Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105254
Name   oriT_pRHBSTW-00167_2 in_silico
Organism   Klebsiella michiganensis strain RHBSTW-00167
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058119 (185268..185316 [-], 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_pRHBSTW-00167_2
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTTTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3604 GenBank   WP_181250924
Name   traI_HV105_RS30145_pRHBSTW-00167_2 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: 190223.95 Da        Isoelectric Point: 6.2880

>WP_181250924.1 conjugative transfer relaxase/helicase TraI [Klebsiella michiganensis]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRNEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKARSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATALETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADIAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIQK
ALSEGKTLPAGQPATLYEALVKDYTGRAPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVAGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(576-628)


  Protein structure



No available structure.




T4CP

ID   3567 GenBank   WP_020316650
Name   traD_HV105_RS30140_pRHBSTW-00167_2 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 85197.99 Da        Isoelectric Point: 4.8865

>WP_020316650.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPAEVTV
SPAPVKATQTTKMPAEEPSVRATEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTEQELAQQ
SAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 187695..213220

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV105_RS29960 (HV105_29960) 184148..184678 + 531 WP_015632491 antirestriction protein -
HV105_RS29965 (HV105_29965) 184716..185123 - 408 WP_020805750 transglycosylase SLT domain-containing protein -
HV105_RS29970 (HV105_29970) 185627..186019 + 393 WP_032419915 conjugal transfer relaxosome DNA-binding protein TraM -
HV105_RS32155 186257..186958 + 702 WP_032419917 hypothetical protein -
HV105_RS29980 (HV105_29980) 187044..187244 + 201 WP_048289787 TraY domain-containing protein -
HV105_RS29985 (HV105_29985) 187313..187681 + 369 WP_020316649 type IV conjugative transfer system pilin TraA -
HV105_RS29990 (HV105_29990) 187695..188000 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HV105_RS29995 (HV105_29995) 188020..188586 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
HV105_RS30000 (HV105_30000) 188573..189313 + 741 WP_020316652 type-F conjugative transfer system secretin TraK traK
HV105_RS30005 (HV105_30005) 189313..190737 + 1425 WP_020316642 F-type conjugal transfer pilus assembly protein TraB traB
HV105_RS30010 (HV105_30010) 190730..191326 + 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
HV105_RS30015 (HV105_30015) 191349..191918 + 570 WP_032419921 type IV conjugative transfer system lipoprotein TraV traV
HV105_RS30020 (HV105_30020) 192050..192460 + 411 WP_032419923 hypothetical protein -
HV105_RS30025 (HV105_30025) 192465..192755 + 291 WP_020316639 hypothetical protein -
HV105_RS30030 (HV105_30030) 192779..192997 + 219 WP_004171484 hypothetical protein -
HV105_RS30035 (HV105_30035) 192998..193315 + 318 WP_020316633 hypothetical protein -
HV105_RS30040 (HV105_30040) 193382..193786 + 405 WP_032419926 hypothetical protein -
HV105_RS30045 (HV105_30045) 193783..194073 + 291 WP_032419928 hypothetical protein -
HV105_RS30050 (HV105_30050) 194081..194479 + 399 WP_020316629 hypothetical protein -
HV105_RS30055 (HV105_30055) 194551..197190 + 2640 WP_020316635 type IV secretion system protein TraC virb4
HV105_RS30060 (HV105_30060) 197190..197579 + 390 WP_020316628 type-F conjugative transfer system protein TrbI -
HV105_RS30065 (HV105_30065) 197579..198205 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HV105_RS30070 (HV105_30070) 198249..199208 + 960 WP_202386622 conjugal transfer pilus assembly protein TraU traU
HV105_RS30075 (HV105_30075) 199221..199859 + 639 WP_020316653 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV105_RS30080 (HV105_30080) 199918..201873 + 1956 WP_020316657 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV105_RS30085 (HV105_30085) 201906..202187 + 282 WP_032419932 hypothetical protein -
HV105_RS30090 (HV105_30090) 202177..202404 + 228 WP_012540032 conjugal transfer protein TrbE -
HV105_RS30095 (HV105_30095) 202415..202741 + 327 WP_020316638 hypothetical protein -
HV105_RS30100 (HV105_30100) 202762..203514 + 753 WP_020316647 type-F conjugative transfer system pilin assembly protein TraF traF
HV105_RS30105 (HV105_30105) 203525..203764 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
HV105_RS30110 (HV105_30110) 203736..204293 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV105_RS30115 (HV105_30115) 204339..204782 + 444 WP_020804675 F-type conjugal transfer protein TrbF -
HV105_RS30120 (HV105_30120) 204760..206139 + 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
HV105_RS30125 (HV105_30125) 206139..208961 + 2823 WP_020316632 conjugal transfer mating-pair stabilization protein TraG traG
HV105_RS30130 (HV105_30130) 208985..209587 + 603 WP_048263624 hypothetical protein -
HV105_RS30135 (HV105_30135) 209838..210569 + 732 WP_016831056 conjugal transfer complement resistance protein TraT -
HV105_RS30140 (HV105_30140) 210929..213220 + 2292 WP_020316650 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5692 GenBank   NZ_CP058119
Plasmid name   pRHBSTW-00167_2 Incompatibility group   IncR
Plasmid size   223875 bp Coordinate of oriT [Strand]   185268..185316 [-]
Host baterium   Klebsiella michiganensis strain RHBSTW-00167

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merD, merA, merC, merP, merT, merR, arsH, arsC, arsB
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9