Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104408
Name   oriT_RHBSTW-00405|unnamed in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00405
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055520 (71783..71831 [-], 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_RHBSTW-00405|unnamed
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3212 GenBank   WP_181466065
Name   traI_HV185_RS28205_RHBSTW-00405|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: 189737.34 Da        Isoelectric Point: 5.9228

>WP_181466065.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAETLELEGKVDKQVFTALLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALEQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKETIDPAEKMVEWMNT
LKETGFDIRGYREAADARAKELASAPAAPVKTDGPDIGDVVTNAIAGLSDRKVQFTYADLLARTVGQLEA
KPGVFERARGGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVTVTPDATVVRLAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQNGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGRQTTADIISEPDKGARYNRLAQEFAVSVREGQESVAQISGTREQGVLNGIIRDTLKNEGALGTKEM
AITALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVANGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQALSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDATRTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIATQKAGLHTPAEQVIHLSIPLLESEALNFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTKVLEGKDAVPPLMDSVPGSLMADLTSGQRAATRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQAPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIQK
ALSEGEILPAGQPATLYEALVKDYADRTPEAQLQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVTGGRKQMASFESAYVGLSRMKLHVQVYTDSREGWVNAIQASPSKATAHDILAP
RNERAVKTADLLFGRAQPLNETAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKNAGIW
LSPLTDKDGRLEAIGGDGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMGRQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   1406 GenBank   WP_020805752
Name   WP_020805752_RHBSTW-00405|unnamed 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   3126 GenBank   WP_064343540
Name   traD_HV185_RS28200_RHBSTW-00405|unnamed 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: 85378.44 Da        Isoelectric Point: 4.9296

>WP_064343540.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTVCVVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIQRRLDARVDGRLSALLEAREAEGSLARALFTPDEPVSESAEEKAGVQPEQTKPAEDS
VLPVPVKTSSKAAEGAGKTPDVPLSGAPVTRVKTVPLIRPEPAASVTGTAAAASTAAVSATAGGTEQELA
QQPVEADQDMLPAGMNEDGVIEDMQAYDAWLAGEQTQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 71216..99198

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV185_RS28000 (HV185_28010) 66408..67283 + 876 WP_060415463 DUF4942 domain-containing protein -
HV185_RS29565 67665..67773 - 109 Protein_85 hypothetical protein -
HV185_RS28005 (HV185_28015) 68061..68399 + 339 WP_020804855 hypothetical protein -
HV185_RS28010 (HV185_28020) 68456..68803 + 348 WP_064182675 hypothetical protein -
HV185_RS28015 (HV185_28025) 68892..69122 + 231 WP_060415465 hypothetical protein -
HV185_RS28020 (HV185_28030) 69169..70002 + 834 WP_060415466 N-6 DNA methylase -
HV185_RS28025 (HV185_28035) 70288..70656 - 369 WP_080848162 hypothetical protein -
HV185_RS28030 (HV185_28040) 70651..71193 + 543 WP_060415467 antirestriction protein -
HV185_RS28035 (HV185_28045) 71216..71638 - 423 WP_073972322 transglycosylase SLT domain-containing protein virB1
HV185_RS28040 (HV185_28050) 72142..72534 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
HV185_RS29570 72772..73473 + 702 WP_223174962 hypothetical protein -
HV185_RS28050 (HV185_28060) 73559..73759 + 201 WP_048289787 TraY domain-containing protein -
HV185_RS28055 (HV185_28065) 73828..74196 + 369 WP_064343525 type IV conjugative transfer system pilin TraA -
HV185_RS28060 (HV185_28070) 74210..74515 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
HV185_RS28065 (HV185_28075) 74531..75097 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
HV185_RS28070 (HV185_28080) 75084..75818 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
HV185_RS28075 (HV185_28085) 75818..77239 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
HV185_RS28080 (HV185_28090) 77232..77666 + 435 WP_181466063 conjugal transfer protein TraP -
HV185_RS28085 (HV185_28095) 77700..78284 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
HV185_RS28090 (HV185_28100) 78897..79085 + 189 WP_053390286 hypothetical protein -
HV185_RS29575 79169..79570 + 402 WP_064343532 hypothetical protein -
HV185_RS28100 (HV185_28110) 79567..79866 + 300 WP_181466064 hypothetical protein -
HV185_RS28105 (HV185_28115) 79954..80337 + 384 WP_042946290 hypothetical protein -
HV185_RS28110 (HV185_28120) 80430..83069 + 2640 WP_064343533 type IV secretion system protein TraC virb4
HV185_RS28115 (HV185_28125) 83069..83461 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
HV185_RS28120 (HV185_28130) 83458..84084 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
HV185_RS28125 (HV185_28135) 84128..85087 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
HV185_RS28130 (HV185_28140) 85100..85747 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV185_RS28135 (HV185_28145) 85744..86127 + 384 WP_053390297 hypothetical protein -
HV185_RS28140 (HV185_28150) 86124..88079 + 1956 WP_064359956 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV185_RS28145 (HV185_28155) 88111..88371 + 261 WP_053390216 hypothetical protein -
HV185_RS28150 (HV185_28160) 88364..88975 + 612 WP_053390217 hypothetical protein -
HV185_RS28155 (HV185_28165) 88965..89207 + 243 WP_053390218 conjugal transfer protein TrbE -
HV185_RS28160 (HV185_28170) 89253..89579 + 327 WP_053390219 hypothetical protein -
HV185_RS28165 (HV185_28175) 89600..90352 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
HV185_RS28170 (HV185_28180) 90363..90599 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
HV185_RS28175 (HV185_28185) 90574..91134 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV185_RS28180 (HV185_28190) 91121..92491 + 1371 WP_049078362 conjugal transfer pilus assembly protein TraH traH
HV185_RS28185 (HV185_28195) 92491..95334 + 2844 WP_049078361 conjugal transfer mating-pair stabilization protein TraG traG
HV185_RS28190 (HV185_28200) 95340..95855 + 516 WP_049078360 conjugal transfer protein TraS -
HV185_RS28195 (HV185_28205) 95918..96664 + 747 WP_049078359 hypothetical protein -
HV185_RS28200 (HV185_28210) 96904..99198 + 2295 WP_064343540 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4847 GenBank   NZ_CP055520
Plasmid name   RHBSTW-00405|unnamed Incompatibility group   ColRNAI
Plasmid size   112388 bp Coordinate of oriT [Strand]   71783..71831 [-]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00405

Cargo genes

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