Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117709
Name   oriT_p117885-NR in_silico
Organism   Raoultella ornithinolytica strain 172117885
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT074086 (34448..34497 [-], 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_p117885-NR
AAATCTGCAAAATATTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11264 GenBank   WP_076752116
Name   traI_I0Q10_RS00375_p117885-NR 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   13151 GenBank   WP_032736842
Name   traD_I0Q10_RS00370_p117885-NR 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: 36873..59933

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I0Q10_RS00205 32907..33137 - 231 WP_076752135 hypothetical protein -
I0Q10_RS00210 33329..33859 + 531 WP_076752134 antirestriction protein -
I0Q10_RS00215 33897..34373 - 477 WP_076752132 transglycosylase SLT domain-containing protein -
I0Q10_RS00220 34805..35197 + 393 WP_032736874 conjugal transfer relaxosome DNA-binding protein TraM -
I0Q10_RS00225 35445..36137 + 693 WP_181717165 hypothetical protein -
I0Q10_RS00230 36222..36422 + 201 WP_060415469 TraY domain-containing protein -
I0Q10_RS00235 36491..36859 + 369 WP_032736871 type IV conjugative transfer system pilin TraA -
I0Q10_RS00240 36873..37178 + 306 WP_032736870 type IV conjugative transfer system protein TraL traL
I0Q10_RS00245 37198..37764 + 567 WP_032736869 type IV conjugative transfer system protein TraE traE
I0Q10_RS00250 37751..38485 + 735 WP_032736867 type-F conjugative transfer system secretin TraK traK
I0Q10_RS00255 38485..39906 + 1422 WP_032736866 F-type conjugal transfer pilus assembly protein TraB traB
I0Q10_RS00260 39899..40060 + 162 WP_154235504 hypothetical protein -
I0Q10_RS00265 40080..40649 + 570 WP_042946293 type IV conjugative transfer system lipoprotein TraV traV
I0Q10_RS00270 40761..41039 + 279 WP_032736865 hypothetical protein -
I0Q10_RS00990 41124..41525 + 402 WP_032736864 hypothetical protein -
I0Q10_RS00280 41522..41821 + 300 WP_032736863 hypothetical protein -
I0Q10_RS00285 41909..42292 + 384 WP_042946290 hypothetical protein -
I0Q10_RS00290 42385..45024 + 2640 WP_032736861 type IV secretion system protein TraC virb4
I0Q10_RS00295 45024..45413 + 390 WP_032736860 type-F conjugative transfer system protein TrbI -
I0Q10_RS00300 45410..46036 + 627 WP_042946288 type-F conjugative transfer system protein TraW traW
I0Q10_RS00305 46080..47039 + 960 WP_088912317 conjugal transfer pilus assembly protein TraU traU
I0Q10_RS00310 47052..47678 + 627 WP_032736857 type-F conjugative transfer system pilin assembly protein TrbC trbC
I0Q10_RS00315 47675..49618 + 1944 WP_032736856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
I0Q10_RS00320 49780..50343 + 564 WP_195156997 hypothetical protein -
I0Q10_RS00325 50333..50569 + 237 WP_076752122 conjugal transfer protein TrbE -
I0Q10_RS00330 50566..50751 + 186 WP_032736852 hypothetical protein -
I0Q10_RS00335 50798..51124 + 327 WP_032736851 hypothetical protein -
I0Q10_RS00340 51145..51897 + 753 WP_042946285 type-F conjugative transfer system pilin assembly protein TraF traF
I0Q10_RS00345 51908..52144 + 237 WP_032736848 type-F conjugative transfer system pilin chaperone TraQ -
I0Q10_RS00350 52131..52694 + 564 WP_224250969 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
I0Q10_RS00355 52681..54051 + 1371 WP_076752120 conjugal transfer pilus assembly protein TraH traH
I0Q10_RS00360 54051..56894 + 2844 WP_076752118 conjugal transfer mating-pair stabilization protein TraG traG
I0Q10_RS00365 56905..57432 + 528 WP_032736843 hypothetical protein -
I0Q10_RS00370 57639..59933 + 2295 WP_032736842 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18142 GenBank   NZ_MT074086
Plasmid name   p117885-NR Incompatibility group   IncFII
Plasmid size   184801 bp Coordinate of oriT [Strand]   34448..34497 [-]
Host baterium   Raoultella ornithinolytica strain 172117885

Cargo genes

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