Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119369
Name   oriT_p602815-NR in_silico
Organism   Raoultella ornithinolytica strain 170602815
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN310380 (144144..144193 [+], 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_p602815-NR
AAATCTGCAAAATATTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12251 GenBank   WP_047727551
Name   traI_H5E28_RS00655_p602815-NR insolico UniProt ID   A0A443VHM8
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190459.15 Da        Isoelectric Point: 5.7342

>WP_047727551.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSETVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGGKWQSLGTDTVGKTGFIENVYANQIAFGKLYREVLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPAEKMVEWVNT
LKESGFDIHSYREDADKRAAEINRAPVSPAKTDGPDISDVVTKAIAGLSDRKVQFTYADMLARTVSQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRHAPF
SDAVSVLAQDRPAMGIVYGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLVGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETLSLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGNQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGVREQGVLNGIIREVLKNEGTLGAKEM
TVTTLTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFLIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVASGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQTLAVGAGPFDGIK
VGHGWVESPGRSVSETATVFASLTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIALQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDSVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQLRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQITPEQVPRKDGAWVPENSVVEFTPAQEETIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKTTRTLNPKADQAQQHVDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESSYVGLSRMKQHVQLYTDNREGWIKAINHSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEALRREMERQTEQATREVSGEEKKVGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVATESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1552)


  Protein structure



No available structure.




T4CP

ID   14368 GenBank   WP_032736842
Name   traD_H5E28_RS00660_p602815-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: 128704..144745

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5E28_RS00660 128704..130998 - 2295 WP_032736842 type IV conjugative transfer system coupling protein TraD virb4
H5E28_RS00665 131205..131732 - 528 WP_032736843 hypothetical protein -
H5E28_RS00670 131743..134586 - 2844 WP_047727552 conjugal transfer mating-pair stabilization protein TraG traG
H5E28_RS00675 134586..135956 - 1371 WP_032736846 conjugal transfer pilus assembly protein TraH traH
H5E28_RS00680 135943..136506 - 564 WP_224250969 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
H5E28_RS00685 136493..136624 - 132 Protein_143 conjugal transfer protein TraQ -
H5E28_RS00915 136614..136733 - 120 Protein_144 hypothetical protein -
H5E28_RS00690 136820..137119 - 300 WP_032736863 hypothetical protein -
H5E28_RS00920 137116..137517 - 402 WP_032736864 hypothetical protein -
H5E28_RS00700 137602..137880 - 279 WP_032736865 hypothetical protein -
H5E28_RS00705 137992..138561 - 570 WP_042946293 type IV conjugative transfer system lipoprotein TraV traV
H5E28_RS00710 138735..140156 - 1422 WP_032736866 F-type conjugal transfer pilus assembly protein TraB traB
H5E28_RS00715 140156..140890 - 735 WP_032736867 type-F conjugative transfer system secretin TraK traK
H5E28_RS00720 140877..141443 - 567 WP_032736869 type IV conjugative transfer system protein TraE traE
H5E28_RS00725 141463..141768 - 306 WP_032736870 type IV conjugative transfer system protein TraL traL
H5E28_RS00730 141782..142150 - 369 WP_032736871 type IV conjugative transfer system pilin TraA -
H5E28_RS00735 142219..142419 - 201 WP_060415469 TraY domain-containing protein -
H5E28_RS00740 142504..143196 - 693 WP_181717165 hypothetical protein -
H5E28_RS00745 143444..143836 - 393 WP_032736874 conjugal transfer relaxosome DNA-binding protein TraM -
H5E28_RS00750 144338..144745 + 408 WP_080346868 transglycosylase SLT domain-containing protein virB1
H5E28_RS00755 144785..145315 - 531 WP_047727555 antirestriction protein -
H5E28_RS00760 145939..146772 - 834 WP_009651958 N-6 DNA methylase -
H5E28_RS00765 146822..146968 - 147 WP_047727556 hypothetical protein -
H5E28_RS00770 147062..147409 - 348 WP_009651960 hypothetical protein -
H5E28_RS00775 147462..147785 - 324 WP_009651959 hypothetical protein -
H5E28_RS00780 147806..147964 - 159 WP_223240703 hypothetical protein -
H5E28_RS00785 148636..148755 - 120 WP_223156217 type I toxin-antitoxin system Hok family toxin -
H5E28_RS00925 148700..148852 - 153 WP_269567326 DUF5431 family protein -
H5E28_RS00790 149011..149337 - 327 WP_038992719 hypothetical protein -

Host bacterium

ID   19799 GenBank   NZ_MN310380
Plasmid name   p602815-NR Incompatibility group   IncFIB
Plasmid size   164851 bp Coordinate of oriT [Strand]   144144..144193 [+]
Host baterium   Raoultella ornithinolytica strain 170602815

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE, silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, pbrA, merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -