Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115089
Name   oriT_pRHBSTW-00909_4 in_silico
Organism   Klebsiella michiganensis strain RHBSTW-00909
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056139 (116498..116546 [+], 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-00909_4
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9651 GenBank   WP_181507344
Name   traI_HV324_RS30465_pRHBSTW-00909_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: 190143.83 Da        Isoelectric Point: 6.2632

>WP_181507344.1 conjugative transfer relaxase/helicase TraI [Klebsiella michiganensis]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDASVVREAPF
SDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGKQATADIISEPDKSARYSRLAQEFAASVREGQESVAQISGTREQNVLNNVIRDTLKNEGALGNRDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLKDREGERLDLKVSAVD
SQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETDLEEAIAQQKAGLHTPAEQAIHLSVPLLESNSLTFTRPQLLATALETGGGKVPMKDIEATIQ
AQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAVAPLMGRVPGSLMTDLTAGQRAATRM
ILETPDRFTVVQGYAGVGKTTQFKAVMSAISLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLQQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGLEQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1156)

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

(634-713)

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

(576-628)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   5671 GenBank   WP_087829209
Name   WP_087829209_pRHBSTW-00909_4 insolico UniProt ID   _
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14907.97 Da        Isoelectric Point: 4.5248

>WP_087829209.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure



No available structure.




T4CP

ID   11260 GenBank   WP_020803851
Name   traD_HV324_RS30470_pRHBSTW-00909_4 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85873.87 Da        Isoelectric Point: 4.9596

>WP_020803851.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFIFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLSLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAM
KYKPRPKIAEGFIQRTPDTRADARLSALLEAREAEGSLARALFTPDAPELAGKDSTPGEQPEPVSQPAPA
EVAVSPAPVNAPPTTKSPAAEPSAGAPASPPPEATVLRNTTVPLIKPKAAGTAATASSAGTPVAPAGGTE
QELVQHSTEQGRDMLPAGMNEDGVIEDMQAYDAWLADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 88307..114084

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV324_RS30470 (HV324_30480) 88307..90619 - 2313 WP_020803851 type IV conjugative transfer system coupling protein TraD virb4
HV324_RS30475 (HV324_30485) 90691..90951 - 261 WP_020803850 hypothetical protein -
HV324_RS32545 90975..91643 - 669 WP_020803846 hypothetical protein -
HV324_RS30485 (HV324_30495) 91826..92353 - 528 WP_020803849 hypothetical protein -
HV324_RS30490 (HV324_30500) 92359..95208 - 2850 WP_032744228 conjugal transfer mating-pair stabilization protein TraG traG
HV324_RS30495 (HV324_30505) 95208..96587 - 1380 WP_162495503 conjugal transfer pilus assembly protein TraH traH
HV324_RS30500 (HV324_30510) 96565..97008 - 444 WP_020804675 F-type conjugal transfer protein TrbF -
HV324_RS30505 (HV324_30515) 97054..97611 - 558 WP_134931968 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV324_RS30510 (HV324_30520) 97583..97822 - 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
HV324_RS30515 (HV324_30525) 98277..99029 - 753 WP_023316406 type-F conjugative transfer system pilin assembly protein TraF traF
HV324_RS30520 (HV324_30530) 99050..99376 - 327 WP_020323521 hypothetical protein -
HV324_RS30525 (HV324_30535) 99387..99614 - 228 WP_012540032 conjugal transfer protein TrbE -
HV324_RS30530 (HV324_30540) 99604..99885 - 282 WP_022644736 hypothetical protein -
HV324_RS30535 (HV324_30545) 99918..101873 - 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV324_RS30540 (HV324_30550) 101932..102570 - 639 WP_064182677 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV324_RS30545 (HV324_30555) 102583..103542 - 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
HV324_RS30550 (HV324_30560) 103586..104212 - 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HV324_RS30555 (HV324_30565) 104212..104601 - 390 WP_020314627 type-F conjugative transfer system protein TrbI -
HV324_RS30560 (HV324_30570) 104601..107240 - 2640 WP_137962958 type IV secretion system protein TraC virb4
HV324_RS30565 (HV324_30575) 107312..107710 - 399 WP_072156904 hypothetical protein -
HV324_RS30570 (HV324_30580) 107718..108008 - 291 WP_020323516 hypothetical protein -
HV324_RS30575 (HV324_30585) 108005..108409 - 405 WP_023316404 hypothetical protein -
HV324_RS30580 (HV324_30590) 108476..108787 - 312 WP_023316403 hypothetical protein -
HV324_RS30585 (HV324_30595) 108788..109006 - 219 WP_023316402 hypothetical protein -
HV324_RS30590 (HV324_30600) 109030..109314 - 285 WP_023316401 hypothetical protein -
HV324_RS30595 (HV324_30605) 109319..109729 - 411 WP_023316400 hypothetical protein -
HV324_RS30600 (HV324_30610) 109861..110430 - 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
HV324_RS30605 (HV324_30615) 110453..111049 - 597 WP_023316398 conjugal transfer pilus-stabilizing protein TraP -
HV324_RS30610 (HV324_30620) 111042..112466 - 1425 WP_137962959 F-type conjugal transfer pilus assembly protein TraB traB
HV324_RS30615 (HV324_30625) 112466..113206 - 741 WP_020804840 type-F conjugative transfer system secretin TraK traK
HV324_RS30620 (HV324_30630) 113193..113759 - 567 WP_064373744 type IV conjugative transfer system protein TraE traE
HV324_RS30625 (HV324_30635) 113779..114084 - 306 WP_087829212 type IV conjugative transfer system protein TraL traL
HV324_RS30630 (HV324_30640) 114098..114466 - 369 WP_087829211 type IV conjugative transfer system pilin TraA -
HV324_RS30635 (HV324_30645) 114528..114692 - 165 WP_032444506 TraY domain-containing protein -
HV324_RS30640 (HV324_30650) 114884..115558 - 675 WP_109545916 hypothetical protein -
HV324_RS30645 (HV324_30655) 115797..116186 - 390 WP_087829209 conjugal transfer relaxosome DNA-binding protein TraM -
HV324_RS30650 (HV324_30660) 116691..117113 + 423 WP_225995934 transglycosylase SLT domain-containing protein -
HV324_RS30655 (HV324_30665) 117136..117678 - 543 WP_020804853 antirestriction protein -

Host bacterium

ID   15524 GenBank   NZ_CP056139
Plasmid name   pRHBSTW-00909_4 Incompatibility group   IncFII
Plasmid size   157649 bp Coordinate of oriT [Strand]   116498..116546 [+]
Host baterium   Klebsiella michiganensis strain RHBSTW-00909

Cargo genes

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