Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115471
Name   oriT_pOC-Colt5.8 in_silico
Organism   Rhizobium rhizogenes strain Colt5.8
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK318973 (92733..92775 [+], 43 nt)
oriT length   43 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: 43 nt

>oriT_pOC-Colt5.8
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9909 GenBank   WP_172694595
Name   traA_HTY31_RS00425_pOC-Colt5.8 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123841.56 Da        Isoelectric Point: 9.8226

>WP_172694595.1 Ti-type conjugative transfer relaxase TraA [Rhizobium rhizogenes]
MAIAHFSASIVSRGGGRSVVLSAAYRHCARMEYEREARTIDYTRKQGLVHEELMLPADAPKWVRAMIADR
SVSGASEAFWNKVEAFEKRADAQLARDLTIALALELTPQQNVALVRDFVEKHILEKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGAKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNSLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPTIHLGVGAKAIERKAKEQGIRPELERIELNEERRSENARRILRRPEIVLDL
ITREKSVFDERDVAKVLHRYVDEPTVFQQLMLRIILNPEVLRLQRDTIDFATGEKLPARYSTGAMIRLEA
TMARQAMWLSNREGRSVPEAALDATFRRHERLSEEQKTAIERIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIESRTLASWELRWNRGRDVLDDKTVFVMDEAGMVASKQMAGFVD
TVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDPTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFKTADG
VRQFDVGDQIVFLKNEGSLGVKNGMIAHVIEAAPNRIVAVVGEGGQRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHRDDLQLYYGRRSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAENRGLHIMQVARTLLRDRLDWTLRQNTKLSDLVHRLRALGERFGLDQSPKTQTMKEAAPMVAG
IKTFPGSVVDTVGDKLGADLALKQQWEEVSARFRYVFADPETAFRAMNFDTVLADKDSARQALQKLEAEP
ASIGPLRGKTGILASKAERESRRIAEINVPALKRDLEQYLRMRETAAQRLQADEQVLRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAAMGYALSNRETKQEIDGFNQAITERFGERTLLANTAREPSGKLYEKLSEG
MKPEQKEQLKEAWPVMRTAQQLAAHERTTQTLKQVEELRLTQRQSPVMKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

MobA/MobL family (MobA_MobL)

(17-243)

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

(855-951)


  Protein structure



No available structure.




T4CP

ID   11551 GenBank   WP_172694571
Name   traG_HTY31_RS00410_pOC-Colt5.8 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: 71142.54 Da        Isoelectric Point: 9.3596

>WP_172694571.1 Ti-type conjugative transfer system protein TraG [Rhizobium rhizogenes]
MTVNRLLLLILPAIIMLAAMFATSGMEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGIIGLFAANGSA
NIKAAGLSVLAGNGVVITIATLREVIRLNSITSRVPAEQSVLAYADPVTMIGVGIAFISGMFALRVAIKG
NAAFSTTAPKRIGGKRAVHGEADWMKIQDAAKLFPEPGGIVIGERYRVDRDSVAAMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVCEHRRQAGRKVIVLD
PTAAGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKGRTLFLLDEVARLGY
LRILETARDAGRKYGIMLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFTSGNPPLRCVRAIWFRRDDMKACVG
ENRFHRTGTGADTHTEHAPPWQKEGTRP

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   11552 GenBank   WP_080868325
Name   t4cp2_HTY31_RS00760_pOC-Colt5.8 insolico UniProt ID   _
Length   822 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 822 a.a.        Molecular weight: 92115.82 Da        Isoelectric Point: 5.6807

>WP_080868325.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALKLFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDSERNEVSRQINMIMSRLG
SGWMVQVEALRVPTIDYPVGDTCHFPDPVTRAIDTERRSHFERESGHFESRHALILTWRPPEPRRSGLAR
YVYSDTASRSATYADTALDSFRTSIREFEQYLANVVSIRRMVTRETEERGGFRVARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPTVENRFLGVVAIDGLAAESWPGILNSLDLMPLTYRWSSRFVF
LDEQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMMMVAETEDAIAEASSQLVAYGYYTPVILL
FDEQQERLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLVNTRNLADLIPLNSVWS
GSPVAPCPFYPPGSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLSLIAAQFRRYADAQIFA
FDKGRSMLPLTRAIGGDHYEIGGDTAEGGEGASPQLAFCPLAELASDSDRAWAAEWIETLVALQGVTVTP
DYRNAISRQLGLMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLALGAFQCFEVEEL
MNMGERNLVPVLLYMFRRVEKRLTGAPSLIILDEAWLMLGHPTFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPEGRRLFDM
SLGPVALSFVGASGKEDLKRIRALHFQHGADWPKHWLQQRGIAHAETLFQAA

  Protein domains


Predicted by InterproScan.

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

(188-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 161752..171422

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTY31_RS00700 (pOC-C5.8_655) 157272..157997 - 726 WP_080868320 nopaline ABC transporter permease NocM -
HTY31_RS00705 (pOC-C5.8_656) 157999..158709 - 711 WP_045025159 nopaline ABC transporter permease NocQ -
HTY31_RS00710 (pOC-C5.8_657) 158782..159633 - 852 WP_003523898 nopaline ABC transporter substrate-binding protein NocT -
HTY31_RS00715 (pOC-C5.8_658) 159698..160471 - 774 WP_080868321 nopaline ABC transporter ATP-binding protein NocP -
HTY31_RS00720 (pOC-C5.8_659) 160721..161623 + 903 WP_137006652 LysR family transcriptional regulator -
HTY31_RS00725 (pOC-C5.8_660) 161752..163059 - 1308 WP_080868322 IncP-type conjugal transfer protein TrbI virB10
HTY31_RS00730 (pOC-C5.8_661) 163074..163550 - 477 WP_045025162 conjugal transfer protein TrbH -
HTY31_RS00735 (pOC-C5.8_662) 163550..164404 - 855 WP_070167554 P-type conjugative transfer protein TrbG virB9
HTY31_RS00740 (pOC-C5.8_663) 164422..165084 - 663 WP_080868323 conjugal transfer protein TrbF virB8
HTY31_RS00745 (pOC-C5.8_664) 165091..166293 - 1203 WP_080868324 P-type conjugative transfer protein TrbL virB6
HTY31_RS00750 (pOC-C5.8_665) 166287..166505 - 219 WP_070167519 entry exclusion protein TrbK -
HTY31_RS00755 (pOC-C5.8_666) 166502..167311 - 810 WP_070167518 P-type conjugative transfer protein TrbJ virB5
HTY31_RS00760 (pOC-C5.8_667) 167283..169751 - 2469 WP_080868325 conjugal transfer protein TrbE virb4
HTY31_RS00765 (pOC-C5.8_668) 169762..170061 - 300 WP_080868326 conjugal transfer protein TrbD virB3
HTY31_RS00770 (pOC-C5.8_669) 170054..170461 - 408 WP_137006655 conjugal transfer pilin TrbC virB2
HTY31_RS00775 (pOC-C5.8_670) 170451..171422 - 972 WP_080868328 P-type conjugative transfer ATPase TrbB virB11
HTY31_RS00780 (pOC-C5.8_671) 171419..172054 - 636 WP_041723972 acyl-homoserine-lactone synthase -

Host bacterium

ID   15904 GenBank   NZ_MK318973
Plasmid name   pOC-Colt5.8 Incompatibility group   -
Plasmid size   172401 bp Coordinate of oriT [Strand]   92733..92775 [+]
Host baterium   Rhizobium rhizogenes strain Colt5.8

Cargo genes

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