Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105980
Name   oriT_pRHBSTW-00433_4 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00433
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056533 (35047..35095 [-], 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-00433_4
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4025 GenBank   WP_032752174
Name   traI_HV193_RS27750_pRHBSTW-00433_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: 190186.86 Da        Isoelectric Point: 6.3180

>WP_032752174.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDASVVREAPF
SDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGKQATADIISEPDKSARYSRLAQEFAASVREGQESVAQISGTREQNVLNNVIRDTLKNEGALGNRDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLKDREGERLDLKVSAVD
SQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETDLEEAIAQQKAGLHTPAEQAIHLSVPLLESNSLTFTRPQLLATALETGGGKVPMKDIEATIQ
AQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAVAPLMGRVPGSLMTDLTAGQRAATRM
ILETPDRFTVVQGYAGVGKTTQFKAVMSAISLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLQQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
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   1781 GenBank   WP_020804860
Name   WP_020804860_pRHBSTW-00433_4 insolico UniProt ID   A0A7H9GLQ1
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15022.07 Da        Isoelectric Point: 4.5248

>WP_020804860.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMRTFFPDEQEEADE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A7H9GLQ1


T4CP

ID   4036 GenBank   WP_020803851
Name   traD_HV193_RS27745_pRHBSTW-00433_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: 37512..64485

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV193_RS27555 (HV193_27575) 33915..34457 + 543 WP_020804853 antirestriction protein -
HV193_RS27560 (HV193_27580) 34480..34902 - 423 WP_020315406 transglycosylase SLT domain-containing protein -
HV193_RS27565 (HV193_27585) 35407..35799 + 393 WP_020804860 conjugal transfer relaxosome DNA-binding protein TraM -
HV193_RS27570 (HV193_27590) 36037..36729 + 693 WP_032426082 conjugal transfer protein TrbJ -
HV193_RS27575 (HV193_27595) 36862..37068 + 207 WP_176212272 TraY domain-containing protein -
HV193_RS27580 (HV193_27600) 37130..37498 + 369 WP_032744235 type IV conjugative transfer system pilin TraA -
HV193_RS27585 (HV193_27605) 37512..37817 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HV193_RS27590 (HV193_27610) 37833..38399 + 567 WP_020804842 type IV conjugative transfer system protein TraE traE
HV193_RS27595 (HV193_27615) 38386..39126 + 741 WP_020804840 type-F conjugative transfer system secretin TraK traK
HV193_RS27600 (HV193_27620) 39126..40550 + 1425 WP_032744233 F-type conjugal transfer pilus assembly protein TraB traB
HV193_RS27605 (HV193_27625) 40543..41139 + 597 WP_023316398 conjugal transfer pilus-stabilizing protein TraP -
HV193_RS27610 (HV193_27630) 41162..41731 + 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
HV193_RS27615 (HV193_27635) 41863..42285 + 423 WP_080901871 hypothetical protein -
HV193_RS27620 (HV193_27640) 42326..43306 + 981 WP_009310076 IS5-like element ISKpn26 family transposase -
HV193_RS28455 43288..43473 + 186 WP_310585744 hypothetical protein -
HV193_RS27625 (HV193_27645) 43478..43762 + 285 WP_023316401 hypothetical protein -
HV193_RS27630 (HV193_27650) 43786..44004 + 219 WP_023316402 hypothetical protein -
HV193_RS27635 (HV193_27655) 44005..44316 + 312 WP_023316403 hypothetical protein -
HV193_RS27640 (HV193_27660) 44383..44787 + 405 WP_023316404 hypothetical protein -
HV193_RS27645 (HV193_27665) 44784..45074 + 291 WP_020323516 hypothetical protein -
HV193_RS27650 (HV193_27670) 45082..45480 + 399 WP_072156904 hypothetical protein -
HV193_RS27655 (HV193_27675) 45552..48191 + 2640 WP_047718076 type IV secretion system protein TraC virb4
HV193_RS27660 (HV193_27680) 48191..48580 + 390 WP_032436749 type-F conjugative transfer system protein TrbI -
HV193_RS27665 (HV193_27685) 48580..49206 + 627 WP_023307538 type-F conjugative transfer system protein TraW traW
HV193_RS27670 (HV193_27690) 49250..50209 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
HV193_RS27675 (HV193_27695) 50222..50860 + 639 WP_020321224 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV193_RS27680 (HV193_27700) 50919..52874 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV193_RS27685 (HV193_27705) 52907..53188 + 282 WP_022644736 hypothetical protein -
HV193_RS27690 (HV193_27710) 53178..53405 + 228 WP_012540032 conjugal transfer protein TrbE -
HV193_RS27695 (HV193_27715) 53416..53742 + 327 WP_020323521 hypothetical protein -
HV193_RS27700 (HV193_27720) 53763..54515 + 753 WP_023316406 type-F conjugative transfer system pilin assembly protein TraF traF
HV193_RS27705 (HV193_27725) 54970..55209 + 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
HV193_RS27710 (HV193_27730) 55181..55738 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV193_RS27715 (HV193_27735) 55784..56227 + 444 WP_020804675 F-type conjugal transfer protein TrbF -
HV193_RS27720 (HV193_27740) 56205..57584 + 1380 WP_162492049 conjugal transfer pilus assembly protein TraH traH
HV193_RS27725 (HV193_27745) 57584..60433 + 2850 WP_032744228 conjugal transfer mating-pair stabilization protein TraG traG
HV193_RS27730 (HV193_27750) 60439..60966 + 528 WP_020803849 hypothetical protein -
HV193_RS28265 61149..61817 + 669 WP_020803846 hypothetical protein -
HV193_RS27740 (HV193_27760) 61841..62101 + 261 WP_020803850 hypothetical protein -
HV193_RS27745 (HV193_27765) 62173..64485 + 2313 WP_020803851 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   6417 GenBank   NZ_CP056533
Plasmid name   pRHBSTW-00433_4 Incompatibility group   IncFII
Plasmid size   74689 bp Coordinate of oriT [Strand]   35047..35095 [-]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00433

Cargo genes

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