Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107630
Name   oriT_M15|p5 in_silico
Organism   Rhizobium oryzihabitans strain M15
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048637 (268313..268350 [-], 38 nt)
oriT length   38 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: 38 nt

>oriT_M15|p5
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5125 GenBank   WP_164056953
Name   traA_G3A56_RS26950_M15|p5 insolico UniProt ID   _
Length   1198 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1198 a.a.        Molecular weight: 131902.78 Da        Isoelectric Point: 9.1452

>WP_164056953.1 Ti-type conjugative transfer relaxase TraA [Rhizobium oryzihabitans]
MAVPHFSVTVVARGSGRSAVLSAAYRHCAKMDYEREARVIDYSRKQGLLHEEFVIPADAPEWLRAMIADR
SVSGASEAFWNRVEMFEKRSDAQLAKDVTIALPIELSADQNIALMRDFIAQHITTKGMVADWVYHDAPGN
PHVHLMTTLRPLSEDGFGAKKVAVVGPDGNPVRNDAGKIVYELWAGGAEDFNAFRDGWFAIQNRHLALAG
LDIRVDGRSFEKQGIDLTPTIHIGVGATAIERKAETAQVAGAAPSLQLERIELQQERRTENAKRIQRNPE
IVLDLITREKSVFEERDVAKVLNRYIDDAVLFQDLMARILQSPQTLRLDRERMDLATGVRAAAKYTTREL
IRVESQMANQAVWLSQRSSHRVKPAVLNSVFTRHDRLSDEQKIAIEHVAGPERIAAVIGRAGTGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSAWELRWNQERDRLDEKIVFVLDEAGMVSSRQM
ALFVEAVTSSGAKLVLVGDPEQLQPIEAGAAFRAISERIGYAELGTIYRQREQWMRDASLDLARGNVSAA
LDAYAQRDLVRTGWTKGDAITALIADWDREYDPAKATLILAHRRVDVRLLNEMARGKLVERGAIEPGHAF
KTEDGTRHFAAGDQIVFLKNEGSIGVKNGMLARVVEAQPGRFVAEIGGGEDRRQVVVEQRFYTNVDHGYA
TTVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHREAAELYVGLEELAQRRGGVLIAHGEAPYEHKPSNR
ASYFVTLGFSDGQERTVWGVDLARAMEASDVRIGDRIGLEHAGSQRVTLPDGKEVERNSWKVVPIEELAM
ARLHERLSRAGSKETTLDYQHASHYRAALRFAEARGLHLMNVARTVVHDRLQWTVRQSLRIAALGARLAA
VATRLGLGGATSTASTTSAIKEAKPMVSGTTTFPRSVAQAVEDRLSADTGLKDSWQEVSGRFHLVFADPQ
AAFKAVNVDAMLTNDTIAATTIVRIAEQPESFGALKGKTGLFAGSAEKQVRDIALVNALALARNLERYLT
VRAEAERKFETEERAARLKVSIEIPALSPSAKQTLERVRDAIDRNDLPAGLEFALADKMVKAELEGFAKA
VSERFGERTLLPIAAKSADGETFQKLTAGMNSAQKSEVQSAWTSMRTVQQLAAHERTTVALRQAEAARQT
QAKGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

MobA/MobL family (MobA_MobL)

(17-243)

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

(954-1049)

AAA domain (AAA_30)

(387-573)


  Protein structure



No available structure.




T4CP

ID   5361 GenBank   WP_164056938
Name   t4cp2_G3A56_RS26865_M15|p5 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: 91200.68 Da        Isoelectric Point: 6.1538

>WP_164056938.1 conjugal transfer protein TrbE [Rhizobium oryzihabitans]
MVALNKFRSTGPSFADLVPYAGLVENGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINAILSRLG
TGWMIQVEAVRVPTTDYPSAERSHFPDTVTRLIDDERRRHFGQESGHFESRHALILTYRPPERRRSGLTR
YIYSDSESRSAKYADTSLDQFRRSIREIEQYLGNNLSVQRMRTREIPERDGCRVARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLATAELEHGLTPRVENRFLGVVAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIIL
FDENRAALLDKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GHPAAPCPFYPPDAPPLMQVASGSTPFRLNLHFDDVGHTLIFGPTGSGKSTLLALIAAQFCRYERAQVFA
FDKGNSMLPLTLGVGGNHYEIAGESGDGANLAFCPFAELSSEADRAWACEWIETLVSLQGVTVAPDHRNA
ISRQVALMATAPGRSLSDFVSGVQMRDIKDALHHYTVDGPMGQLLDAEADGLTLGRFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGSPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVILATQSISDAERS
GIIDVLKESCPTKICLPNGGAREPGTREFYVRLGFNERQIEIVANAIPKREYYVTSPDGRRLFDMSLGPV
TLSFVGASGKADLARIRALSSTHGREWPGQWLIERGVNRYE

  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   5362 GenBank   WP_164056956
Name   traG_G3A56_RS26965_M15|p5 insolico UniProt ID   _
Length   645 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 645 a.a.        Molecular weight: 69624.67 Da        Isoelectric Point: 9.0645

>WP_164056956.1 Ti-type conjugative transfer system protein TraG [Rhizobium oryzihabitans]
MKVTRALLAVIPPLVMIAVALLLPGIEQWIAAFGSTAKAKMTLGRIGLSLPYALAAAIGVIALFAANGSI
NIKTAGCGVAIGSTTVIVIATIRESARVLQFAGQVPTGKSALSYLDPGTMGGATAAFFCGLFAMRVAMLG
NAAFARSEPKRIRGKRALYGEAEWMALPQAERLFGEGGGIVVGERYRVDRDSTAAISFRADAKETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGSTLIVLDPSNEVAPMVKAHRSAAGRDVVVLD
PKNPDVGFNALDWIGRHGGTKEEDIAAVASWIMSDSGRASGVRDDFFRASGLQLLTAIIADVCLSGHTLK
ERQTLRTVRTNLSEPEPVLRARLQEIYDNSESDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYA
GLVSGSTFSTDDIANGKTDVFVALDLKTLETHSGLARVIIGSFLNAIYNRDGAMPGRALFLLDEVARLGF
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDATSKWFESASWISFAAINDPETADYISRRCGTTT
VEIDQVSRNFQARGSSRTRSKQLASRPLIQPHEVLRMRSDEQIVFTGGNPPLRCGRAMWFRRDDMTSCVG
DNRFHKKPEPVEIAE

  Protein domains


Predicted by InterproScan.

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

(164-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 248000..262897

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G3A56_RS28610 (G3A56_26830) 243609..243785 - 177 WP_210255077 hypothetical protein -
G3A56_RS26835 (G3A56_26835) 243955..245199 - 1245 WP_164056933 plasmid replication protein RepC -
G3A56_RS26840 (G3A56_26840) 245356..246348 - 993 WP_164056934 plasmid partitioning protein RepB -
G3A56_RS26845 (G3A56_26845) 246433..247619 - 1187 Protein_246 plasmid partitioning protein RepA -
G3A56_RS26850 (G3A56_26850) 248000..248965 + 966 WP_164056935 P-type conjugative transfer ATPase TrbB virB11
G3A56_RS26855 (G3A56_26855) 248955..249350 + 396 WP_164056936 TrbC/VirB2 family protein virB2
G3A56_RS26860 (G3A56_26860) 249343..249642 + 300 WP_164056937 conjugal transfer protein TrbD virB3
G3A56_RS26865 (G3A56_26865) 249652..252087 + 2436 WP_164056938 conjugal transfer protein TrbE virb4
G3A56_RS26870 (G3A56_26870) 252080..252889 + 810 WP_164056939 P-type conjugative transfer protein TrbJ virB5
G3A56_RS26875 (G3A56_26875) 252886..253089 + 204 WP_164056940 entry exclusion protein TrbK -
G3A56_RS26880 (G3A56_26880) 253083..254264 + 1182 WP_164056941 P-type conjugative transfer protein TrbL virB6
G3A56_RS26885 (G3A56_26885) 254286..254948 + 663 WP_164056942 conjugal transfer protein TrbF virB8
G3A56_RS26890 (G3A56_26890) 254965..255795 + 831 WP_164056943 P-type conjugative transfer protein TrbG virB9
G3A56_RS26895 (G3A56_26895) 255799..256245 + 447 WP_164056944 conjugal transfer protein TrbH -
G3A56_RS26900 (G3A56_26900) 256261..257561 + 1301 Protein_257 IncP-type conjugal transfer protein TrbI -
G3A56_RS26905 (G3A56_26905) 257606..258271 - 666 WP_164056945 acyl-homoserine-lactone synthase -
G3A56_RS26910 (G3A56_26910) 258388..259077 - 690 WP_246231472 LuxR family transcriptional regulator -
G3A56_RS26915 (G3A56_26915) 259575..259874 + 300 WP_164056947 transcriptional repressor TraM -
G3A56_RS26920 (G3A56_26920) 259886..260590 - 705 WP_164056948 transcriptional regulator TraR -
G3A56_RS26925 (G3A56_26925) 261010..261648 + 639 WP_164056971 XRE family transcriptional regulator -
G3A56_RS26930 (G3A56_26930) 261649..262263 + 615 WP_164056949 RES family NAD+ phosphorylase -
G3A56_RS26935 (G3A56_26935) 262286..262897 - 612 WP_164056950 TraH family protein virB1
G3A56_RS26940 (G3A56_26940) 262915..264081 - 1167 WP_164056951 conjugal transfer protein TraB -
G3A56_RS26945 (G3A56_26945) 264071..264640 - 570 WP_164056952 conjugative transfer signal peptidase TraF -

Host bacterium

ID   8065 GenBank   NZ_CP048637
Plasmid name   M15|p5 Incompatibility group   -
Plasmid size   339368 bp Coordinate of oriT [Strand]   268313..268350 [-]
Host baterium   Rhizobium oryzihabitans strain M15

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -