Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115088
Name   oriT_pRHBSTW-00909_3 in_silico
Organism   Klebsiella michiganensis strain RHBSTW-00909
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056138 (119653..119702 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pRHBSTW-00909_3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9650 GenBank   WP_064359958
Name   traI_HV324_RS29965_pRHBSTW-00909_3 insolico UniProt ID   A0A7D6JMG2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 189724.34 Da        Isoelectric Point: 5.9228

>WP_064359958.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAETLELEGKVDKQVFTALLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALEQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKETIDPAEKMVEWMNT
LKETGFDIRGYREAADARAKELASAPAAPVKTDGPDIGDVVTNAIAGLSDRKVQFTYADLLARTVGQLEA
KPGVFERARGGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVTVTPDATVVRLAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQNGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGRQTTADIISEPDKGARYNRLAQEFAVSVREGQESVAQISGTREQGVLNGIIRDTLKNEGALGTKEM
AITALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVANGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQALSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDATRTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIATQKAGLHTPAEQVIHLSIPLLESEALTFTRPQLLATALETGGGKVPMTEIDATIQ
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   5670 GenBank   WP_053390193
Name   WP_053390193_pRHBSTW-00909_3 insolico UniProt ID   A0A8G2A327
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14883.89 Da        Isoelectric Point: 4.3779

>WP_053390193.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVADKINAIVEKRRVEGAKDKDISFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LESVIKTQFTVNKVLGIECLSPHVSGNPRWEWPGLIENIRDDVQEVMLRFFPDEESEDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   11259 GenBank   WP_064343540
Name   traD_HV324_RS29960_pRHBSTW-00909_3 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: 119086..157077

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV324_RS29760 (HV324_29770) 114276..115151 + 876 WP_060415463 DUF4942 domain-containing protein -
HV324_RS29765 (HV324_29775) 115931..116269 + 339 WP_020804855 hypothetical protein -
HV324_RS29770 (HV324_29780) 116326..116673 + 348 WP_064182675 hypothetical protein -
HV324_RS29775 (HV324_29785) 116762..116992 + 231 WP_060415465 hypothetical protein -
HV324_RS29780 (HV324_29790) 117039..117872 + 834 WP_060415466 N-6 DNA methylase -
HV324_RS29785 (HV324_29795) 118158..118526 - 369 WP_080848162 hypothetical protein -
HV324_RS29790 (HV324_29800) 118521..119063 + 543 WP_060415467 antirestriction protein -
HV324_RS29795 (HV324_29805) 119086..119508 - 423 WP_073972322 transglycosylase SLT domain-containing protein virB1
HV324_RS29800 (HV324_29810) 120014..120406 + 393 WP_053390193 conjugal transfer relaxosome DNA-binding protein TraM -
HV324_RS29805 (HV324_29815) 120644..121345 + 702 WP_094898581 hypothetical protein -
HV324_RS29810 (HV324_29820) 121506..121667 + 162 WP_172686697 TraY domain-containing protein -
HV324_RS29815 (HV324_29825) 121732..122100 + 369 WP_064386081 type IV conjugative transfer system pilin TraA -
HV324_RS29820 (HV324_29830) 122114..122419 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
HV324_RS29825 (HV324_29835) 122435..123001 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
HV324_RS29830 (HV324_29840) 122988..123722 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
HV324_RS29835 (HV324_29845) 123722..125143 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
HV324_RS29840 (HV324_29850) 125136..125570 + 435 WP_020322358 conjugal transfer protein TraP -
HV324_RS29845 (HV324_29855) 125604..126188 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
HV324_RS29850 (HV324_29860) 126801..126989 + 189 WP_053390286 hypothetical protein -
HV324_RS32520 127073..127474 + 402 WP_064343532 hypothetical protein -
HV324_RS29860 (HV324_29870) 127471..127770 + 300 WP_053390308 hypothetical protein -
HV324_RS29865 (HV324_29875) 127858..128241 + 384 WP_064359955 hypothetical protein -
HV324_RS29870 (HV324_29880) 128334..130973 + 2640 WP_064343533 type IV secretion system protein TraC virb4
HV324_RS29875 (HV324_29885) 130973..131365 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
HV324_RS29880 (HV324_29890) 131362..131988 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
HV324_RS29885 (HV324_29895) 132032..132991 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
HV324_RS29890 (HV324_29900) 133004..133651 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV324_RS29895 (HV324_29905) 133648..134031 + 384 WP_053390297 hypothetical protein -
HV324_RS29900 (HV324_29910) 134028..135983 + 1956 WP_064343537 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV324_RS29905 (HV324_29915) 136015..136275 + 261 WP_053390216 hypothetical protein -
HV324_RS29910 (HV324_29920) 136268..136879 + 612 WP_053390217 hypothetical protein -
HV324_RS29915 (HV324_29925) 136869..137111 + 243 WP_053390218 conjugal transfer protein TrbE -
HV324_RS29920 (HV324_29930) 137157..137483 + 327 WP_053390219 hypothetical protein -
HV324_RS29925 (HV324_29935) 137504..138256 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
HV324_RS29930 (HV324_29940) 138267..138503 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
HV324_RS29935 (HV324_29945) 138478..139038 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV324_RS29940 (HV324_29950) 139025..140395 + 1371 WP_049078362 conjugal transfer pilus assembly protein TraH traH
HV324_RS29945 (HV324_29955) 140395..143238 + 2844 WP_049078361 conjugal transfer mating-pair stabilization protein TraG traG
HV324_RS29950 (HV324_29960) 143244..143759 + 516 WP_049078360 conjugal transfer protein TraS -
HV324_RS29955 (HV324_29965) 143822..144568 + 747 WP_049078359 hypothetical protein -
HV324_RS29960 (HV324_29970) 144808..147102 + 2295 WP_064343540 type IV conjugative transfer system coupling protein TraD virb4
HV324_RS29965 (HV324_29975) 147102..152360 + 5259 WP_064359958 conjugative transfer relaxase/helicase TraI -
HV324_RS29970 (HV324_29980) 152443..153168 + 726 WP_049078358 type-F conjugative transfer system pilin acetylase TraX -
HV324_RS29975 (HV324_29985) 153325..153915 + 591 WP_049078357 fertility inhibition protein FinO -
HV324_RS29980 (HV324_29990) 154018..154431 + 414 WP_114499528 hypothetical protein -
HV324_RS32760 (HV324_29995) 154584..154775 + 192 Protein_183 DsbA family protein -
HV324_RS29990 (HV324_30000) 155011..157077 - 2067 WP_004098991 ATP-binding protein virb4
HV324_RS29995 (HV324_30005) 157074..158465 - 1392 WP_004098990 SIR2 family protein -
HV324_RS30000 (HV324_30010) 158473..159042 - 570 WP_004098989 recombinase family protein -

Host bacterium

ID   15523 GenBank   NZ_CP056138
Plasmid name   pRHBSTW-00909_3 Incompatibility group   IncFII
Plasmid size   166165 bp Coordinate of oriT [Strand]   119653..119702 [-]
Host baterium   Klebsiella michiganensis strain RHBSTW-00909

Cargo genes

Drug resistance gene   -
Virulence gene   katA
Metal resistance gene   merR, merT, merP, merC, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -