Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102682
Name   oriT_pB323S2c in_silico
Organism   Bradyrhizobium barranii subsp. barranii strain 323S2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP049702 (75671..75707 [+], 37 nt)
oriT length   37 nt
IRs (inverted repeats)      17..23, 28..34  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 37 nt

>oriT_pB323S2c
CCAAGGGCGCAGTAATACGTCGCTGACGCGACGTCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1980 GenBank   WP_166354441
Name   traA_G6321_RS54590_pB323S2c insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 123111.13 Da        Isoelectric Point: 10.2256

>WP_166354441.1 Ti-type conjugative transfer relaxase TraA [Bradyrhizobium barranii]
MAITHFTPQLIGRGDGRSAVLAAAYRHCAKMEFEAEGRTVDYSNKRGMAHEEFLVPADAPAWLRTIIADR
SVAGASEAFWNKVEAFEKRADAQFAKEFIIALPVELTTEQNIALMRQFVVEQVLSRRQVADWVYHDEPGN
PHVHLMTTLRPLTEDGFGPKRVAVIGEDGQPLRMQSGKIAYRLWAGDKQEFLEQRNGWLDLQNQHLALNG
HEIRVDGRSYAERGIDVVPTTHIGVAAKAIQRRAEREGRDPNLERLRVFDENRAETLRRIQRRPEIVLDM
ISREKSVFDQRDVGKLLHRYVDDVGTFQDLMARVLQSPDALRLEGESVDFATGARAPAKYTTRELIRLEA
EMARRADHLSGSAAFTVKAQVIAAVSARHANLSVEQRAAIAHVVSGERIAAVVGRAGAGKTTMMRAAREV
WEAAGYRVVVGALAGKAAEGLEKEAAIQSRTLASWELRWKSGRDGLDDRTVFVLDEAGMVASRQMALFVE
TASKAGSKLVLVGDPEQLQPIEAGAAFRAIVERIGYAELETIYRQRQQWMRDASLDLARGRTGEALSAYR
HHGRLFGSELKAQAIDNLIADWNRDYDPSKSTLILAHLRRDVRALNDMARAKLVERGLIEEGHAFRTEDG
ERRFAAGDQIVFLKNEGSLGVKNGMIGKVVAAEPKRLVAEIGDGEGRRHVEVDQRFYRNIDHGYATTVHK
AQGATVDRVKVLATLSLDKHLTYVALTRHREDVALYYGRRSFQKAGGLIPILSQRRAKESTLDYECGALY
RDALRFAANRGLNIFKVARTLANDRLRWTVRQKQRLADVARRLRALGEKLGLLDSRKPIIRTAHKEAKPM
VAGVTTFTKSLTDTVEDRILADPAIKKQWEDVSTRFRLVFADPERAFRATNFDAMLKDPAAASSTMARLA
ASPESFGALRGKVGLLAGKSDKQVRQRAEANAPALKRDIERYLRLRAEAEHKHEAEERAIRHRVAIDIPA
LSREARRVLERVRDAIDRNDLPSALEFALADRMVKAEIDGFNKAVAERFGDRTFLSNAAREPNGQPFEKA
AAGMDPARREQLKEAWPAMRAAQQLAAGERTAQALKQAEGQRLTQSQGQTLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)

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

(858-954)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-735)


  Protein structure



No available structure.




T4CP

ID   1620 GenBank   WP_166354547
Name   t4cp2_G6321_RS54265_pB323S2c insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91446.12 Da        Isoelectric Point: 6.0776

>WP_166354547.1 conjugal transfer protein TrbE [Bradyrhizobium barranii]
MVALRSFRHSGPSFADLVPYAGLVANGVVLLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINTILARLG
SGWMIQVEAVRVPTTDYPARQDCYFPDPVTRAIDDERRSRFEQERGHFESRHAIILSWRPPERRRAGLAR
YIYSDAESRSASYADTAIESFRTSVREVEQYLASVLSIRRMETREVEERDGTRMARYDELFQFIRFCITG
ENHPIRLPDIPMYLDWLATAELQHGLSPMVENRFLGVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFMF
LDDQDARQKLERTRKKWQQKVRPFIDQLFQTQSRSIDQDAAAMVAEAEDAIAEASSQLVAYGYYTPVIVL
FDESSARLQEKAEAVRRLIQAEGFGARIETLNATEAFLGSLPGNWYANIREPLINTRNLADLIPLNSVWS
GNPTAPCPFFPPASPPLMQVASGSSPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYAGAQIFA
FDKGRSMMPLTLAAGGDHYEIGGDEVDSAAALAFCPLSDLSTDTDRAWAAEWVETLVAVQGVLITPDHRN
AISRQIGLMVKARGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAERDGLQLGSFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLTGNPSLIILDEAWLMLGHSVFRDKIREWLKVLRKANCAVLLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAVPKREYYVASPEGRRLFNMALGP
VALSFVGASGKDDLKRILALKKAEANWPVHWLKERGIGHAETLLATS

  Protein domains


Predicted by InterproScan.

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

(189-400)

  Protein structure



No available structure.



ID   1621 GenBank   WP_166354583
Name   traG_G6321_RS54575_pB323S2c insolico UniProt ID   _
Length   597 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 597 a.a.        Molecular weight: 64040.25 Da        Isoelectric Point: 9.1616

>WP_166354583.1 Ti-type conjugative transfer system protein TraG [Bradyrhizobium barranii]
MKANKIALAIVPAVLMTGLCLALTGIEAWLSKFGTTPKAHLVLGRIGIALPYVIAAAIGVVFLFAAAGAT
AIRSAGWSVVFGVLIVVAIAAAREIARLHSFANALPAGDRLLAYADPSTVIGATITALVAVFGLRVAMRG
NAAFAAAAPRRIHGRRAIHGESDWMTMSEAARLFPEAGGIVVGERYRVDRDAVAGQPFRADDAETWGAAG
KSALLCFDASFGSSHGIAFAGSGGFKTTSVTVPTALKWGGGLVVLDPSNEVAPMVRGHRHGAGRQVFVLD
PRSSGVGFNVLDWIGQHGATKEEDIAAVASWIMTDNPRQGSARDDFFRASALQLLTALIADVCLSGHTEK
KDQHLRQVRANLSEPEPKLRQRLQAIYDNSESGFVKENVAPFIAMTPETFSGVYANAVKETHWLSYANYA
ALVSGSSFTTAELAEGRTDVFINLDLKTLENHAGLARVIIGSLLNAIYNRNGEVTSRTLFLLDEVARLGY
LRILETARDAGRKYGITLLMLYQSIGQMREAYGGRDATSKWFESASWISFSAINDPETADYISKRCGDTT
VEVDQLSRSSQMSGSSRTRSKQLARRPLILPHEVLHP

  Protein domains


Predicted by InterproScan.

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

(163-596)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 7766..17314

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6321_RS54215 (G6321_54215) 3939..4427 - 489 WP_166354698 DUF1353 domain-containing protein -
G6321_RS54220 (G6321_54220) 4981..6627 - 1647 WP_166354529 hypothetical protein -
G6321_RS54225 (G6321_54225) 6690..7409 - 720 WP_166354531 alpha/beta hydrolase -
G6321_RS54230 (G6321_54230) 7766..9070 - 1305 WP_166354533 IncP-type conjugal transfer protein TrbI virB10
G6321_RS54235 (G6321_54235) 9082..9534 - 453 WP_166354535 conjugal transfer protein TrbH -
G6321_RS54240 (G6321_54240) 9537..10376 - 840 WP_166354537 P-type conjugative transfer protein TrbG virB9
G6321_RS54245 (G6321_54245) 10394..11056 - 663 WP_166354539 conjugal transfer protein TrbF virB8
G6321_RS54250 (G6321_54250) 11093..12253 - 1161 WP_166354541 P-type conjugative transfer protein TrbL virB6
G6321_RS54255 (G6321_54255) 12270..12455 - 186 WP_166354543 entry exclusion protein TrbK -
G6321_RS54260 (G6321_54260) 12452..13249 - 798 WP_166354545 P-type conjugative transfer protein TrbJ virB5
G6321_RS54265 (G6321_54265) 13221..15674 - 2454 WP_166354547 conjugal transfer protein TrbE virb4
G6321_RS54270 (G6321_54270) 15684..15983 - 300 WP_166354329 conjugal transfer protein TrbD virB3
G6321_RS54275 (G6321_54275) 15976..16356 - 381 WP_166354549 TrbC/VirB2 family protein virB2
G6321_RS54280 (G6321_54280) 16346..17314 - 969 WP_166354551 P-type conjugative transfer ATPase TrbB virB11
G6321_RS54285 (G6321_54285) 17330..17883 - 554 Protein_17 GNAT family N-acetyltransferase -
G6321_RS54290 (G6321_54290) 18296..19510 + 1215 WP_080660038 plasmid partitioning protein RepA -
G6321_RS54295 (G6321_54295) 19507..20535 + 1029 WP_166354553 plasmid partitioning protein RepB -
G6321_RS54300 (G6321_54300) 20815..22131 + 1317 WP_166354555 plasmid replication protein RepC -

Host bacterium

ID   3126 GenBank   NZ_CP049702
Plasmid name   pB323S2c Incompatibility group   -
Plasmid size   198976 bp Coordinate of oriT [Strand]   75671..75707 [+]
Host baterium   Bradyrhizobium barranii subsp. barranii strain 323S2

Cargo genes

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