Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119733
Name   oriT_pRHBSTW-00676_2 in_silico
Organism   Klebsiella michiganensis strain RHBSTW-00676
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055986 (183240..183288 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pRHBSTW-00676_2
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12470 GenBank   WP_064352027
Name   traI_HV264_RS28515_pRHBSTW-00676_2 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190278.04 Da        Isoelectric Point: 6.1200

>WP_064352027.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMEERWQGKGAEALGLDGKAVDKAVFTELLKGKLPDGSDLTRM
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTVAVKQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQIAFGKLYREALKPLVE
KLGYETEVVGKHGMWEMKDVLVEPFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIQGYREAADTRAEEIARAPAAPVQTDGLDIADVVTKAIAGLSDRKVQFTYADVLARTVGQLE
AKPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDAGVVREKP
FSDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGKQATADIISEPDKSARYSRLAQEFAVSVREGQESVAQISGTREQNVLNSVIRDTLKNEGALGSRD
MTVTALTPVWLDSKSRGVRDYYREGMVMERWDPEARKHDRFVIDRVTASSNMLTLKDREGERLDLKVSVV
DSQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLLVGSSPFDGI
KVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDKARTTEKLARHTAFSVVSE
QLKARSGEADLEAAIAQQKAGLHTPAEQAIHLSIPLLESNSLTFTRPQLLATALETGGGKVPMKDIEATI
QAQIKAGSLLNVPVASGHGNDMLISRQTWDAEKSVLTRVLEGKDAVAPLMDRVPGSLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFKAVMSAINLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLH
DTQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDVSRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQ
DALKEGKEIPPVTPVSLHDAIVKDYTGRTPAAQANTLIITHLNADRRALNGLIHDARVQNGEVSKDEVTL
PVLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDSEGNTRFLSPREASAEGVTL
YRPEHVTVSQGDRMRFSKSDPERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAIT
AHGAQGASEPFAIALEGMEGRRKAMVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLE
PQNARAVRNAGQLYGRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDRDGRLEAIGGEGRIMGDETARFVALQNSRNGESLLAGNMGEGVRAARNHPDSGVIVRLAGDDR
PWNPEAITGGRIWAAPLPNLPLPDTGADTTPPPDVLAQRAAEEAQRRELERQTEQATREVAGEEKKAGEP
GERIKEVIGDVIRGLERDRPGEEKTPLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

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

(577-629)

TrwC relaxase (TrwC)

(10-284)

AAA domain (AAA_30)

(971-1158)

DNA helicase TraI (TraI_C)

(1433-1555)


  Protein structure



No available structure.




T4CP

ID   14651 GenBank   WP_064352026
Name   traD_HV264_RS28520_pRHBSTW-00676_2 insolico UniProt ID   _
Length   759 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 759 a.a.        Molecular weight: 84981.63 Da        Isoelectric Point: 4.8119

>WP_064352026.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIMLYVLFILFWGLCGLLLMFRLSWQTFVNGSVYWWCTTLAPMR
DIMRSQPVYTIQYYGHSLEFTAEQILSDKYTVWCGEQLWTSFVFAAVVSLIICIIAFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLSLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDNDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDARLSALLEAREAEGSLARALFTPDAPEPEQSDADSRTSPGQPEPESAP
VSPAPVKSASTAETLAAPPSVKASEAPQATVTTVPLTRPAPAATPAASSATASTTGGTEQELAQQPAEQG
QEMMPAGMNEDGEIEDMQVYDAWLADEQTQREMQRREEVNINHSHRRDEQDDIEIGGNF

  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: 158159..183846

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV264_RS28520 (HV264_28525) 158159..160438 - 2280 WP_064352026 type IV conjugative transfer system coupling protein TraD virb4
HV264_RS28525 (HV264_28530) 160675..161211 - 537 WP_064352025 hypothetical protein -
HV264_RS28530 (HV264_28535) 161222..164071 - 2850 WP_064352024 conjugal transfer mating-pair stabilization protein TraG traG
HV264_RS28535 (HV264_28540) 164071..165441 - 1371 WP_047722560 conjugal transfer pilus assembly protein TraH traH
HV264_RS28540 (HV264_28545) 165428..166006 - 579 WP_047722561 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV264_RS28545 (HV264_28550) 165978..166217 - 240 WP_047722563 type-F conjugative transfer system pilin chaperone TraQ -
HV264_RS28550 (HV264_28555) 166228..166980 - 753 WP_047722564 type-F conjugative transfer system pilin assembly protein TraF traF
HV264_RS28555 (HV264_28560) 166999..167325 - 327 WP_047722565 hypothetical protein -
HV264_RS28560 (HV264_28565) 167554..167784 - 231 WP_047722568 conjugal transfer protein TrbE -
HV264_RS28565 (HV264_28570) 167774..168055 - 282 WP_064352023 hypothetical protein -
HV264_RS28570 (HV264_28575) 168088..169962 - 1875 WP_047722571 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV264_RS28575 (HV264_28580) 169959..170576 - 618 WP_064352022 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV264_RS28580 (HV264_28585) 170589..171572 - 984 WP_160887030 conjugal transfer pilus assembly protein TraU traU
HV264_RS28585 (HV264_28590) 171592..172218 - 627 WP_047722574 type-F conjugative transfer system protein TraW traW
HV264_RS28590 (HV264_28595) 172215..172655 - 441 WP_101836779 type-F conjugative transfer system protein TrbI -
HV264_RS28595 (HV264_28600) 172655..175294 - 2640 WP_047722575 type IV secretion system protein TraC virb4
HV264_RS28600 (HV264_28605) 175418..175744 - 327 WP_052958980 hypothetical protein -
HV264_RS28605 (HV264_28610) 175741..176145 - 405 WP_047722576 hypothetical protein -
HV264_RS28610 (HV264_28615) 176142..176363 - 222 WP_047722577 hypothetical protein -
HV264_RS28615 (HV264_28620) 176387..176680 - 294 WP_047722579 hypothetical protein -
HV264_RS28620 (HV264_28625) 176825..177028 - 204 WP_047722580 hypothetical protein -
HV264_RS28625 (HV264_28630) 177175..177744 - 570 WP_047722665 type IV conjugative transfer system lipoprotein TraV traV
HV264_RS28630 (HV264_28635) 177839..179254 - 1416 WP_047722582 F-type conjugal transfer pilus assembly protein TraB traB
HV264_RS28635 (HV264_28640) 179254..179994 - 741 WP_047722583 type-F conjugative transfer system secretin TraK traK
HV264_RS28640 (HV264_28645) 179981..180547 - 567 WP_047722585 type IV conjugative transfer system protein TraE traE
HV264_RS28645 (HV264_28650) 180567..180872 - 306 WP_047722586 type IV conjugative transfer system protein TraL traL
HV264_RS28650 (HV264_28655) 180886..181248 - 363 WP_047722588 type IV conjugative transfer system pilin TraA -
HV264_RS28655 (HV264_28660) 181309..181512 - 204 WP_171972759 TraY domain-containing protein -
HV264_RS28660 (HV264_28665) 181667..182341 - 675 WP_047722589 hypothetical protein -
HV264_RS28665 (HV264_28670) 182542..182937 - 396 WP_047722590 conjugal transfer relaxosome DNA-binding protein TraM -
HV264_RS28670 (HV264_28675) 183361..183846 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
HV264_RS28675 (HV264_28680) 183879..184208 - 330 WP_011977736 DUF5983 family protein -
HV264_RS28680 (HV264_28685) 184241..185062 - 822 WP_004182076 DUF932 domain-containing protein -
HV264_RS28685 (HV264_28690) 185890..186453 - 564 WP_004182054 methyltransferase -
HV264_RS28690 (HV264_28695) 186501..187856 - 1356 WP_004182052 DUF3560 domain-containing protein -
HV264_RS28695 (HV264_28700) 187908..188138 - 231 WP_064352021 hypothetical protein -
HV264_RS28700 (HV264_28705) 188230..188457 - 228 WP_004182050 hypothetical protein -

Host bacterium

ID   20163 GenBank   NZ_CP055986
Plasmid name   pRHBSTW-00676_2 Incompatibility group   IncFIB
Plasmid size   206301 bp Coordinate of oriT [Strand]   183240..183288 [+]
Host baterium   Klebsiella michiganensis strain RHBSTW-00676

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, merR, merT, merP, merC, merA, merD, merE, arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -