Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106750
Name   oriT_ZM13|pD in_silico
Organism   Ancylobacter polymorphus strain ZM13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP083243 (26553..26607 [-], 55 nt)
oriT length   55 nt
IRs (inverted repeats)      22..28, 33..39  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 55 nt

>oriT_ZM13|pD
CCCCGCCAGGGCCGGCGCAGGACGTCGCGGCAGCGACGTATTACTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4451 GenBank   WP_244451514
Name   traA_K9D25_RS24490_ZM13|pD 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: 123151.40 Da        Isoelectric Point: 10.0859

>WP_244451514.1 Ti-type conjugative transfer relaxase TraA [Ancylobacter polymorphus]
MAITHFTPQLIGRGNGRSAVLSAAYRHCARMEYEAEARTVDYSNKRNLAHEEFLLPADAPEWARALIADR
SVAGAVEAFWNRVEAFEKREDAQFGREFIIALPVELSKEQNIALMRQFVLEQVLARGQVADWVYHDEPGN
PHVHLMTTLRPLTEDGFGPKRIPVIGEDGEVLRNKAGKIVYRLWSGEKTEFLEQRNGWLDLQNQHLALAG
LEIRVDGRSYAERGIDLVPTTHIGVGAKAIQRKSTREGEAVDLERLKLFEAQRTENRRRILLRPEIVLDL
LSSEKSVFDQRDIVKVLHRYVDDAGTFQQLMARILQSPELLRIERESVDFATGERLPARYTTRELIRVEA
GMARQAIWLSGRSSHGVRERVLEQVFARHERLSEEQRTAIEHVTKPGGIAAVVGRAGAGKTTMMKAAREA
WEVGGYRVVGAALAGKAAEGLEKEAGIQSRTLASWELRWKEGRDTLDSSTVLVLDEAGMIASKQMARFVE
AAVKAGAKLVLIGDPDQLQPIEAGAAFRAVVERIGYAELETIYRQREDWKRAASMDLARGRIAEALSAYQ
QQGRVLGSVLKAEAVASLIADWNRDYDPARSSLILAHLRRDVRMLNTMAREKLVERGLLSEGHAFRTEDG
VRRFDVGDQIVFLKNDSALGVKNGMIGKVVEAAPNRIVAAIGEGDQRRQVTVDQHVYRNLDHGYATTIHK
AQGATVDRVKVLASLSLDRHLTYVALTRHREDMALYYGRRSFAFNGGLAKVLSRRNAKETTLDYERGTLY
RQALRFAENRGLHIVNVARTLLRDRVDWTVRQKRKFADLAQRLRGIGARLGLFDPRQTHSPKEAAAMVAG
VTLFTKSIKDTVEEKLRANPAVTKQWDEVSTRFRYVFADPETAFRAMNFDAVLSDPTAAKTALDRLVSEP
QALGPLKGKTGLLAGKADREDRRVAELNVTALKRDIERYLNLREAAVQKLQADEQALRHRVSIDIPALSP
AAHRVLERVRDAIDRNDLPAALGYAISNREVKGEIDGFNKAIAERFGERTLLTNAAREPAGKIFDKAADG
LAPGERQKLAEAWPTMRTAQQLAAQERTAATLKQAETLRQSQRQTPVMKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-565)

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

(855-950)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(681-734)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   4490 GenBank   WP_244451511
Name   traG_K9D25_RS24475_ZM13|pD insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 69041.33 Da        Isoelectric Point: 9.7468

>WP_244451511.1 Ti-type conjugative transfer system protein TraG [Ancylobacter polymorphus]
MNRLLIAMIQVVVMVAVAIFTAGAEHWLAGFGKTEAARLMLGRAGLALPYVLSAGVGVILLFAAAGAIAI
RAVGWGVVTGSAAVIGIATIREGARLAALADRVPAGQYVLAYADPGTMIGAAIALVCAMFALRVAIRGNA
AFAAASPRRIKGRRAIHGETDWMRMETAGKLFGDAGGIVIGERYRVDRDSVAGIAFRADSRDSWGSGGRS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPSALKWGGGLVVLDPSSEVAPMVIGHRRKAGRKVVVLDPA
DAATGFNALDWIGRFGGTKEEDIVAVATWVMTDTARQASARDDFFRASAMQLLTALIADVCLSGHTEKKD
QTLRQVRANLSEPEPKLRERLTRIYEQSGSDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYAAL
ISGHSFTTDELADGGTDIFIALDLKVLEAHPGLARVIIGALMNAIYNRNGEVKDRTLFLLDEVARLGFLR
ILETARDAGRKYGITMTLLFQSIGQMREAYGGRDATSKWFESASWISFAAINDPETADYISRRCGDTTVE
VDQLSRSSQMSGASRTRSKQLARRPLILPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMRSCVGEN
RFHRKEAVR

  Protein domains


Predicted by InterproScan.

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

(161-635)

  Protein structure



No available structure.



ID   4491 GenBank   WP_244451470
Name   t4cp2_K9D25_RS24575_ZM13|pD insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91292.72 Da        Isoelectric Point: 5.9109

>WP_244451470.1 conjugal transfer protein TrbE [Ancylobacter polymorphus]
MVAIRSFRHSGPSFSDLVPYAAIVANGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
TGWMIQVEAVRVATSDYPAREECHFPDAVTRAIDDERRAHFQEGRGHFESRHALILTWRPPERRRSGLAR
YVYSDSESRAARYADTVLDNFLTSIREVEQYLGNVLSIRRMVTRSVEERGGFQTARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLATAEFSHGLTPMVDSRYLAVVGIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDDQEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDALAMVAETEDAIAQASSQLVAYGYYTPVIVL
FDDSEARLREKAEAVRRLVQAEGFGARIETINATEAFLGSLPGNWYANIREPLINTRNLADLIPLNSVWS
GEPTAPCPYYPPGSPPLMLVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYAQAQIFA
FDKGRSMLPLTLAAGGDHYEIGESDGAGAPTLAFCPLAELRTDGDRAWASEWIETLVALQGVTITPDHRN
AISRQIGLMASANGRSLSDFVSGVQMREIKEALHHYTVDGPMGQLLDAESDGLSLRSFQTFEIEQLMNMG
ERSLVPVLLYLFRRIEKRLTGAPSLIVLDEAWLMLGHPTFRDKIREWLKVLRKANCAVILATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPEGRRLFDMALGP
VALSFAGASGKEDLKQIAALKAEHGDGWPARWLQQRGIGDAEALLHQS

  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: 23981..50200

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
K9D25_RS24440 (K9D25_24440) 19516..19674 + 159 Protein_18 DUF736 family protein -
K9D25_RS24445 (K9D25_24445) 19743..19937 + 195 WP_244451506 hypothetical protein -
K9D25_RS24450 (K9D25_24450) 19989..20237 - 249 WP_244451507 WGR domain-containing protein -
K9D25_RS24455 (K9D25_24455) 20322..20795 - 474 WP_244451508 thermonuclease family protein -
K9D25_RS24460 (K9D25_24460) 21388..21750 + 363 WP_244451509 hypothetical protein -
K9D25_RS24465 (K9D25_24465) 22109..22612 + 504 WP_244451510 hypothetical protein -
K9D25_RS24470 (K9D25_24470) 22720..23892 - 1173 WP_244451526 DUF1173 domain-containing protein -
K9D25_RS24475 (K9D25_24475) 23981..25900 - 1920 WP_244451511 Ti-type conjugative transfer system protein TraG virb4
K9D25_RS24480 (K9D25_24480) 25893..26108 - 216 WP_244451512 type IV conjugative transfer system coupling protein TraD -
K9D25_RS24485 (K9D25_24485) 26113..26409 - 297 WP_244451513 conjugal transfer protein TraC -
K9D25_RS24490 (K9D25_24490) 26663..29965 + 3303 WP_244451514 Ti-type conjugative transfer relaxase TraA -
K9D25_RS24495 (K9D25_24495) 29962..30489 + 528 WP_244451515 conjugative transfer signal peptidase TraF -
K9D25_RS24500 (K9D25_24500) 30491..31645 + 1155 WP_244451516 conjugal transfer protein TraB -
K9D25_RS24505 (K9D25_24505) 31660..32265 + 606 WP_244451517 TraH family protein virB1
K9D25_RS24510 (K9D25_24510) 32463..34238 - 1776 WP_244451518 phospholipase D-like domain-containing protein -
K9D25_RS24515 (K9D25_24515) 34235..37780 - 3546 WP_244451519 AAA domain-containing protein -
K9D25_RS24520 (K9D25_24520) 37948..38592 - 645 WP_244451520 RES family NAD+ phosphorylase -
K9D25_RS24525 (K9D25_24525) 38589..39386 - 798 WP_244451521 hypothetical protein -
K9D25_RS24530 (K9D25_24530) 39512..39787 - 276 WP_244451522 hypothetical protein -
K9D25_RS24535 (K9D25_24535) 40164..40484 + 321 WP_244451523 transcriptional repressor TraM -
K9D25_RS24540 (K9D25_24540) 40676..41962 - 1287 WP_244451524 IncP-type conjugal transfer protein TrbI virB10
K9D25_RS24545 (K9D25_24545) 41975..42427 - 453 WP_244451466 conjugal transfer protein TrbH -
K9D25_RS24550 (K9D25_24550) 42431..43207 - 777 WP_244451527 P-type conjugative transfer protein TrbG virB9
K9D25_RS24555 (K9D25_24555) 43285..43944 - 660 WP_244451467 conjugal transfer protein TrbF virB8
K9D25_RS24560 (K9D25_24560) 43963..45150 - 1188 WP_244451468 P-type conjugative transfer protein TrbL virB6
K9D25_RS24565 (K9D25_24565) 45144..45344 - 201 WP_244451469 entry exclusion protein TrbK -
K9D25_RS24570 (K9D25_24570) 45341..46099 - 759 WP_244451528 P-type conjugative transfer protein TrbJ virB5
K9D25_RS24575 (K9D25_24575) 46113..48569 - 2457 WP_244451470 conjugal transfer protein TrbE virb4
K9D25_RS24580 (K9D25_24580) 48579..48878 - 300 WP_029349440 conjugal transfer protein TrbD virB3
K9D25_RS24585 (K9D25_24585) 48871..49242 - 372 WP_126280986 TrbC/VirB2 family protein virB2
K9D25_RS24590 (K9D25_24590) 49232..50200 - 969 WP_029349434 P-type conjugative transfer ATPase TrbB virB11
K9D25_RS24595 (K9D25_24595) 50216..50839 - 624 WP_244451529 acyl-homoserine-lactone synthase TraI -
K9D25_RS24600 (K9D25_24600) 51224..52441 + 1218 WP_244451471 plasmid partitioning protein RepA -
K9D25_RS24605 (K9D25_24605) 52441..53469 + 1029 WP_244451472 plasmid partitioning protein RepB -
K9D25_RS24610 (K9D25_24610) 53744..55093 + 1350 WP_244451473 plasmid replication protein RepC -

Host bacterium

ID   7187 GenBank   NZ_CP083243
Plasmid name   ZM13|pD Incompatibility group   -
Plasmid size   83314 bp Coordinate of oriT [Strand]   26553..26607 [-]
Host baterium   Ancylobacter polymorphus strain ZM13

Cargo genes

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