Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117988
Name   oriT_p2_M47_H.defensa in_silico
Organism   Candidatus Hamiltonella defensa strain MI47
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022934 (8104..8182 [-], 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_p2_M47_H.defensa
GGACAAGATATGTTTTGAAGCACCGCTTGCAAGCAAGCGGCCCTTCAAAACTCTTGGTCAGGGCTTCGCCCCGACACCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11410 GenBank   WP_095034927
Name   traI_CJJ18_RS10970_p2_M47_H.defensa 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   13334 GenBank   WP_164703738
Name   t4cp2_CJJ18_RS12110_p2_M47_H.defensa insolico UniProt ID   _
Length   474 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 474 a.a.        Molecular weight: 53562.54 Da        Isoelectric Point: 6.4249

>WP_164703738.1 type IV secretory system conjugative DNA transfer family protein [Candidatus Hamiltonella defensa]
MARELWLNLDDALRHIQLIATTGAGKTEAILSVYLNALCWGRGMCLSDGKAENRLAFAVWSLARRFGRED
DVYILNFLTAGNSKFSDLMKDNKSRPQSNSINLFANASETFIIQLMDSLLPKVGSNETGWQEKAKAMIAA
LIYALCYKREKDGLFLSQRVIQDYLPLRKIVTLYQEAKKNHWHEEGYKPLEHYLNTLAGFDMALIDSPLE
WSKTVWEQHGFLIQQFTRMLSLFNDIYGHVFPQGAGDIDLKDVLHNDRILVVLIPALELSNPEAVTLGKL
YISGLRMTLSQDLGGQLEGKREDVLLSQKFAQKFPYPIIFDELGAYFASGLDKMAAQMRSLQYMLMIAAQ
DVQSMMDKSMREFFTVSANQRTKWFMALEDAQDTFNLIRSAAGKGYYSELSSVKRKGSLSGSRYEDADTH
HIRERDNIELTELKALNKGEGVIVFQDAVVRSAAIFIPDEEKLSSKLPCGLTGL

  Protein domains


Predicted by InterproScan.

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

(3-155)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 26701..54945

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CJJ18_RS11070 (CJJ18_11070) 21950..22546 + 597 WP_234811177 toxin co-regulated pilus biosynthesis Q family protein -
CJJ18_RS11075 (CJJ18_11075) 22524..24224 + 1701 WP_095034941 PilN family type IVB pilus formation outer membrane protein -
CJJ18_RS11080 (CJJ18_11080) 24236..24574 - 339 WP_095034942 helix-turn-helix domain-containing protein -
CJJ18_RS11085 (CJJ18_11085) 24555..24934 - 380 Protein_30 type II toxin-antitoxin system RelE/ParE family toxin -
CJJ18_RS13560 24998..25732 + 735 WP_268807596 type 4b pilus protein PilO2 -
CJJ18_RS13565 25663..26307 + 645 WP_268807597 type 4b pilus protein PilO2 -
CJJ18_RS11095 (CJJ18_11095) 26294..26704 + 411 WP_095034943 type IV pilus biogenesis protein PilP -
CJJ18_RS11100 (CJJ18_11100) 26701..28248 + 1548 WP_095034944 GspE/PulE family protein virB11
CJJ18_RS11105 (CJJ18_11105) 28235..29275 + 1041 WP_234813674 type II secretion system F family protein -
CJJ18_RS11110 (CJJ18_11110) 29310..29819 + 510 WP_095034945 type 4 pilus major pilin -
CJJ18_RS11115 (CJJ18_11115) 30072..31307 + 1236 WP_095034946 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
CJJ18_RS11120 (CJJ18_11120) 31346..31777 + 432 WP_095034947 type IV pilus biogenesis protein PilM -
CJJ18_RS13275 32012..32401 + 390 WP_234813502 prepilin peptidase -
CJJ18_RS11130 (CJJ18_11130) 32444..32914 + 471 WP_095034948 lytic transglycosylase domain-containing protein virB1
CJJ18_RS11135 (CJJ18_11135) 32968..33411 + 444 WP_095034949 DotD/TraH family lipoprotein -
CJJ18_RS11140 (CJJ18_11140) 33408..34216 + 809 Protein_42 type IV secretion system DotC family protein -
CJJ18_RS11145 (CJJ18_11145) 34203..35368 + 1166 Protein_43 plasmid transfer ATPase TraJ -
CJJ18_RS11150 (CJJ18_11150) 35430..35690 + 261 WP_015873087 IcmT/TraK family protein traK
CJJ18_RS11155 (CJJ18_11155) 35705..37993 + 2289 WP_095034950 LPD7 domain-containing protein -
CJJ18_RS11160 (CJJ18_11160) 37990..38346 + 357 WP_123875548 hypothetical protein -
CJJ18_RS11165 (CJJ18_11165) 38444..38875 + 432 WP_095034952 conjugal transfer protein TraL traL
CJJ18_RS13280 38900..39127 + 228 WP_234813663 hypothetical protein traM
CJJ18_RS11170 (CJJ18_11170) 39124..39570 + 447 WP_234813664 DotI/IcmL/TraM family protein traM
CJJ18_RS13285 39609..39929 + 321 WP_164703737 hypothetical protein -
CJJ18_RS11175 (CJJ18_11175) 39917..40573 + 657 WP_234813632 DotH/IcmK family type IV secretion protein traN
CJJ18_RS11180 (CJJ18_11180) 40577..41596 + 1020 WP_234813665 conjugal transfer protein TraO traO
CJJ18_RS11185 (CJJ18_11185) 41891..42496 + 606 WP_095034953 conjugal transfer protein TraP traP
CJJ18_RS11190 (CJJ18_11190) 42510..43049 + 540 WP_095034954 conjugal transfer protein TraQ traQ
CJJ18_RS11195 (CJJ18_11195) 43107..43502 + 396 WP_095034955 DUF6750 family protein traR
CJJ18_RS11200 (CJJ18_11200) 43532..44038 + 507 WP_095034956 TraT conjugal transfer protein traT
CJJ18_RS11205 (CJJ18_11205) 44232..47287 + 3056 Protein_57 ATP-binding protein -
CJJ18_RS11210 (CJJ18_11210) 47348..48529 + 1182 WP_234813666 conjugal transfer protein TraW traW
CJJ18_RS13290 (CJJ18_11215) 48526..48876 + 351 WP_095034957 hypothetical protein -
CJJ18_RS11225 (CJJ18_11225) 49157..51304 + 2148 WP_095034959 DotA/TraY family protein traY
CJJ18_RS11230 (CJJ18_11230) 51379..52017 + 639 WP_095034960 plasmid IncI1-type surface exclusion protein ExcA -
CJJ18_RS11235 (CJJ18_11235) 52062..52367 - 306 WP_095034961 type II toxin-antitoxin system RelE/ParE family toxin -
CJJ18_RS11240 (CJJ18_11240) 52354..52647 - 294 WP_095034962 CopG family ribbon-helix-helix protein -
CJJ18_RS11245 (CJJ18_11245) 52826..53935 + 1110 WP_095034963 conjugal transfer protein TrbA trbA
CJJ18_RS13295 54011..54436 + 426 WP_234813667 hypothetical protein trbB
CJJ18_RS13300 54436..54945 + 510 WP_234813668 DsbC family protein trbB
CJJ18_RS12110 55315..56739 + 1425 WP_164703738 type IV secretory system conjugative DNA transfer family protein -
CJJ18_RS12115 56877..57083 + 207 WP_123875551 hypothetical protein -
CJJ18_RS11265 (CJJ18_11265) 57170..57370 - 201 WP_095034965 hypothetical protein -

Host bacterium

ID   18421 GenBank   NZ_CP022934
Plasmid name   p2_M47_H.defensa Incompatibility group   -
Plasmid size   57469 bp Coordinate of oriT [Strand]   8104..8182 [-]
Host baterium   Candidatus Hamiltonella defensa strain MI47

Cargo genes

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