Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107348
Name   oriT_ISRA437|unnamed in_silico
Organism   Bradyrhizobium sp. ISRA437
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP094522 (122307..122344 [+], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 38 nt

>oriT_ISRA437|unnamed
TCCAAGGGCGCAGTAATACGTCGCTGACGCGACGTCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4899 GenBank   WP_280978580
Name   traA_MTX18_RS35520_ISRA437|unnamed 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: 123258.33 Da        Isoelectric Point: 10.3384

>WP_280978580.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [unclassified Bradyrhizobium]
MAITHFTPQLIGRGDGRSAVLAAAYRHCAKMEFEAEGRTVDYSGKRGMIHEEFQVPADAPAWLRSMIADR
SVAGASEAFWNRVEAFEKRADAQFAKEFIIALPVEQTTEQNIALMRQFVVEQVLSRGQVADWVYHDEPGN
PHVHLMTTLRPLTENGFGPKRVAVIGEDGQPTRMKSGKIAYRLWAGDKQEFLEQRNGWLDLQNQHLAMNG
HEIRVDGRSYVERGIDVVPTTHIGVAAKAIQRRAEREGRDPDLERLRVFDENRAETLRRIQRRPEIVLDM
ISREKSIFDERDVGKLLHRYVDDAGTFHHLMARVLQSPDALRLEGESVDFATAARAPAKYTTRELIRLEA
DMARRAIHLSGSTAFAIKTPVIAAVSARHANLSAEQRSAIEHFASGTRITAVVGRAGAGKTTMMRAAREV
WEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWKSGRDGLNDRTVFVLDEAGMVASRQMALFVE
TASKAGAKLVLVGDPEQLQPIEAGAAFRAIVERIGYAELETIYRQRQQWMRDASLDLARGRTARALSAYR
HHGRLFGSELKAQAIDNLIADWNRDYDPSKSTLILAHLRRDVRALNEMARGKLVERGLVGEGYVFRTEDG
ERRFAAGDQIVFLKNEGSLGVKNGMIGKVVEAAPAFLVAEIGEGDGRRRVEVDQRFYRNIDHGYATTVHK
AQGATVDRVKVLATLSLDKHLTYVALTRHREDVALYYGRRSFQKAGGVIPILSQRRAKETTLDYERGSLY
RDALRFAANRGLHIVNVARTLMRDRLRWTVRQKLRLPEFGRRLRALGEKLGLIDSRKPIMNTAHKEEKPM
VAGVTTFPKSLIDTVEDSILADPAIKKQWEQVSTRFRLVFAAPERAFRATNFDAVLKDSTAATSTLARLA
SNPESFGALRGKTGLLAGKADKQERQRAEANVPALKRDIERYLRLRAEAEHKHEAEERAIRQRVAIDIPA
LSRDARRVLERVRDAIDRNDLPSALEFALADRMVKAEIDGFNKAIAERFGDRTFLPNAAREANGPAFEKA
AAGMDPARRDQLKEAWPAMRAAQQLAAQERSAQALKQAEAQRLTQSQGQTLK

  Protein domains


Predicted by InterproScan.

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

(859-954)

AAA domain (AAA_30)

(382-565)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-735)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5101 GenBank   WP_280978493
Name   t4cp2_MTX18_RS34995_ISRA437|unnamed 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: 91343.09 Da        Isoelectric Point: 6.3242

>WP_280978493.1 MULTISPECIES: conjugal transfer protein TrbE [unclassified Bradyrhizobium]
MVALRSFRHSGPSFADLVPYAGLVANGIVLLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINTILARLG
SGWMIQVEAVRVPTTDYPARRDCHFPDPVTRAIDDERRGRFEQERGHFESRHAIILTWRPPERRRAGLAR
YIYSDVESRSASYADTAIESFRTSIREVEQYLASVLTIRRMETREIEERDGTRMARYDELFQFIRFCITG
ENHPIRLPDIPMYLDWLATAELQHGLSPTVENRFLGVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFIF
LDDQDARQKLERTRKKWQQKVRPFIDQLFQTQSRSIDHDAAAMVAEAEDAIAEASSQLAAYGYYTPVLVL
FDESSARLQEKAEAVRRLIQAEGFGARIETLNATEAFLGSLPGNWYANIREPLISTRNLADLIPLNSVWS
GNPIAPCPFYPPSSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYAGAQIFA
FDKGRSMLPLTLAAGGDHYEIGGDDAGGAAALAFCPLSDLLTDTDRAWAAEWIETLVAVQGVVITPDHRN
AISRQVGLMAEARGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAERDGLQLGSFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLSGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAVPKREYYVASPEGRRLFNMALGP
VALSFVGASGKEDLKRILALKKGKANWPVHWLKERGIGHAETLLADF

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.



ID   5102 GenBank   WP_280978577
Name   traG_MTX18_RS35505_ISRA437|unnamed insolico UniProt ID   _
Length   646 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 646 a.a.        Molecular weight: 70108.01 Da        Isoelectric Point: 9.4757

>WP_280978577.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [unclassified Bradyrhizobium]
MKANKVALAIAPGVLMAGLCLALTGIEAWLSKFGTTPKAHLVLGRIGIALPYVMAAATGVIFLFAAAGAT
AIRYAGWSVVFGGLLMVAIAASREIARLHSFANAVPAGKELLAYTDPSTVIGATIAALTAVFGFRVAMRG
NAAFAAAEPRRIRGQRAIHGESNWMAITEAARLFPEPGGIVVGERYRVDRDAVADQSFRADDPETWGAGG
KSPLLCFDASFGSSHGIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSNEVAPMVTTHRHGAGRQVFVLD
PRSSEIGFNILDWIGEHGATKEEDIAAVASWIMTDNPRQGSARDDFFRASALQLLTALIADVCLSGHTEK
KDQHLRQVRANLSEPEPKLRQRLQTIYDNSESGFVKENVAPFIAMTPETFSGVYANAVKETHWLSYANYA
ALVSGSSFTTAELAEGRTDVFINLDLKTLENHAGLARVIIGSLLNAIYNRNGEANGRTLFLLDEVARLGY
LRILETARDAGRKYGITLLMLYQSIGQMREAYGGRDATSKWFESASWISFSAINDPETADYISKRCGDTT
VEVDQLSRSSQMSGSSRTRSKQLARRPLMLPHEVLRMRTDEQIIFTAGNPPLRCGRAIWFRRADMRTCVG
ENRFHRREAGGRSRRS

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 7540..17111

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MTX18_RS34945 (MTX18_34845) 2988..4760 + 1773 WP_280978484 GMC family oxidoreductase N-terminal domain-containing protein -
MTX18_RS34950 (MTX18_34850) 4842..5747 - 906 WP_280978485 LysR family transcriptional regulator -
MTX18_RS34955 (MTX18_34855) 6224..6490 + 267 WP_280978486 hypothetical protein -
MTX18_RS34960 (MTX18_34860) 7540..8847 - 1308 WP_280978487 IncP-type conjugal transfer protein TrbI virB10
MTX18_RS34965 (MTX18_34865) 8859..9311 - 453 WP_280978488 conjugal transfer protein TrbH -
MTX18_RS34970 (MTX18_34870) 9314..10153 - 840 WP_280978489 P-type conjugative transfer protein TrbG virB9
MTX18_RS34975 (MTX18_34875) 10171..10833 - 663 WP_280978490 conjugal transfer protein TrbF virB8
MTX18_RS34980 (MTX18_34880) 10877..11992 - 1116 WP_280978619 P-type conjugative transfer protein TrbL virB6
MTX18_RS34985 (MTX18_34885) 12055..12243 - 189 WP_280978491 entry exclusion protein TrbK -
MTX18_RS34990 (MTX18_34890) 12240..13046 - 807 WP_280978492 P-type conjugative transfer protein TrbJ virB5
MTX18_RS34995 (MTX18_34895) 13018..15471 - 2454 WP_280978493 conjugal transfer protein TrbE virb4
MTX18_RS35000 (MTX18_34900) 15481..15780 - 300 WP_027584282 conjugal transfer protein TrbD virB3
MTX18_RS35005 (MTX18_34905) 15773..16153 - 381 WP_280978494 TrbC/VirB2 family protein virB2
MTX18_RS35010 (MTX18_34910) 16143..17111 - 969 WP_280978495 P-type conjugative transfer ATPase TrbB virB11
MTX18_RS35015 (MTX18_34915) 17129..17752 - 624 WP_280978496 acyl-homoserine-lactone synthase TraI -
MTX18_RS35020 (MTX18_34920) 18309..18740 - 432 WP_280978497 hypothetical protein -
MTX18_RS35025 (MTX18_34925) 19344..20558 + 1215 WP_280978498 plasmid partitioning protein RepA -
MTX18_RS35030 (MTX18_34930) 20555..21589 + 1035 WP_280978499 plasmid partitioning protein RepB -

Host bacterium

ID   7784 GenBank   NZ_CP094522
Plasmid name   ISRA437|unnamed Incompatibility group   -
Plasmid size   316663 bp Coordinate of oriT [Strand]   122307..122344 [+]
Host baterium   Bradyrhizobium sp. ISRA437

Cargo genes

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