Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117993
Name   oriT_p5D_Hdefensa-2 in_silico
Organism   Candidatus Hamiltonella defensa strain 5D
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021665 (8103..8181 [-], 79 nt)
oriT length   79 nt
IRs (inverted repeats)      23..30, 33..40  (CCGCTTGC..GCAAGCGG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 79 nt

>oriT_p5D_Hdefensa-2
GGACAAGATATGTTTTGAAGCACCGCTTGCAAGCAAGCGGCCCTTCAAAACTCTTGGTCAGGGCTTCGCCCCGACACCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11414 GenBank   WP_095034927
Name   traI_CCS40_RS10760_p5D_Hdefensa-2 insolico UniProt ID   _
Length   627 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 627 a.a.        Molecular weight: 72459.28 Da        Isoelectric Point: 9.0352

>WP_095034927.1 TraI/MobA(P) family conjugative relaxase [Candidatus Hamiltonella defensa]
MIVGKAKKRRDGKSSFLTLLAYTTTRDDHHHDDVIDPETQKARLSQSKEAIFERLMGYIHRHGDADKSLI
TERFPDGRHQVLFDQVLCETNTLSVATAAVEMQAVALKNTRCKDPVYHFFLSWPETDSPTVEQIFESARH
SLKALGMSDHQYVTAIHRDTDHLHCHVAANRIHPVTYKVADDAYDISKLHKASREMELKYGWTRTNGCHV
INENNRIVRSCSKEKSMPDDAKKLEYYSDQESLYGYAVRECRSEISEILKADSIYWERIHAVLIRAGLEL
KKKGAGLAIYHRAHPEQTPLKASRLHPDLTLSHLEPRAGPFESSPKVDTYDKDRLVFGYVIEKSYDRRLH
ARDHSARHERRLARAEAREELKLRYQHDKKEAKCPSFDAKNRFRTLSMTFRFRRAHVCVAVRDPLMRKLA
WHVLAFEREKAMAQLRLQLKQERAHWHRAPENRRLSYRLWVEQQALKGDKAAISQLRGWAYQAKRDERTA
YLSDTVIECAVSDDIAPVELKGYTHHIHRDGAILYKKEGVTQMIDRGETIEMARPFENEGDNMVAGLRLA
EQKSGEKRVFSGPREYVEKACSLVRDLNEMGETSLTLTDSLQQKRVCEMRPQDKPAPISFDSPNLTP

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(512-608)

Relaxase/Mobilisation nuclease domain (Relaxase)

(89-318)


  Protein structure



No available structure.




T4CP

ID   13339 GenBank   WP_187356329
Name   trbC_CCS40_RS11040_p5D_Hdefensa-2 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: 73110.36 Da        Isoelectric Point: 7.4673

>WP_187356329.1 F-type conjugative transfer protein TrbC [Candidatus Hamiltonella defensa]
MIALVLGCLWPVTLLIGLPACVILLIIFCDRPFRMPIRLPTDIGGPDLTTEREGFKARKGWSGLFSFITR
TRHCEQAAGILCLGYARGKSLARELWLNLDDALRHIQLIATTGAGKTEAILSVYLNALCWGRGMCLSDGK
AENRLAFAVWSLARRFGREDDVYILNFLTAGNSKFSDLMKDNKSRPQSNSINLFANASETFIIQLMDSLL
PKVGSNETGWQEKAKAMIAALIYALCYKREKDGLFLSQRVIQDYLPLRKIVTLYQEAKKNHWHEEGYKPL
EHYLNTLAGFDMALIDSPLEWSKTVWEQHGFLIQQFTRMLSLFNDIYGHVFPQGAGDIDLKDVLHNDRIL
VVLIPALELSNPEAVTLGKLYISGLRMTLSQDLGGQLEGKREDVLLSQKFAQKFPYPIIFDELGAYFASG
LDKMAAQMRSLQYMLMIAAQDVQSMMDKSMREFFTVSANQRTKWFMALEDAQDTFNLIRSAAGKGYYSEL
SSVKRKGSLSGSRYEDADTHHIRERDNIELTELKALNKGEGVIVFQDAVVRSAAIFIPDEEKLSSKLPLR
INRFIELKRPDFDALCEVVPELRHKGAAFKQEVQGILQRLKTADTQENKGTLNVRLFDKTLHHLCEITQN
LDHRNDLSYTPRSEE

  Protein domains


Predicted by InterproScan.

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

(92-244)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 27295..54943

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CCS40_RS10860 (CCS40_10900) 22517..24217 + 1701 WP_095034941 PilN family type IVB pilus formation outer membrane protein -
CCS40_RS10865 (CCS40_10905) 24229..24567 - 339 WP_095034942 helix-turn-helix domain-containing protein -
CCS40_RS10870 (CCS40_10910) 24548..24928 - 381 WP_148121498 type II toxin-antitoxin system RelE/ParE family toxin -
CCS40_RS10875 (CCS40_10915) 24992..26302 + 1311 WP_148121499 type 4b pilus protein PilO2 -
CCS40_RS10880 (CCS40_10920) 26289..26699 + 411 WP_095034943 type IV pilus biogenesis protein PilP -
CCS40_RS12690 26696..27298 + 603 WP_235655681 hypothetical protein -
CCS40_RS12695 27295..27888 + 594 WP_235655682 ATPase, T2SS/T4P/T4SS family virB11
CCS40_RS12700 27963..28241 + 279 WP_235655683 hypothetical protein -
CCS40_RS12705 28228..28782 + 555 WP_235655684 type II secretion system F family protein -
CCS40_RS12710 28776..29291 + 516 WP_235655676 type II secretion system F family protein -
CCS40_RS10895 (CCS40_10935) 29303..29812 + 510 WP_095034945 type 4 pilus major pilin -
CCS40_RS10900 (CCS40_10940) 30065..31300 + 1236 WP_095034946 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
CCS40_RS10905 (CCS40_10945) 31339..31770 + 432 WP_095034947 type IV pilus biogenesis protein PilM -
CCS40_RS12715 31776..32063 + 288 WP_235655677 hypothetical protein -
CCS40_RS12720 32006..32395 + 390 WP_234813502 prepilin peptidase -
CCS40_RS10915 (CCS40_10955) 32438..32908 + 471 WP_095034948 lytic transglycosylase domain-containing protein virB1
CCS40_RS10920 (CCS40_10960) 32962..33405 + 444 WP_095034949 DotD/TraH family lipoprotein -
CCS40_RS10925 (CCS40_10965) 33402..34210 + 809 Protein_47 type IV secretion system DotC family protein -
CCS40_RS10930 (CCS40_10970) 34197..35363 + 1167 WP_148121500 plasmid transfer ATPase TraJ virB11
CCS40_RS10935 (CCS40_10975) 35425..35685 + 261 WP_015873087 IcmT/TraK family protein traK
CCS40_RS10940 (CCS40_10980) 35700..37013 + 1314 WP_148121501 DUF5710 domain-containing protein -
CCS40_RS10945 (CCS40_10985) 37022..37795 + 774 WP_148121502 LPD7 domain-containing protein -
CCS40_RS10950 (CCS40_10990) 37795..38340 + 546 WP_148121503 hypothetical protein -
CCS40_RS10955 (CCS40_10995) 38437..38868 + 432 WP_095034952 conjugal transfer protein TraL traL
CCS40_RS12725 38893..39120 + 228 WP_234813663 hypothetical protein traM
CCS40_RS10960 (CCS40_11000) 39117..39563 + 447 WP_234813664 DotI/IcmL/TraM family protein traM
CCS40_RS10965 (CCS40_11005) 39602..40567 + 966 WP_234811143 DotH/IcmK family type IV secretion protein traN
CCS40_RS10970 (CCS40_11010) 40571..41590 + 1020 WP_234813665 conjugal transfer protein TraO traO
CCS40_RS12975 41611..41742 + 132 WP_268877281 hypothetical protein traO
CCS40_RS10975 (CCS40_11015) 41885..42490 + 606 WP_095034953 conjugal transfer protein TraP traP
CCS40_RS10980 (CCS40_11020) 42504..43043 + 540 WP_095034954 conjugal transfer protein TraQ traQ
CCS40_RS10985 (CCS40_11025) 43101..43496 + 396 WP_095034955 DUF6750 family protein traR
CCS40_RS10990 (CCS40_11030) 43526..44128 + 603 WP_148121504 TraT conjugal transfer protein traT
CCS40_RS10995 (CCS40_11035) 44227..47297 + 3071 Protein_63 ATP-binding protein -
CCS40_RS11000 (CCS40_11040) 47342..48523 + 1182 WP_234813666 conjugal transfer protein TraW traW
CCS40_RS11005 (CCS40_11045) 48520..49068 + 549 WP_148121505 conjugal transfer protein TraX -
CCS40_RS11010 (CCS40_11050) 49153..51300 + 2148 WP_095034959 DotA/TraY family protein traY
CCS40_RS11015 (CCS40_11055) 51375..52013 + 639 WP_095034960 plasmid IncI1-type surface exclusion protein ExcA -
CCS40_RS11020 (CCS40_11060) 52058..52363 - 306 WP_095034961 type II toxin-antitoxin system RelE/ParE family toxin -
CCS40_RS11025 (CCS40_11065) 52350..52643 - 294 WP_095034962 CopG family ribbon-helix-helix protein -
CCS40_RS11030 (CCS40_11070) 52822..53931 + 1110 WP_095034963 conjugal transfer protein TrbA trbA
CCS40_RS11035 (CCS40_11075) 54008..54943 + 936 WP_148121506 DsbC family protein trbB
CCS40_RS11040 55043..56980 + 1938 WP_187356329 F-type conjugative transfer protein TrbC -
CCS40_RS11050 (CCS40_11090) 57168..57368 - 201 WP_095034965 hypothetical protein -

Host bacterium

ID   18426 GenBank   NZ_CP021665
Plasmid name   p5D_Hdefensa-2 Incompatibility group   -
Plasmid size   57467 bp Coordinate of oriT [Strand]   8103..8181 [-]
Host baterium   Candidatus Hamiltonella defensa strain 5D

Cargo genes

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