Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117931
Name   oriT_pHNNC189-2 in_silico
Organism   Raoultella ornithinolytica strain NC189
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN175502 (134099..134148 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..13, 18..24  (GCAAAAT..ATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pHNNC189-2
AAATCTGCAAAATATTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11385 GenBank   WP_076752116
Name   traI_JYH36_RS00540_pHNNC189-2 insolico UniProt ID   A0A9Q9JMY5
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190488.11 Da        Isoelectric Point: 5.7342

>WP_076752116.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSETVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGGKWQSLGTDTVGKTGFIENVYANQIAFGKLYREVLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPAEKMVEWVNT
LKESGFDIHSYREDADKRAAEINRAPVSPAKTDGPDISDVVTKAIAGLSDRKVQFTYADMLARTVSQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRHAPF
SDAVSVLAQDRPAMGIVYGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLVGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETLSLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGNQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGVREQGVLNGIIREVLKNEGTLGAKEM
TVTTLTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFLIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVASGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQTLAVGAGPFDGIK
VGHGWVESPGRSVSETATVFASLTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIALQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDSVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQLRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQITPEQVPRKDGAWVPENSVVEFTPAQEETIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKTTRTLNPKADQAQQHVDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESSYVGLSRMKQHVQVYTDNREGWIRAINHSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKVGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVATESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(634-713)

DNA helicase TraI (TraI_C)

(1432-1552)

AAA domain (AAA_30)

(970-1156)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(576-628)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4CP

ID   13299 GenBank   WP_032736842
Name   traD_JYH36_RS00545_pHNNC189-2 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 85398.61 Da        Isoelectric Point: 5.0675

>WP_032736842.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTICVVTFFVASWVLGRQGKL
QSEDENTGGRQLSDKPKDVARQMKRDGAASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMRGDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYNPRPKIAEGFIQRRLDTRIDERLSAQLEAREAEGSLVRALFTPDEPVSEPAEEKAGVQPEQTKPAKDS
VLPVPVKTSSMAAEGAGKTPAVPLSGAPVTRVKTVPLIRPKPAASVTGTAAAASTAAVSATAGGTEQELA
QQPVEADQDMLPAGMNEDGVIEDMQAYDAWLEGEQIQRDMQRREEVNINHSRSEQDDIEIGGNF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 108663..131723

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JYH36_RS00545 108663..110957 - 2295 WP_032736842 type IV conjugative transfer system coupling protein TraD virb4
JYH36_RS00550 111164..111691 - 528 WP_032736843 hypothetical protein -
JYH36_RS00555 111702..114545 - 2844 WP_076752118 conjugal transfer mating-pair stabilization protein TraG traG
JYH36_RS00560 114545..115915 - 1371 WP_032736846 conjugal transfer pilus assembly protein TraH traH
JYH36_RS00565 115902..116465 - 564 WP_224250969 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JYH36_RS00570 116452..116688 - 237 WP_032736848 type-F conjugative transfer system pilin chaperone TraQ -
JYH36_RS00575 116699..117451 - 753 WP_042946285 type-F conjugative transfer system pilin assembly protein TraF traF
JYH36_RS00580 117472..117798 - 327 WP_032736851 hypothetical protein -
JYH36_RS00585 117845..118030 - 186 WP_032736852 hypothetical protein -
JYH36_RS00590 118027..118263 - 237 WP_076752122 conjugal transfer protein TrbE -
JYH36_RS00595 118253..118765 - 513 WP_204884858 hypothetical protein -
JYH36_RS00600 118978..120921 - 1944 WP_032736856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JYH36_RS00605 120918..121544 - 627 WP_032736857 type-F conjugative transfer system pilin assembly protein TrbC trbC
JYH36_RS00610 121557..122516 - 960 WP_088912317 conjugal transfer pilus assembly protein TraU traU
JYH36_RS00615 122560..123186 - 627 WP_042946288 type-F conjugative transfer system protein TraW traW
JYH36_RS00620 123183..123572 - 390 WP_032736860 type-F conjugative transfer system protein TrbI -
JYH36_RS00625 123572..126211 - 2640 WP_032736861 type IV secretion system protein TraC virb4
JYH36_RS00630 126304..126687 - 384 WP_042946290 hypothetical protein -
JYH36_RS00635 126775..127074 - 300 WP_032736863 hypothetical protein -
JYH36_RS01040 127071..127472 - 402 WP_032736864 hypothetical protein -
JYH36_RS00645 127557..127835 - 279 WP_032736865 hypothetical protein -
JYH36_RS00650 127947..128516 - 570 WP_042946293 type IV conjugative transfer system lipoprotein TraV traV
JYH36_RS00655 128690..130111 - 1422 WP_204884859 F-type conjugal transfer pilus assembly protein TraB traB
JYH36_RS00660 130111..130845 - 735 WP_032736867 type-F conjugative transfer system secretin TraK traK
JYH36_RS00665 130832..131398 - 567 WP_032736869 type IV conjugative transfer system protein TraE traE
JYH36_RS00670 131418..131723 - 306 WP_032736870 type IV conjugative transfer system protein TraL traL
JYH36_RS00675 131737..132105 - 369 WP_032736871 type IV conjugative transfer system pilin TraA -
JYH36_RS00680 132174..132374 - 201 WP_060415469 TraY domain-containing protein -
JYH36_RS00685 132459..133151 - 693 WP_181717165 hypothetical protein -
JYH36_RS00690 133399..133791 - 393 WP_032736874 conjugal transfer relaxosome DNA-binding protein TraM -
JYH36_RS00695 134223..134699 + 477 WP_076752132 transglycosylase SLT domain-containing protein -
JYH36_RS00700 134737..135267 - 531 WP_076752134 antirestriction protein -
JYH36_RS00705 135459..135689 + 231 WP_076752135 hypothetical protein -

Host bacterium

ID   18364 GenBank   NZ_MN175502
Plasmid name   pHNNC189-2 Incompatibility group   IncFIB
Plasmid size   196122 bp Coordinate of oriT [Strand]   134099..134148 [+]
Host baterium   Raoultella ornithinolytica strain NC189

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7