Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101743
Name   oriT_pRHBSTW-00189_4 in_silico
Organism   Klebsiella grimontii strain RHBSTW-00189
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXQY010000004 (74322..74370 [-], 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-00189_4
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1474 GenBank   WP_182189506
Name   traI_HV116_RS28655_pRHBSTW-00189_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: 190481.00 Da        Isoelectric Point: 5.9706

>WP_182189506.1 conjugative transfer relaxase/helicase TraI [Klebsiella grimontii]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQIFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIAFGKIYQNTLRADVES
LGYRTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTSDASVVRQAPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(969-1156)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   589 GenBank   WP_004197733
Name   WP_004197733_pRHBSTW-00189_4 insolico UniProt ID   A0A0E3KB00
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14835.90 Da        Isoelectric Point: 4.6012

>WP_004197733.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
AlphaFold DB A0A0E3KB00


T4CP

ID   1151 GenBank   WP_064343438
Name   traD_HV116_RS28650_pRHBSTW-00189_4 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85584.66 Da        Isoelectric Point: 5.3307

>WP_064343438.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGEQPEPVSQPA
PAVMTVTPAPVKSPPTTKRPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAGTAATASSAGTPAAAAGGTE
QVLAQQSAEQGQAMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDLEIGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 73764..103907

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV116_RS28435 (HV116_28440) 68866..69216 + 351 WP_004153414 hypothetical protein -
HV116_RS28440 (HV116_28445) 69846..70199 + 354 WP_004152748 hypothetical protein -
HV116_RS28445 (HV116_28450) 70256..70603 + 348 WP_004152749 hypothetical protein -
HV116_RS28450 (HV116_28455) 70698..70844 + 147 WP_004152750 hypothetical protein -
HV116_RS28455 (HV116_28460) 70895..71728 + 834 WP_004152751 N-6 DNA methylase -
HV116_RS28460 (HV116_28465) 72548..73369 + 822 WP_004152492 DUF932 domain-containing protein -
HV116_RS28465 (HV116_28470) 73402..73731 + 330 WP_011977736 DUF5983 family protein -
HV116_RS28470 (HV116_28475) 73764..74249 - 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
HV116_RS28475 (HV116_28480) 74682..75071 + 390 WP_004197733 conjugal transfer relaxosome DNA-binding protein TraM -
HV116_RS28480 (HV116_28485) 75310..75984 + 675 WP_004197737 hypothetical protein -
HV116_RS28485 (HV116_28490) 76134..76352 + 219 WP_172619300 TraY domain-containing protein -
HV116_RS28490 (HV116_28495) 76402..76770 + 369 WP_042946346 type IV conjugative transfer system pilin TraA -
HV116_RS28495 (HV116_28500) 76784..77089 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HV116_RS28500 (HV116_28505) 77109..77675 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
HV116_RS28505 (HV116_28510) 77662..78402 + 741 WP_032738531 type-F conjugative transfer system secretin TraK traK
HV116_RS28510 (HV116_28515) 78402..79826 + 1425 WP_042946342 F-type conjugal transfer pilus assembly protein TraB traB
HV116_RS28515 (HV116_28520) 79819..80415 + 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
HV116_RS28520 (HV116_28525) 80438..81007 + 570 WP_023340942 type IV conjugative transfer system lipoprotein TraV traV
HV116_RS28525 (HV116_28530) 81139..81549 + 411 WP_020805613 hypothetical protein -
HV116_RS28530 (HV116_28535) 81554..81838 + 285 WP_023316401 hypothetical protein -
HV116_RS28535 (HV116_28540) 81862..82080 + 219 WP_023316402 hypothetical protein -
HV116_RS28540 (HV116_28545) 82081..82392 + 312 WP_023316403 hypothetical protein -
HV116_RS28545 (HV116_28550) 82459..82863 + 405 WP_042939116 hypothetical protein -
HV116_RS28550 (HV116_28555) 82860..83150 + 291 WP_023340940 hypothetical protein -
HV116_RS28555 (HV116_28560) 83158..83556 + 399 WP_074186017 hypothetical protein -
HV116_RS28560 (HV116_28565) 83628..86267 + 2640 WP_042946320 type IV secretion system protein TraC virb4
HV116_RS28565 (HV116_28570) 86264..86656 + 393 WP_042946321 type-F conjugative transfer system protein TrbI -
HV116_RS28570 (HV116_28575) 86656..87282 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HV116_RS28575 (HV116_28580) 87326..88285 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
HV116_RS28580 (HV116_28585) 88300..88848 + 549 WP_022631518 hypothetical protein -
HV116_RS28585 (HV116_28590) 89569..90171 + 603 WP_022631520 hypothetical protein -
HV116_RS28590 (HV116_28595) 90315..90962 + 648 WP_039698503 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV116_RS28595 (HV116_28600) 91021..92976 + 1956 WP_049192820 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV116_RS28600 (HV116_28605) 93008..93262 + 255 WP_004195500 conjugal transfer protein TrbE -
HV116_RS28605 (HV116_28610) 93240..93488 + 249 WP_004152675 hypothetical protein -
HV116_RS28610 (HV116_28615) 93501..93827 + 327 WP_004194451 hypothetical protein -
HV116_RS28615 (HV116_28620) 93848..94600 + 753 WP_042946327 type-F conjugative transfer system pilin assembly protein TraF traF
HV116_RS28620 (HV116_28625) 94611..94850 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
HV116_RS28625 (HV116_28630) 94822..95394 + 573 WP_009309876 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV116_RS28630 (HV116_28635) 95387..95815 + 429 WP_004152689 hypothetical protein -
HV116_RS28635 (HV116_28640) 95802..97172 + 1371 WP_009309877 conjugal transfer pilus assembly protein TraH traH
HV116_RS28640 (HV116_28645) 97172..100045 + 2874 WP_009309878 conjugal transfer mating-pair stabilization protein TraG traG
HV116_RS28645 (HV116_28650) 100780..101472 + 693 WP_009309879 hypothetical protein -
HV116_RS28650 (HV116_28655) 101598..103907 + 2310 WP_064343438 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2187 GenBank   NZ_JABXQY010000004
Plasmid name   pRHBSTW-00189_4 Incompatibility group   IncFIB
Plasmid size   115072 bp Coordinate of oriT [Strand]   74322..74370 [-]
Host baterium   Klebsiella grimontii strain RHBSTW-00189

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9