Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103708
Name   oriT_JS187-vir|unnamed3 in_silico
Organism   Klebsiella pneumoniae strain JS187-vir
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MZ475702 (71725..71774 [-], 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_JS187-vir|unnamed3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2749 GenBank   WP_014343483
Name   traI_LL121_RS00645_JS187-vir|unnamed3 insolico UniProt ID   A0A0H3H1C0
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190459.18 Da        Isoelectric Point: 6.1353

>WP_014343483.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREATDARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGINAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVTF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRASTRM
ILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDLHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
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)

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

(634-713)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1155)


  Protein structure


Source ID Structure
AlphaFold DB A0A0H3H1C0


T4CP

ID   2586 GenBank   WP_110133658
Name   traD_LL121_RS00640_JS187-vir|unnamed3 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 84917.94 Da        Isoelectric Point: 5.0045

>WP_110133658.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDAWLADDQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  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: 71167..99622

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LL121_RS00430 (MGOKJAAN_00085) 66323..66640 + 318 WP_014343505 hypothetical protein -
LL121_RS00435 (MGOKJAAN_00086) 67481..67837 + 357 WP_014343501 hypothetical protein -
LL121_RS00440 (MGOKJAAN_00087) 67898..68110 + 213 WP_014343500 hypothetical protein -
LL121_RS00445 (MGOKJAAN_00088) 68121..68345 + 225 WP_014343499 hypothetical protein -
LL121_RS00450 (MGOKJAAN_00089) 68426..68746 + 321 WP_014343498 type II toxin-antitoxin system RelE/ParE family toxin -
LL121_RS00455 (MGOKJAAN_00090) 68736..69014 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
LL121_RS00460 (MGOKJAAN_00091) 69018..69122 + 105 Protein_91 transcriptional regulator -
LL121_RS00465 (MGOKJAAN_00092) 69951..70772 + 822 WP_004152492 DUF932 domain-containing protein -
LL121_RS00470 (MGOKJAAN_00093) 70805..71134 + 330 WP_013214015 DUF5983 family protein -
LL121_RS00475 (MGOKJAAN_00094) 71167..71652 - 486 WP_014343495 transglycosylase SLT domain-containing protein virB1
LL121_RS00480 (MGOKJAAN_00095) 72043..72459 + 417 WP_014343494 conjugal transfer relaxosome DNA-binding protein TraM -
LL121_RS00485 (MGOKJAAN_00096) 72659..73396 + 738 WP_013214018 conjugal transfer protein TrbJ -
LL121_RS00490 73511..73717 + 207 WP_171773970 TraY domain-containing protein -
LL121_RS00495 (MGOKJAAN_00097) 73779..74147 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LL121_RS00500 (MGOKJAAN_00098) 74161..74466 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LL121_RS00505 (MGOKJAAN_00099) 74486..75052 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
LL121_RS00510 (MGOKJAAN_00100) 75039..75779 + 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
LL121_RS00515 (MGOKJAAN_00101) 75779..77203 + 1425 WP_013214020 F-type conjugal transfer pilus assembly protein TraB traB
LL121_RS00520 (MGOKJAAN_00102) 77275..77859 + 585 WP_014343493 type IV conjugative transfer system lipoprotein TraV traV
LL121_RS00525 (MGOKJAAN_00103) 78182..78400 + 219 WP_004195468 hypothetical protein -
LL121_RS00530 (MGOKJAAN_00104) 78401..78712 + 312 WP_013214022 hypothetical protein -
LL121_RS00535 (MGOKJAAN_00105) 78779..79183 + 405 WP_004197817 hypothetical protein -
LL121_RS00540 (MGOKJAAN_00107) 79560..79958 + 399 WP_014343490 hypothetical protein -
LL121_RS00545 (MGOKJAAN_00108) 80030..82669 + 2640 WP_013214024 type IV secretion system protein TraC virb4
LL121_RS00550 (MGOKJAAN_00109) 82669..83058 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
LL121_RS00555 (MGOKJAAN_00110) 83058..83693 + 636 WP_013214026 type-F conjugative transfer system protein TraW traW
LL121_RS00560 (MGOKJAAN_00111) 83728..84129 + 402 WP_004194979 hypothetical protein -
LL121_RS00565 (MGOKJAAN_00112) 84126..85115 + 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
LL121_RS00570 (MGOKJAAN_00113) 85128..85766 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
LL121_RS00575 (MGOKJAAN_00114) 85825..87780 + 1956 WP_014343489 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LL121_RS00580 (MGOKJAAN_00115) 87812..88066 + 255 WP_004152674 conjugal transfer protein TrbE -
LL121_RS00585 (MGOKJAAN_00116) 88044..88292 + 249 WP_013214029 hypothetical protein -
LL121_RS00590 (MGOKJAAN_00117) 88305..88631 + 327 WP_013214030 hypothetical protein -
LL121_RS00595 (MGOKJAAN_00118) 88652..89404 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
LL121_RS00600 (MGOKJAAN_00119) 89415..89654 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
LL121_RS00605 (MGOKJAAN_00120) 89626..90183 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LL121_RS00610 (MGOKJAAN_00121) 90229..90672 + 444 WP_014343488 F-type conjugal transfer protein TrbF -
LL121_RS00615 (MGOKJAAN_00122) 90650..92029 + 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
LL121_RS00620 (MGOKJAAN_00123) 92029..94878 + 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
LL121_RS00625 (MGOKJAAN_00124) 94881..95414 + 534 WP_014343486 conjugal transfer protein TraS -
LL121_RS00630 (MGOKJAAN_00125) 95600..96331 + 732 WP_013023830 conjugal transfer complement resistance protein TraT -
LL121_RS00635 (MGOKJAAN_00126) 96524..97213 + 690 WP_014343485 hypothetical protein -
LL121_RS00640 (MGOKJAAN_00127) 97340..99622 + 2283 WP_110133658 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4151 GenBank   NZ_MZ475702
Plasmid name   JS187-vir|unnamed3 Incompatibility group   IncFII
Plasmid size   110080 bp Coordinate of oriT [Strand]   71725..71774 [-]
Host baterium   Klebsiella pneumoniae strain JS187-vir

Cargo genes

Drug resistance gene   blaKPC-2, blaTEM-1B
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9