Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105313
Name   oriT_pRHBSTW-00832_4 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00832
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056310 (57364..57412 [-], 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-00832_4
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3630 GenBank   WP_181247953
Name   traI_HV292_RS29345_pRHBSTW-00832_4 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: 190153.89 Da        Isoelectric Point: 5.9563

>WP_181247953.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSETVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYASQIAFGKLYREMLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPAEKMVEWVNT
LKETGFDIHSYREDADKRAAEITRAPVSPVKTDGPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
RPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSLTPDASVVRQAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSRDFLAGDARLAGETVTG
KSALQDGTAFIPGGTLVVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPDKHVRYSRLAQEFAVSVREGQESVAQISGTREQNALNNVIRDTLKNEGVLGAKEI
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWTLFRADKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVENPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDVARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQAIHLSIPLLESENLTFTRPQLLATALETGGGKVPMAEIDATIQ
SQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTKVLEGKDAVPPLMDSVPGSLMADLTSGQRAATRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQAPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIQK
ALSEGEILPAGQPATLYEALVKDYADRTPEAQLQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVTGGRKQMASFESAYVGLSRMKLHVQVYTDSREGWVNAIQASPSKATAHDILAP
RNERAVKTADLLFGRAQPLNETAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKNAGIW
LSPLTDKDGRLEAIGGDGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMGRQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1630 GenBank   WP_022644939
Name   WP_022644939_pRHBSTW-00832_4 insolico UniProt ID   W8QGP1
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15048.16 Da        Isoelectric Point: 4.5248

>WP_022644939.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVAEKINAIVEKRRVEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LEYVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMLRFFPDEDNEVEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB W8QGP1


T4CP

ID   3599 GenBank   WP_181247952
Name   traD_HV292_RS29340_pRHBSTW-00832_4 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 85822.74 Da        Isoelectric Point: 4.9170

>WP_181247952.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTAFVFAAIVSLTVCVVTFFVASWVLGRQGKQ
QSEDEDTGGRQLSDKPKDVARQIKRDGVASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEREYLKPSEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRMDGRLSAQLEAREAEGSHARMLFTPDEVAKDEGDTGNSPEAIKPAGDRIP
TPVNATPPEKTPPAEASGNAPVTPQPATPAMRVTTVPLTRPRPVVPASGATAVAAATDVSAATSGGTAQE
LAQQPVEADQNMLPAGMNEDGVIEDMQAYDAWLEGEQIQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 60989..85915

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV292_RS29160 (HV292_29160) 56232..56774 + 543 WP_181247948 antirestriction protein -
HV292_RS29165 (HV292_29165) 56797..57219 - 423 WP_020315406 transglycosylase SLT domain-containing protein -
HV292_RS29170 (HV292_29170) 57725..58117 + 393 WP_022644939 conjugal transfer relaxosome DNA-binding protein TraM -
HV292_RS29175 (HV292_29175) 58352..58849 + 498 WP_181247949 hypothetical protein -
HV292_RS29180 (HV292_29180) 58888..59868 - 981 WP_009310076 IS5-like element ISKpn26 family transposase -
HV292_RS29185 (HV292_29185) 60338..60538 + 201 WP_060415469 TraY domain-containing protein -
HV292_RS29190 (HV292_29190) 60607..60975 + 369 WP_060415470 type IV conjugative transfer system pilin TraA -
HV292_RS29195 (HV292_29195) 60989..61294 + 306 WP_053390196 type IV conjugative transfer system protein TraL traL
HV292_RS29200 (HV292_29200) 61314..61880 + 567 WP_053390197 type IV conjugative transfer system protein TraE traE
HV292_RS29205 (HV292_29205) 61867..62601 + 735 WP_053390198 type-F conjugative transfer system secretin TraK traK
HV292_RS29210 (HV292_29210) 62601..64022 + 1422 WP_075606927 F-type conjugal transfer pilus assembly protein TraB traB
HV292_RS29215 (HV292_29215) 64015..64611 + 597 WP_075606926 conjugal transfer pilus-stabilizing protein TraP -
HV292_RS29220 (HV292_29220) 64634..65203 + 570 WP_075606925 type IV conjugative transfer system lipoprotein TraV traV
HV292_RS29225 (HV292_29225) 65315..65593 + 279 WP_053390295 hypothetical protein -
HV292_RS29230 (HV292_29230) 65600..65788 + 189 WP_053390294 hypothetical protein -
HV292_RS29960 65872..66273 + 402 WP_064343532 hypothetical protein -
HV292_RS29240 (HV292_29240) 66270..66569 + 300 WP_053390308 hypothetical protein -
HV292_RS29245 (HV292_29245) 66657..67040 + 384 WP_042946290 hypothetical protein -
HV292_RS29250 (HV292_29250) 67133..69772 + 2640 WP_064343533 type IV secretion system protein TraC virb4
HV292_RS29255 (HV292_29255) 69772..70164 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
HV292_RS29260 (HV292_29260) 70161..70787 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
HV292_RS29265 (HV292_29265) 70831..71790 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
HV292_RS29270 (HV292_29270) 71803..72429 + 627 WP_181247950 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV292_RS29275 (HV292_29275) 72426..74381 + 1956 WP_102016187 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV292_RS29280 (HV292_29280) 74413..74673 + 261 WP_181247951 hypothetical protein -
HV292_RS29285 (HV292_29285) 74666..75277 + 612 WP_060415486 hypothetical protein -
HV292_RS29290 (HV292_29290) 75267..75509 + 243 WP_060415487 conjugal transfer protein TrbE -
HV292_RS29295 (HV292_29295) 75555..75881 + 327 WP_060415488 hypothetical protein -
HV292_RS29300 (HV292_29300) 75902..76654 + 753 WP_060415489 type-F conjugative transfer system pilin assembly protein TraF traF
HV292_RS29305 (HV292_29305) 76665..76901 + 237 WP_032736848 type-F conjugative transfer system pilin chaperone TraQ -
HV292_RS29310 (HV292_29310) 76915..77451 + 537 WP_180807780 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV292_RS29315 (HV292_29315) 77438..78808 + 1371 WP_102016205 conjugal transfer pilus assembly protein TraH traH
HV292_RS29320 (HV292_29320) 78808..81633 + 2826 WP_060415492 conjugal transfer mating-pair stabilization protein TraG traG
HV292_RS29325 (HV292_29325) 81650..82321 + 672 WP_088883382 hypothetical protein -
HV292_RS29330 (HV292_29330) 82568..83260 + 693 WP_162762153 hypothetical protein -
HV292_RS29335 (HV292_29335) 83281..83544 + 264 WP_142372547 hypothetical protein -
HV292_RS29340 (HV292_29340) 83615..85915 + 2301 WP_181247952 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5751 GenBank   NZ_CP056310
Plasmid name   pRHBSTW-00832_4 Incompatibility group   IncFII
Plasmid size   97542 bp Coordinate of oriT [Strand]   57364..57412 [-]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00832

Cargo genes

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