Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107809
Name   oriT_p.BB_2 in_silico
Organism   Pannonibacter phragmitetus BB
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032314 (54811..54844 [-], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_p.BB_2
TCCAAGGGCGCAGTAATACGTCGCTGACGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5243 GenBank   WP_119396928
Name   traA_P874_RS24785_p.BB_2 insolico UniProt ID   _
Length   1101 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1101 a.a.        Molecular weight: 121993.92 Da        Isoelectric Point: 10.1042

>WP_119396928.1 Ti-type conjugative transfer relaxase TraA [Pannonibacter phragmitetus]
MAITHFTPQIIGRADGRSAVLSTAYRHCAKMEHAAEARTVDYSGKRNLAHEEFLLPVDAPKWAREMIADR
SVAGAAEAFWNKVEAFEKRADAQFAKEFIVALPMELSKAQNIALVRQFVHEQVLGRGQVADWVYHDDPGN
PHVHLMTTLRPLTESGFGAKKVAVIGADGQTVRTKTGKIQYRLWAGEKAEFLEQRQRWLDLQNQHLAFGG
FEIRVDGRSYAERGIDLVPTTHIGPGAKAIERRAMREGRDTRLERLASHAAARAVNAERIQARPEIVLDL
VSCEKSVFDERDIAKVLHRYVDDPGAFQQLLARIVQSPDCLRLESGTVDFATGARLPDKLTTRELIRLEA
EMVSRASALVKAKGFGVRKKIVADVFARHDRLSDEQRTAIEHATSGARIATVVGRAGAGKTTMMRAAREA
WEAAGYTVVGGALAGKAAEGLETEAKIPSRTLASWELRWNEARNRLDRKTIFVMDEAGMVASKQMATFVE
AVSKAGAKLVLVGDAEQLQPIEAGAAFRAIVERTGYAELETIYRQKDAWMRTASVDLARGNVTAALSAYG
GRGMVIGEKLKAQAVDSLIASWNGEYDPEKSTLILAHLRRDVRELNRLAREKLVERGIVGEGHAFQTEEG
TRHFDAGDQIVFLRNEGALGVKNGMIGRVVEAGPGRIVAETGEGEGKHRIEVEERFYRNLDLGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLFYGERSFQIAGGLDTLLSRRNAKETTLDYAAGRFY
RHALSFANSRGLHLMRVARTLARDRLDWTLRQKRRLADLGRKFRAVGTRIGLFDTTLSAVQSKKEAEPMV
KGVTTFAKSITDVAAERVHAEKEVARQWEEVSDRFRLVFSDPEAAFRAMRFDAVLADPAVASERLGQLAR
EPAAIGALRGREGILASRAERQARQEAEANVPALGREIERYLRLREAATRRLEADETALRRRASIDIPAL
SPAAHAVLEKVRDAIDRNDLSAALGFALADRMAKAEIDGFNKAVSERFGERTLLSNGVQDTDGAVFRKQA
LGLPAAERERLAAAWPIMRTGQQLAAHERTVKALKETEALRQSQRQSQVLK

  Protein domains


Predicted by InterproScan.

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

(857-953)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-735)

AAA domain (AAA_30)

(382-566)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5488 GenBank   WP_119396914
Name   t4cp2_P874_RS24715_p.BB_2 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 90982.20 Da        Isoelectric Point: 5.2576

>WP_119396914.1 conjugal transfer protein TrbE [Pannonibacter phragmitetus]
MVALRQFRNTRPSFSDLLPYAGLVDDGVILLKDGSVMAGWYFAGPDSESSTNLERNEVSRQINTILSRLG
SGWMIQVEAVRIPTVAYPAREQCHFPDPATRAIDNERRAHFEAESGHFESQHAIILTYRPPERRRSGLAR
YVYSDSESRSETYADVVLDTFRTSIREFEQYLANVLSIRRMVTRTVADPESGREIRYDELFQFIRFCIVG
ESHPVRLPAIPMYLDWLATAEFHHGLSPVVDGRYLAVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFIF
LDDQEARAKLERTRKKWQQKVRPFFDQLFQTQSRAVDQDAMTMVAEAEDAIAEASSQLVAFGYYTPVIVL
FDSNDTRLRDQAEAVRRLVQAEGFGARIETLNATEAYLGSLPGNSYANVREPLVNTRNLADLIPLNSVWS
GSTTAPCPFYPTGSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSLLPLTIAADGDHYEVGAGEGTSLSFCPLAELSTEGDRAWASEWIETLIAMQGVAITPDHRNAIS
RQVGLMASARGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQTFEIEELMNMGERN
LVPVLLYLFRRIEKRLTGAPSLIVLDEAWLMLGHPTFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAGEPGTREFYERIGFNERQIEIVATATPKREYYVASPEGRRLFDMALGPVAL
AFAGASGKEDLKRIDQLHKDHGPDWPAAWLMERGIGNAEAILTRD

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.



ID   5489 GenBank   WP_119396931
Name   traG_P874_RS24800_p.BB_2 insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 68674.64 Da        Isoelectric Point: 9.9621

>WP_119396931.1 Ti-type conjugative transfer system protein TraG [Pannonibacter phragmitetus]
MTPNKLALLLGPVIIMTGACLALTGMEHWLAGFARTPDTRLMLGRIGIALPYLAAGGTGVVFLFAARGAI
SIRLAGWGVVAGTLVVITIAAVREIGRLAASVMTVPPGTSIVEYTDPATLTGAVVAAGGGVFGLRVAIRG
NAAFASAAPRRVRGKRAIHGESAWMTISAARRLFPKSGGIVVGEACRVDRQAGGGRGFRADDRETWGAGG
KSQLLCFDGSFGSSHGLVFAGSGGFKTTSVTVPTALKWGGGLVALDPSNEVAPMVIGHRRKAGRSVFVLD
PKEPGTGFNVLDWIGRFGGTKEEDVVAVATWVVTDTARQTSIRDDFFRASALQLITVLIADVCLSGHTEK
ENQHLRQMRANLSEPEPKLRERLQLIYDNSESAFVKENVAPFIAMTPETFSGVYANAVKETHWLSYPNYA
ALVSGDSFSTDDLADGDTDVFVNLDLKTLEAHPGLARTIIGALANAIYNRNGKVKGRTLFLLDEVARLGY
LRILETARDAGRKYGISLLLLFQSIGQMRETYGGRDATSKWFESASWISFAAINDPETADYISRRCGNTT
VEVDQLSRTSRMSGSSRTRSRQLSARPLILPEEVLRMRGDEQIVFTSGNPPLRCGRAIWFRREDMKSVVG
ENRFQRT

  Protein domains


Predicted by InterproScan.

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

(164-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36567..46054

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
P874_RS24680 (DW354_RS24680) 31643..32305 - 663 WP_119396910 hypothetical protein -
P874_RS24685 (DW354_RS24685) 32310..33647 - 1338 WP_009452548 plasmid replication protein RepC -
P874_RS24690 (DW354_RS24690) 33813..34823 - 1011 WP_009452547 plasmid partitioning protein RepB -
P874_RS24695 (DW354_RS24695) 34899..36086 - 1188 WP_040673324 plasmid partitioning protein RepA -
P874_RS24700 (DW354_RS24700) 36567..37538 + 972 WP_119396911 P-type conjugative transfer ATPase TrbB virB11
P874_RS24705 (DW354_RS24705) 37528..37905 + 378 WP_119396912 TrbC/VirB2 family protein virB2
P874_RS24710 (DW354_RS24710) 37898..38197 + 300 WP_119396913 conjugal transfer protein TrbD virB3
P874_RS24715 (DW354_RS24715) 38203..40650 + 2448 WP_119396914 conjugal transfer protein TrbE virb4
P874_RS24720 (DW354_RS24720) 40670..41422 + 753 WP_247648218 P-type conjugative transfer protein TrbJ virB5
P874_RS24725 (DW354_RS24725) 41419..41628 + 210 WP_162936539 entry exclusion protein TrbK -
P874_RS24730 (DW354_RS24730) 41609..42775 + 1167 WP_119396917 P-type conjugative transfer protein TrbL virB6
P874_RS24735 (DW354_RS24735) 42778..43440 + 663 WP_119396918 conjugal transfer protein TrbF virB8
P874_RS24740 (DW354_RS24740) 43461..44285 + 825 WP_119396919 P-type conjugative transfer protein TrbG virB9
P874_RS24745 (DW354_RS24745) 44289..44756 + 468 WP_119396920 conjugal transfer protein TrbH -
P874_RS24750 (DW354_RS24750) 44753..46054 + 1302 WP_119396921 IncP-type conjugal transfer protein TrbI virB10
P874_RS24755 (DW354_RS24755) 46135..46839 + 705 WP_162936540 autoinducer binding domain-containing protein -
P874_RS24760 (DW354_RS24760) 46855..47193 - 339 WP_162936541 transcriptional repressor TraM -
P874_RS24765 (DW354_RS24765) 47524..48147 - 624 WP_119396924 acyl-homoserine-lactone synthase -
P874_RS24770 (DW354_RS24770) 48231..48980 - 750 WP_119396925 LuxR family transcriptional regulator -
P874_RS24775 (DW354_RS24775) 49743..50978 - 1236 WP_119396926 conjugal transfer protein TraB -

Host bacterium

ID   8244 GenBank   NZ_CP032314
Plasmid name   p.BB_2 Incompatibility group   -
Plasmid size   116285 bp Coordinate of oriT [Strand]   54811..54844 [-]
Host baterium   Pannonibacter phragmitetus BB

Cargo genes

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