
Name   traA_BA011_RS38865_Vaf10|unnamed4 insolico UniProt ID   A0A1B1CP89
Length   1193 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  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


T4CP

ID   1731 GenBank   WP_028744195
Name   t4cp2_BA011_RS38770_Vaf10|unnamed4 insolico UniProt ID   _
Length   811 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 811 a.a.        Molecular weight: 90925.37 Da        Isoelectric Point: 5.8208

>WP_028744195.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINSILSRLG
TGWMIQVEAVRVPTTEYPSAERSHFPDAVTLLIDHERRRHFGQERGHFESRHALILTYRPPERRRSGLTR
YIYSDNESRSAKYADTALDAFRRSIREIEQYLGNVLSVQRMQTREVSERDGARVARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLATAELEHGLTPRVEGRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIVL
FDESRSALQEKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GQPFAPCPFYPPDAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYEKAQVFA
FDKGNSMLTLTLGVGGDHYEIGGESGEGASLAFCPLSELSTDADRAWASEWIETLVSLQGVTIAPDHRNA
ISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGLLLDAEEDGLTLGRFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVILATQSISDAERS
GIIDVLKESCPTKICLPNGAARETGTREFYERIGFNARQIEIVANAIPKREYYVTSPDGRRLFDMSLGPV
TLSFVGASGKADLARIRALSSTHGLEWPGQWLIERGINRNE

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(457-492)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(186-400)

  Protein structure



No available structure.



ID   1732 GenBank   WP_065284729
Name   traG_BA011_RS38880_Vaf10|unnamed4 insolico UniProt ID   _
Length   656 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 656 a.a.        Molecular weight: 70653.58 Da        Isoelectric Point: 9.4607

>WP_065284729.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTPKRILVAGIPAVAMLAIALTVPGIERWLSAFGTTDQAKLVLGRIGLALPYALAGACGVMFLFGTKGSI
NVKTSGWSVAAGGLVVIIVAALREGSRLLAFAGRVPADRALLSYADPSTIAGAAVTLLSVFFALRVARTG
NAAFARSEPRRIRGKRALHGEADWMTMQGSEKLFPETGGIVIGERYRVDRDDPAAAGFRAGEPTTWGRGG
SAPLLCFDGSFGSSHGIVFAGSGGYKTTSVTIPTALKWGGSLVVLDPSNEVAPMVMEHRRKAGRRVIVLD
PKNAGSGFNALDWIGRHGGTKEEDIAAVASWIMSDSGRATGVRDDFFRASGLQLLTAMIADVCLSGHTDA
KHQTLRQVRANLSEPEPKLRARLQEIYDSSASDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYTNYA
ALVSGSTFSTDALADGETDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGEVKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRESYGGRDAASKWFESVSWISFAAINDPDTADYISKRCGMTT
VEIDQVSRSFQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNPPLRCGRAIWFRRDDMKACVG
TNRFHKIGGPAGSTSDRADAECNEQG

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 89802..106274

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BA011_RS38740 (BA011_36320) 85756..87000 - 1245 WP_065284716 plasmid replication protein RepC -
BA011_RS38745 (BA011_36325) 87158..88150 - 993 WP_028744193 plasmid partitioning protein RepB -
BA011_RS38750 (BA011_36330) 88232..89422 - 1191 WP_018009855 plasmid partitioning protein RepA -
BA011_RS38755 (BA011_36335) 89802..90767 + 966 WP_065284717 P-type conjugative transfer ATPase TrbB virB11
BA011_RS38760 (BA011_36340) 90757..91149 + 393 WP_011654762 TrbC/VirB2 family protein virB2
BA011_RS38765 (BA011_36345) 91142..91441 + 300 WP_011654761 conjugal transfer protein TrbD virB3
BA011_RS38770 (BA011_36350) 91452..93887 + 2436 WP_028744195 conjugal transfer protein TrbE virb4
BA011_RS38775 (BA011_36355) 93880..94689 + 810 WP_011654759 P-type conjugative transfer protein TrbJ virB5
BA011_RS38780 (BA011_36360) 94686..94886 + 201 WP_028744197 entry exclusion protein TrbK -
BA011_RS38785 (BA011_36365) 94880..96061 + 1182 WP_065284718 P-type conjugative transfer protein TrbL virB6
BA011_RS43795 96083..96229 + 147 Protein_108 conjugal transfer protein TrbF -
BA011_RS38800 (BA011_36380) 97471..97989 + 519 Protein_110 VirB8/TrbF family protein -
BA011_RS38805 (BA011_36385) 98041..98835 + 795 WP_237352882 P-type conjugative transfer protein TrbG virB9
BA011_RS38810 (BA011_36390) 98839..99285 + 447 WP_028744199 conjugal transfer protein TrbH -
BA011_RS38815 (BA011_36395) 99301..100602 + 1302 WP_065284720 IncP-type conjugal transfer protein TrbI virB10
BA011_RS38820 (BA011_36400) 100803..101102 + 300 WP_027690597 transcriptional repressor TraM -
BA011_RS38825 (BA011_36405) 101103..101807 - 705 WP_027690598 autoinducer binding domain-containing protein -
BA011_RS38830 (BA011_36410) 102090..103706 + 1617 WP_065284721 hypothetical protein -
BA011_RS38835 (BA011_36415) 103696..104691 + 996 WP_065284722 dienelactone hydrolase-related enzyme -
BA011_RS38840 (BA011_36420) 104840..105019 + 180 WP_018010295 hypothetical protein -
BA011_RS38845 (BA011_36425) 105016..105633 + 618 WP_065284723 hypothetical protein -
BA011_RS38850 (BA011_36430) 105657..106274 - 618 WP_018010297 TraH family protein virB1
BA011_RS38855 (BA011_36435) 106290..107456 - 1167 WP_065284724 conjugal transfer protein TraB -
BA011_RS38860 (BA011_36440) 107446..108012 - 567 WP_065284725 conjugative transfer signal peptidase TraF -

Host bacterium

ID   3240 GenBank   NZ_CP016292
Plasmid name   Vaf10|unnamed4 Incompatibility group   -
Plasmid size   309378 bp Coordinate of oriT [Strand]   111666..111708 [-]
Host baterium   Rhizobium leguminosarum strain Vaf10

Cargo genes

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