Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104418
Name   oriT_pRHBSTW-00123_3 in_silico
Organism   Enterobacter roggenkampii strain RHBSTW-00123
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055399 (87489..87537 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pRHBSTW-00123_3
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3218 GenBank   WP_023332871
Name   traI_HV081_RS23665_pRHBSTW-00123_3 insolico UniProt ID   _
Length   1751 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1751 a.a.        Molecular weight: 191031.21 Da        Isoelectric Point: 6.0768

>WP_023332871.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGKAGDYYTKEDNYYVIGSMDERWQGKGAEALGLEGKTVDKALFTELLKGKLPDGSDLSRI
QDGMNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIEAHNQAVTEAIRQVETLAATRVMVDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQIAFGKIYREVLKPLVE
GLGYETEVVGKHGMWEMKDVPVEPFSTRTQEINAAAGPDASLKSRDVATLDTRKAKETLDPAQKVTEWLS
TLKETGFNLKEYREAADQRAKTQREVPSPEAPAGPNVDDIVTQAISGLSDRKVQFTYTELLARTVSQMEA
RPGVIETARAGIEAAIGREQLIPLDREKGIFTSGIHVLDELSVRALSQEVLRQNHVSMVPEKATARQTSF
SDAVTVLAQDRPAIGIVSGQGGAAGQRERVTEMAMMAREQGRDVHIIAADNRSLEFLLKEEKLAGEIITG
KSALQDGTAFVPGGTLIIDQAEKLSLKETINLLDGAMRNNVQILMSDSGKRSGTGSALTVMKESGVTAYK
WQGGKQTTASVISEPDRNQRFTRMASDFVASVRDGQESVVQIRGPREQGILTGLIRENLRNEGLIGSHEE
TITALTPVWLDSKNRGIRDNYREGMVMERWDPEKRIHDRFIIDRVTAVSNTLTLKDEKGESLNLKVSAVD
NTWTLFRPQQLPVAEGERLAILGKIPETRLKGGDTVQVLKAENGVLTVQHPGQKTTQKLAAGNTPFTGIK
VGHGWVENPGRSVSETATVFASLSQRELDNATLNALAQSGSQVRLYSAQNEQKTVEKLGRHTAFSVVTEQ
LKTRAGEQDISAAIAHQKSQLHTPAEQAIHLAVPSLESDKLTFTRPQLLVAAHEFSDGTVPFSDIEKTIG
EQIKSGDLLHVPVAAGHGNDLLISRQTWDAEKSLLTMVLEGKNAVTPLMAKVPGSLMEGLTSGQRNATRM
ILETRDRFTLVQGYAGVGKTTQFRAVMSAVNLLPEDSRPKVIGLGPTHRAVGEMQSAGVEAQTTASFLHD
TQLLMRSGQTPDFSNTLFLVDESSMLGLSDTAKAMSLIAAGGGRAVSSGDTDQLQSIAPGQPFRLMQKRS
AADVAIMQEIVRQVPELRPAVYSLIDRDIHSALSTIERVEPAQVPRKENAWVPESSVMEFTPEQEKAIQK
AIGEGEVLPDISPVSLYDAIVRDYTGRTESAQAQTLIITHLNDDRRVLNRMIHDEKMRNGELGEDSVTLP
VLVTSNIRDGELRKVSTWEAHKGAIALVDNQYHQIVGVSKADQLITLRSDEGTERLISPREASAEGVTLY
RQESITVSPGDRMRFSKSDTERGYVANSVWRVESISGDSVTLNDGKSTRTVTPAADKAEAHVDLAYAITT
HGAQGASEPFSIELEGVTGARERMVSFESAYVALSRMKQHTQVYTDDRKGWTDAVSRSQEKASAHDVLEP
LNDRAVKSAEQLFGRAIPLTESPAGRAALQQSGIARGQSTGKFISPGKKYPLPHVALPAFDRNGKSAGIW
LSPLTDKDGRLQAIGGEGRVMGNEEARFVALQGSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPGAITGGRVWGDIDAVVTGGSGANIPLPPDLLAQKTAEELQRKQIEKQAQETARELTGEKRKQDEVGE
QIKDIITDVVRGLERQKGQHERFQLPDEPENRLRNEAVQKVVADNQQQDRLQQIERDMVRDLTREKTLGG
D

  Protein domains


Predicted by InterproScan.

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

(634-713)

TrwC relaxase (TrwC)

(10-284)

AAA domain (AAA_30)

(970-1156)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(576-627)


  Protein structure



No available structure.




Auxiliary protein

ID   1408 GenBank   WP_001568107
Name   WP_001568107_pRHBSTW-00123_3 insolico UniProt ID   _
Length   128 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 128 a.a.        Molecular weight: 14784.78 Da        Isoelectric Point: 4.6362

>WP_001568107.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVQAYPSDEVVDKINAIVEKRRAEGAKEKDISFSSVATMLLELGLRVYEAQMERKESGFNQKEFNKVL
LENVMKTQFTISKVLAMDSLSPHINGDDRFDFKSMVMNIRDDAREVVERFFPSQDEEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   3129 GenBank   WP_023332870
Name   traD_HV081_RS23660_pRHBSTW-00123_3 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 82700.58 Da        Isoelectric Point: 5.9222

>WP_023332870.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRFRMFGQIANIILYVLFLFFWVLCGLILMYRLSWQTFVNGAVYWWCTTLGPMR
DIIRSQPVYTINYYGQQLQYTSEQILKDKYTIWCGEQLWTGFVFAGTVSLIICIVAFFVASWVLGHQGKQ
QSEDEVTGGRQLSEKPKEVARKMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSIDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRSVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKGIA
EFAAGEIGEKEIKKASENYSYGADPVRDGVSTGKEQKRETIVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRQLNQAIDDKLAAVLAAREAEGQSARILFMPDPVETVPVEKTDEKPASPVAAVPTP
QEDKAKVPPVTASNTFHKPASAAAAAASASVTQAGGVEQELHEKPEEQLPLPPGVNKDGEIEDMNAWDEW
QSSSDVLRDMHRREEVNINHSHHVDRDDINLGSNF

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 86930..113000

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV081_RS23485 (HV081_23495) 81983..82270 + 288 WP_000323025 type II toxin-antitoxin system mRNA interferase RelE -
HV081_RS23490 (HV081_23500) 82321..83355 - 1035 Protein_96 IS481 family transposase -
HV081_RS24065 83456..83518 + 63 Protein_97 hypothetical protein -
HV081_RS24070 83490..83588 + 99 Protein_98 Hok/Gef family protein -
HV081_RS23500 (HV081_23510) 83683..84891 + 1209 WP_015386429 IS256 family transposase -
HV081_RS23990 85173..85304 - 132 WP_255344245 hypothetical protein -
HV081_RS23505 (HV081_23515) 85702..86523 + 822 WP_023332864 DUF932 domain-containing protein -
HV081_RS23510 (HV081_23520) 86589..86897 + 309 WP_023332865 DUF5983 family protein -
HV081_RS23515 (HV081_23525) 86930..87415 - 486 WP_032629900 transglycosylase SLT domain-containing protein virB1
HV081_RS23520 (HV081_23530) 87838..88224 + 387 WP_001568107 conjugal transfer relaxosome DNA-binding protein TraM -
HV081_RS23525 (HV081_23535) 88444..89133 + 690 WP_001568106 helix-turn-helix domain-containing protein -
HV081_RS23530 (HV081_23540) 89308..89472 + 165 WP_071594636 TraY domain-containing protein -
HV081_RS23535 (HV081_23545) 89551..89919 + 369 WP_001568105 type IV conjugative transfer system pilin TraA -
HV081_RS23540 (HV081_23550) 89999..90367 + 369 WP_001568104 type IV conjugative transfer system pilin TraA -
HV081_RS23545 (HV081_23555) 90381..90686 + 306 WP_024191986 type IV conjugative transfer system protein TraL traL
HV081_RS23550 (HV081_23560) 90705..91271 + 567 WP_001568102 type IV conjugative transfer system protein TraE traE
HV081_RS23555 (HV081_23565) 91258..91998 + 741 WP_001568101 type-F conjugative transfer system secretin TraK traK
HV081_RS23560 (HV081_23570) 91998..93410 + 1413 WP_001568100 F-type conjugal transfer pilus assembly protein TraB traB
HV081_RS23565 (HV081_23575) 93403..93639 + 237 WP_001568098 hypothetical protein virb4
HV081_RS23570 (HV081_23580) 93658..94227 + 570 WP_001568094 type IV conjugative transfer system lipoprotein TraV traV
HV081_RS23960 94341..94754 + 414 WP_001568093 hypothetical protein -
HV081_RS23580 (HV081_23590) 94759..95157 + 399 WP_001568092 hypothetical protein -
HV081_RS23585 (HV081_23595) 95620..98259 + 2640 WP_001568090 type IV secretion system protein TraC virb4
HV081_RS23590 (HV081_23600) 98259..98636 + 378 WP_001568089 type-F conjugative transfer system protein TrbI -
HV081_RS23595 (HV081_23605) 98633..99262 + 630 WP_023332867 type-F conjugative transfer system protein TraW traW
HV081_RS23600 (HV081_23610) 99294..100265 + 972 WP_176602138 conjugal transfer pilus assembly protein TraU traU
HV081_RS23605 (HV081_23615) 100278..100904 + 627 WP_001568086 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV081_RS23610 (HV081_23620) 100901..102793 + 1893 WP_001568085 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV081_RS23615 (HV081_23625) 102806..103066 + 261 WP_001568084 conjugal transfer protein TrbE -
HV081_RS23620 (HV081_23630) 103063..103395 + 333 WP_001568083 hypothetical protein -
HV081_RS23625 (HV081_23635) 103411..104160 + 750 WP_001568082 type-F conjugative transfer system pilin assembly protein TraF traF
HV081_RS23630 (HV081_23640) 104171..104404 + 234 WP_001568081 type-F conjugative transfer system pilin chaperone TraQ -
HV081_RS23635 (HV081_23645) 104424..104960 + 537 WP_032160235 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV081_RS23640 (HV081_23650) 104947..106317 + 1371 WP_023332869 conjugal transfer pilus assembly protein TraH traH
HV081_RS23645 (HV081_23655) 106317..109166 + 2850 WP_001568078 conjugal transfer mating-pair stabilization protein TraG traG
HV081_RS23650 (HV081_23660) 109172..109699 + 528 WP_024191983 conjugal transfer protein TraS -
HV081_RS23655 (HV081_23665) 109877..110608 + 732 WP_001568076 conjugal transfer complement resistance protein TraT -
HV081_RS23660 (HV081_23670) 110793..113000 + 2208 WP_023332870 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4857 GenBank   NZ_CP055399
Plasmid name   pRHBSTW-00123_3 Incompatibility group   IncFIA
Plasmid size   121982 bp Coordinate of oriT [Strand]   87489..87537 [-]
Host baterium   Enterobacter roggenkampii strain RHBSTW-00123

Cargo genes

Drug resistance gene   -
Virulence gene   mrkA, mrkB, mrkC, mrkD, mrkF
Metal resistance gene   ncrY, ncrC, ncrB, ncrA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -