Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105220
Name   oriT_RHBSTW-00165|unnamed in_silico
Organism   Klebsiella grimontii strain RHBSTW-00165
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055365 (41276..41324 [+], 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_RHBSTW-00165|unnamed
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3591 GenBank   WP_181481502
Name   traI_HV104_RS28140_RHBSTW-00165|unnamed 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: 190442.61 Da        Isoelectric Point: 5.6407

>WP_181481502.1 conjugative transfer relaxase/helicase TraI [Klebsiella grimontii]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSETVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYASQIAFGKLYREMLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPSEKMVEWVNT
LKETGFDIHSYREDADKRAAEIARAPVSPVKTDGPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
RPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRHAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLAGDARLAGETVTG
KSALQDGTAFIPGGSLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGNQTTADIISEPDKNVRYSRLAQEFAVSVREGQESVAQISGTREQNALNNVIRDTLKNEGVLGAKEI
TVTALTPVWLDSKSRGVRDYYREGMVMERWDSETRKHDRFVIDRVTASSNMLTLRGKEGERLDLKVSAVD
SQWTLFRADKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFVSVTQRELDNATLNQLAQSGSHIRLYSAQDVARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQAIHLSIPLLESENLTFTRPQLLATALETGGGKVPMTEIESTIR
RQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDSVPGSLMADLTSGQRAATRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAINLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLTDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDINSALTTIEQVTPAQVPRQDGAWVPDNSVVEFTPAQEEAIQK
ALNKGESVPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNDDRRALNSLIHDARRDNGETGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLTDSEGKERLISPREASAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKTTRTMDPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDSREGWIKAIRNSPEKATAHDILEP
RNDRAVKNAGQLFGRAQPLDETAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDKDGRLESIGGEGRIMGDETARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEALTGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQHREMERQTEQATREVSGEEKKAGEPG
EQIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQESAVQQVATESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1156)

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

(576-628)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1553)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   1606 GenBank   WP_022644939
Name   WP_022644939_RHBSTW-00165|unnamed 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   3551 GenBank   WP_060415494
Name   traD_HV104_RS28145_RHBSTW-00165|unnamed 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: 85951.95 Da        Isoelectric Point: 4.9227

>WP_060415494.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTVCVVTFFVASWVLGRQGKQ
QSEDEDTGGRQLSDKPKDVARQIKRDGVASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEREYLKPSEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRMDERLSAQLEAREAEGSHARMLFTPDEVAKDEGDTGNSPEAIKPAGDRIP
TPVNATPSEKTPPAEASGNAPVTPQPATPVMRVTTVPLTRPRPVVPASGATAVAAATDVSAVTSGGTAQE
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: 14869..41891

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV104_RS28145 (HV104_28155) 14869..17169 - 2301 WP_060415494 type IV conjugative transfer system coupling protein TraD virb4
HV104_RS28150 (HV104_28160) 17416..18087 - 672 WP_088883382 hypothetical protein -
HV104_RS28155 (HV104_28165) 18104..20929 - 2826 WP_060415492 conjugal transfer mating-pair stabilization protein TraG traG
HV104_RS28160 (HV104_28170) 20929..22299 - 1371 WP_032736846 conjugal transfer pilus assembly protein TraH traH
HV104_RS28165 (HV104_28175) 22286..22849 - 564 WP_224250969 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV104_RS28170 (HV104_28180) 22836..23072 - 237 WP_032736848 type-F conjugative transfer system pilin chaperone TraQ -
HV104_RS28175 (HV104_28185) 23083..23835 - 753 WP_181481503 type-F conjugative transfer system pilin assembly protein TraF traF
HV104_RS28180 (HV104_28190) 23856..24182 - 327 WP_060415488 hypothetical protein -
HV104_RS28185 (HV104_28195) 24228..24470 - 243 WP_060415487 conjugal transfer protein TrbE -
HV104_RS28190 (HV104_28200) 24460..25071 - 612 WP_060415486 hypothetical protein -
HV104_RS28195 (HV104_28205) 25064..25324 - 261 WP_060415485 hypothetical protein -
HV104_RS28200 (HV104_28210) 25356..27311 - 1956 WP_181481504 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV104_RS28205 (HV104_28215) 27308..27934 - 627 WP_060415483 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV104_RS28210 (HV104_28220) 27947..28906 - 960 WP_088912317 conjugal transfer pilus assembly protein TraU traU
HV104_RS28215 (HV104_28225) 28950..29576 - 627 WP_060415482 type-F conjugative transfer system protein TraW traW
HV104_RS28220 (HV104_28230) 29573..29962 - 390 WP_060415481 type-F conjugative transfer system protein TrbI -
HV104_RS28225 (HV104_28235) 29962..32601 - 2640 WP_060415480 type IV secretion system protein TraC virb4
HV104_RS28230 (HV104_28240) 32694..33077 - 384 WP_181481505 hypothetical protein -
HV104_RS28235 (HV104_28245) 33165..33464 - 300 WP_060415478 hypothetical protein -
HV104_RS31230 33461..33862 - 402 WP_060415477 hypothetical protein -
HV104_RS28245 (HV104_28255) 33946..34134 - 189 WP_053390294 hypothetical protein -
HV104_RS28250 (HV104_28260) 34141..34419 - 279 WP_060415476 hypothetical protein -
HV104_RS28255 (HV104_28265) 34531..35100 - 570 WP_060415475 type IV conjugative transfer system lipoprotein TraV traV
HV104_RS28260 (HV104_28270) 35265..35873 - 609 WP_060415474 conjugal transfer protein TraP -
HV104_RS28265 (HV104_28275) 35866..37287 - 1422 WP_060415473 F-type conjugal transfer pilus assembly protein TraB traB
HV104_RS28270 (HV104_28280) 37287..38021 - 735 WP_060415472 type-F conjugative transfer system secretin TraK traK
HV104_RS28275 (HV104_28285) 38008..38574 - 567 WP_060415471 type IV conjugative transfer system protein TraE traE
HV104_RS28280 (HV104_28290) 38594..38899 - 306 WP_053390196 type IV conjugative transfer system protein TraL traL
HV104_RS28285 (HV104_28295) 38913..39281 - 369 WP_060415470 type IV conjugative transfer system pilin TraA -
HV104_RS28290 (HV104_28300) 39350..39550 - 201 WP_060415469 TraY domain-containing protein -
HV104_RS28295 (HV104_28305) 39635..40336 - 702 WP_022644938 hypothetical protein -
HV104_RS28300 (HV104_28310) 40571..40963 - 393 WP_022644939 conjugal transfer relaxosome DNA-binding protein TraM -
HV104_RS28305 (HV104_28315) 41469..41891 + 423 WP_073972322 transglycosylase SLT domain-containing protein virB1
HV104_RS28310 (HV104_28320) 41914..42456 - 543 WP_060415467 antirestriction protein -
HV104_RS28315 (HV104_28325) 42451..42819 + 369 WP_080848162 hypothetical protein -
HV104_RS28320 (HV104_28330) 43105..43938 - 834 WP_060415466 N-6 DNA methylase -
HV104_RS28325 (HV104_28335) 43985..44215 - 231 WP_060415465 hypothetical protein -
HV104_RS28330 (HV104_28340) 44304..44651 - 348 WP_064182675 hypothetical protein -
HV104_RS28335 (HV104_28345) 44708..45046 - 339 WP_020804855 hypothetical protein -
HV104_RS28340 (HV104_28350) 45826..46701 - 876 WP_060415463 DUF4942 domain-containing protein -

Host bacterium

ID   5658 GenBank   NZ_CP055365
Plasmid name   RHBSTW-00165|unnamed Incompatibility group   IncFII
Plasmid size   123417 bp Coordinate of oriT [Strand]   41276..41324 [+]
Host baterium   Klebsiella grimontii strain RHBSTW-00165

Cargo genes

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