Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119228
Name   oriT_pWLK-101716 in_silico
Organism   Raoultella ornithinolytica strain WLK218
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP038275 (80271..80319 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pWLK-101716
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12167 GenBank   WP_137055834
Name   traI_E4K08_RS00300_pWLK-101716 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190598.14 Da        Isoelectric Point: 5.5946

>WP_137055834.1 conjugative transfer relaxase/helicase TraI [Raoultella ornithinolytica]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSETVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGGKWQSLGTDTVGKTGFIENVYANQIAFGKLYREVLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPAEKMVEWVNT
LKESGFDIHSYREDADKRAAEINRAPVSPAKTDGPDISDVVTKAIAGLSDRKVQFTYADMLARTVSQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASLTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIALQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDSVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQLRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQITPEQVPRKDGAWVPENSVVEFTPAQEETIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKTTRTLNPKADQAQQHVDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESSYVGLSRMKQHVQVYTDNREGWIRAINHSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKVGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVATESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1156)

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

(577-628)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1552)


  Protein structure



No available structure.




Auxiliary protein

ID   6949 GenBank   WP_020805752
Name   WP_020805752_pWLK-101716 insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   14249 GenBank   WP_032736842
Name   traD_E4K08_RS00305_pWLK-101716 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: 54833..77892

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
E4K08_RS00305 (E4K08_00305) 54833..57127 - 2295 WP_032736842 type IV conjugative transfer system coupling protein TraD virb4
E4K08_RS00310 (E4K08_00310) 57334..57861 - 528 WP_032736843 hypothetical protein -
E4K08_RS00315 (E4K08_00315) 57872..60715 - 2844 WP_076752118 conjugal transfer mating-pair stabilization protein TraG traG
E4K08_RS00320 (E4K08_00320) 60715..62085 - 1371 WP_032736846 conjugal transfer pilus assembly protein TraH traH
E4K08_RS00325 (E4K08_00325) 62072..62635 - 564 WP_224250969 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
E4K08_RS00330 (E4K08_00330) 62622..62858 - 237 WP_032736848 type-F conjugative transfer system pilin chaperone TraQ -
E4K08_RS00335 (E4K08_00335) 62869..63621 - 753 WP_042946285 type-F conjugative transfer system pilin assembly protein TraF traF
E4K08_RS00340 (E4K08_00340) 63642..63968 - 327 WP_032736851 hypothetical protein -
E4K08_RS00345 (E4K08_00345) 64015..64200 - 186 WP_032736852 hypothetical protein -
E4K08_RS00350 (E4K08_00350) 64197..64433 - 237 WP_076752122 conjugal transfer protein TrbE -
E4K08_RS00355 (E4K08_00355) 64423..65034 - 612 WP_032736855 hypothetical protein -
E4K08_RS00360 (E4K08_00360) 65148..67091 - 1944 WP_032736856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
E4K08_RS00365 (E4K08_00365) 67088..67714 - 627 WP_032736857 type-F conjugative transfer system pilin assembly protein TrbC trbC
E4K08_RS00370 (E4K08_00370) 67727..68686 - 960 WP_088912317 conjugal transfer pilus assembly protein TraU traU
E4K08_RS00375 (E4K08_00375) 68730..69356 - 627 WP_042946288 type-F conjugative transfer system protein TraW traW
E4K08_RS00380 (E4K08_00380) 69353..69742 - 390 WP_032736860 type-F conjugative transfer system protein TrbI -
E4K08_RS00385 (E4K08_00385) 69742..72381 - 2640 WP_137055835 type IV secretion system protein TraC virb4
E4K08_RS00390 (E4K08_00390) 72474..72857 - 384 WP_042946290 hypothetical protein -
E4K08_RS00395 (E4K08_00395) 72945..73244 - 300 WP_053390308 hypothetical protein -
E4K08_RS30855 73241..73642 - 402 WP_032736864 hypothetical protein -
E4K08_RS00405 (E4K08_00405) 73727..74005 - 279 WP_032736865 hypothetical protein -
E4K08_RS00410 (E4K08_00410) 74117..74686 - 570 WP_042946293 type IV conjugative transfer system lipoprotein TraV traV
E4K08_RS30525 74706..74867 - 162 WP_154235504 hypothetical protein -
E4K08_RS00415 (E4K08_00415) 74860..76280 - 1421 Protein_78 F-type conjugal transfer pilus assembly protein TraB -
E4K08_RS00420 (E4K08_00420) 76280..77014 - 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
E4K08_RS00425 (E4K08_00425) 77001..77567 - 567 WP_114499520 type IV conjugative transfer system protein TraE traE
E4K08_RS00430 (E4K08_00430) 77587..77892 - 306 WP_032736870 type IV conjugative transfer system protein TraL traL
E4K08_RS00435 (E4K08_00435) 77906..78274 - 369 WP_064343525 type IV conjugative transfer system pilin TraA -
E4K08_RS30860 78629..79330 - 702 WP_223174962 hypothetical protein -
E4K08_RS00450 (E4K08_00450) 79568..79960 - 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
E4K08_RS00455 (E4K08_00455) 80464..80886 + 423 WP_020315406 transglycosylase SLT domain-containing protein -
E4K08_RS00460 (E4K08_00460) 80909..81451 - 543 WP_020314754 antirestriction protein -
E4K08_RS30865 (E4K08_00465) 82100..82219 - 120 Protein_87 SAM-dependent DNA methyltransferase -
E4K08_RS00470 (E4K08_00470) 82304..82534 - 231 WP_020314756 hypothetical protein -

Host bacterium

ID   19658 GenBank   NZ_CP038275
Plasmid name   pWLK-101716 Incompatibility group   IncFIA
Plasmid size   101716 bp Coordinate of oriT [Strand]   80271..80319 [+]
Host baterium   Raoultella ornithinolytica strain WLK218

Cargo genes

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