Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104235
Name   oriT_pF5.1b in_silico
Organism   Pararhizobium polonicum strain F5.1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM004503 (56573..56616 [+], 44 nt)
oriT length   44 nt
IRs (inverted repeats)      21..27, 32..38  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 44 nt

>oriT_pF5.1b
GGTTCCAAGGGCGCAATTATACGTCGCTGATGCGACGTGCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3109 GenBank   WP_068951002
Name   traA_ADU59_RS01115_pF5.1b insolico UniProt ID   A0A546YXT6
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123345.21 Da        Isoelectric Point: 10.0430

>WP_068951002.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium/Agrobacterium group]
MAIAHFSASIVSRGGGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLVHEEFMLPADAPKWVRAMIADR
SVAGASEAFWNKVEAFEKRADAQLARDLTIALPLELPAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTGDGFGTKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPTIHLGVGAKAIERKAKEQGIRPELERIELNEDRRSENARRILRRPEIVLDL
ITREKSVFDERDVAKVLHRYVDDPALFQQLMLRIILNPEVLRLQRDTIDFSTGQKVPARYSTRAMIRLEA
TMVRQTTWLSGKETHAVSASVLDTTFQRHARLSEEQKTAIERIAGPTRIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIHSRTLASWELRWNRGRDVLDRKTVFVMDEAGMVASKQMARFVD
TAVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNVMAREKLVERGVVGEGHVFKTADG
IRQFDAGDQIVFLKNETSLGVKNGMIAHVVEAAPNRIVAVVGEGDKRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDVQLYYGRRSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAEGRGLNIVQVARTLVRDRLDWTLRQKMKLVELGQRLAVFAERLGLHHPLKTQTMKEAAPMVAG
IKTFSGSVADTLSDRLGADPALKQQWEEVSARFAYVFADPETAFRAMNFDAVLADKDSARQALGKLEAEP
ASIGALKGKTGILASKTEREARRVAELNVPALTRDLAQYLRMRETATQRMETEEQALRQRVSIDIPALSP
AACVVLERVRDAIDRNDLPAALGYALSNRETKLEIDGFNKAVTERFGERTLLTNAARQPSGTLFDKLSNG
MQPAQKEQLKEAWPVMRTTQQLAAHERTTQTLKQAEELRLSQRQSPVMKQ

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-567)


  Protein structure


Source ID Structure
AlphaFold DB A0A546YXT6


T4CP

ID   3012 GenBank   WP_068950865
Name   traG_ADU59_RS01100_pF5.1b insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71095.45 Da        Isoelectric Point: 9.3596

>WP_068950865.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium/Agrobacterium group]
MTMNRLLLLILPAIIMLAAMFATSGMEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGIIGLFAANGSA
NIKAAGLSVLAGSGVVITIATLREVIRLNSIASSVPAEQSVLAYADPVTMIGASIAFISGMFALRVAIKG
NAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPERGGIIIGERYRVDRDSVAAMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVCEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKGRTLFLLDEVARLGY
LRILETARDAGRKYGIMLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
ENRFHRTGTGTDTHTEHAPPWQKEGTRP

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   3013 GenBank   WP_068950992
Name   t4cp2_ADU59_RS01500_pF5.1b insolico UniProt ID   _
Length   820 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 820 a.a.        Molecular weight: 91760.55 Da        Isoelectric Point: 5.5728

>WP_068950992.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALKLFRHSGPSFADLVPYAGLVDNGVMLLKDGSLMAGWYFAGPDSESSTDTERNEVSRQINMILSRLG
SGWMIQVEALRVPTIDYPARDTCHFPDPVTRAIDSERRSHFERESGHFESRHALILTWRPPEPRRSGLTR
YVYSDTASRSATYADTALDSFRTSIREVEQYLANVVSIRRMVTRETEERGGFRIARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPTIENRFLGVVAIDGLAAESWPGILNSLDLMPLTYRWSSRFVF
LDEQEARSRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMMMVAETEDAIAETASQLVAYGYYTPVIVL
FDEQQPRLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPVAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQVFA
FDKGGSMLPLTLGIDGDHYQIGGDGAGEGGSPQLAFCPLAELSTDGDRAWAAEWIETLVALQGVTVTPDY
RNAISRQLALMAESRGRSLSDFVSGVQMRAIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEELMN
MGERNLVPVLLYMFRRVEKRLTGAPSLIILDEAWLMLGHPTFRDKIREWLKVLRKANCAVVLATQSISDA
ERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPEGRRLFDMSL
GPVALSFVGASGKEDLKRIRALHFDHGADWPLHWLQQRGIAHADTLFPVA

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 132996..142645

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ADU59_RS29470 128188..128445 - 258 WP_234885315 (2Fe-2S)-binding protein -
ADU59_RS01440 (ADU59_01450) 128468..129577 - 1110 WP_068950964 FAD-dependent oxidoreductase -
ADU59_RS01445 (ADU59_01455) 129671..130576 + 906 WP_068950966 LysR substrate-binding domain-containing protein -
ADU59_RS29475 130852..131514 - 663 Protein_121 IncP-type conjugal transfer protein TrbI -
ADU59_RS01460 (ADU59_01470) 132051..132728 + 678 WP_068950972 HAD hydrolase-like protein -
ADU59_RS01465 (ADU59_01475) 132996..134300 - 1305 WP_068950975 IncP-type conjugal transfer protein TrbI virB10
ADU59_RS01470 (ADU59_01480) 134313..134789 - 477 WP_068950977 conjugal transfer protein TrbH -
ADU59_RS01475 (ADU59_01485) 134789..135643 - 855 WP_068950979 P-type conjugative transfer protein TrbG virB9
ADU59_RS01480 (ADU59_01490) 135661..136323 - 663 WP_068950981 conjugal transfer protein TrbF virB8
ADU59_RS01485 (ADU59_01495) 136338..137525 - 1188 WP_012478019 P-type conjugative transfer protein TrbL virB6
ADU59_RS01490 (ADU59_01500) 137519..137737 - 219 WP_068950983 entry exclusion protein TrbK -
ADU59_RS01495 (ADU59_01505) 137734..138543 - 810 WP_068950985 P-type conjugative transfer protein TrbJ virB5
ADU59_RS01500 (ADU59_01510) 138515..140977 - 2463 WP_068950992 conjugal transfer protein TrbE virb4
ADU59_RS01505 (ADU59_01515) 140988..141287 - 300 WP_068950994 conjugal transfer protein TrbD virB3
ADU59_RS01510 (ADU59_01520) 141280..141684 - 405 WP_083198079 conjugal transfer pilin TrbC virB2
ADU59_RS01515 (ADU59_01525) 141674..142645 - 972 WP_068950996 P-type conjugative transfer ATPase TrbB virB11
ADU59_RS01520 (ADU59_01530) 142642..143277 - 636 WP_068950998 acyl-homoserine-lactone synthase -

Host bacterium

ID   4674 GenBank   NZ_CM004503
Plasmid name   pF5.1b Incompatibility group   -
Plasmid size   143492 bp Coordinate of oriT [Strand]   56573..56616 [+]
Host baterium   Pararhizobium polonicum strain F5.1

Cargo genes

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