Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120006
Name   oriT_pINF352_1 in_silico
Organism   Klebsiella variicola strain INF352
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP083791 (248742..248791 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pINF352_1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12611 GenBank   WP_015065542
Name   traI_LB484_RS27630_pINF352_1 insolico UniProt ID   K7R3U7
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190318.03 Da        Isoelectric Point: 6.2890

>WP_015065542.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALAVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
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)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   14809 GenBank   WP_015065541
Name   traD_LB484_RS27635_pINF352_1 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: 86025.00 Da        Isoelectric Point: 5.0577

>WP_015065541.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 219335..249349

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LB484_RS27635 (LB484_27635) 219335..221647 - 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4
LB484_RS27640 (LB484_27640) 221776..222465 - 690 WP_015065540 hypothetical protein -
LB484_RS27645 (LB484_27645) 222657..223388 - 732 WP_032329926 conjugal transfer complement resistance protein TraT -
LB484_RS27650 (LB484_27650) 223697..224221 - 525 WP_015065538 hypothetical protein -
LB484_RS27655 (LB484_27655) 224232..227075 - 2844 WP_023157999 conjugal transfer mating-pair stabilization protein TraG traG
LB484_RS27660 (LB484_27660) 227075..228454 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
LB484_RS27665 (LB484_27665) 228432..228875 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
LB484_RS27670 (LB484_27670) 228921..229478 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LB484_RS27675 (LB484_27675) 229450..229689 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
LB484_RS27680 (LB484_27680) 229700..230452 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
LB484_RS27685 (LB484_27685) 230473..230799 - 327 WP_015065534 hypothetical protein -
LB484_RS27690 (LB484_27690) 230812..231060 - 249 WP_004152675 hypothetical protein -
LB484_RS27695 (LB484_27695) 231038..231292 - 255 WP_015065558 conjugal transfer protein TrbE -
LB484_RS27700 (LB484_27700) 231324..233279 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LB484_RS27705 (LB484_27705) 233338..233985 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
LB484_RS27710 (LB484_27710) 234064..234240 - 177 WP_162866177 hypothetical protein -
LB484_RS27715 (LB484_27715) 234261..235250 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
LB484_RS27720 (LB484_27720) 235247..235648 - 402 WP_023158005 hypothetical protein -
LB484_RS27725 (LB484_27725) 235683..236318 - 636 WP_023158006 type-F conjugative transfer system protein TraW traW
LB484_RS27730 (LB484_27730) 236318..236707 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
LB484_RS27735 (LB484_27735) 236707..239346 - 2640 WP_023158007 type IV secretion system protein TraC virb4
LB484_RS27740 (LB484_27740) 239418..239816 - 399 WP_023158008 hypothetical protein -
LB484_RS27745 (LB484_27745) 239824..240213 - 390 WP_023158009 hypothetical protein -
LB484_RS27750 (LB484_27750) 240256..240660 - 405 WP_016831042 hypothetical protein -
LB484_RS27755 (LB484_27755) 240727..241038 - 312 WP_014386200 hypothetical protein -
LB484_RS27760 (LB484_27760) 241039..241257 - 219 WP_014386199 hypothetical protein -
LB484_RS27765 (LB484_27765) 241281..241570 - 290 Protein_256 hypothetical protein -
LB484_RS27770 (LB484_27770) 241575..241985 - 411 WP_016831039 hypothetical protein -
LB484_RS27775 (LB484_27775) 242117..242701 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
LB484_RS27780 (LB484_27780) 242724..243320 - 597 Protein_259 conjugal transfer pilus-stabilizing protein TraP -
LB484_RS27785 (LB484_27785) 243313..244737 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
LB484_RS27790 (LB484_27790) 244737..245477 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
LB484_RS27795 (LB484_27795) 245464..246030 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
LB484_RS27800 (LB484_27800) 246050..246355 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LB484_RS27805 (LB484_27805) 246369..246737 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LB484_RS27810 (LB484_27810) 246799..247005 - 207 WP_171773970 TraY domain-containing protein -
LB484_RS27815 (LB484_27815) 247138..247857 - 720 WP_016831034 conjugal transfer protein TrbJ -
LB484_RS27820 (LB484_27820) 248057..248473 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
LB484_RS27825 (LB484_27825) 248864..249349 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
LB484_RS27830 (LB484_27830) 249382..249711 - 330 WP_011977736 DUF5983 family protein -
LB484_RS27835 (LB484_27835) 249744..250565 - 822 WP_004182076 DUF932 domain-containing protein -
LB484_RS27840 (LB484_27840) 251393..251956 - 564 WP_004182054 methyltransferase -
LB484_RS27845 (LB484_27845) 252004..253359 - 1356 WP_004182052 DUF3560 domain-containing protein -
LB484_RS27850 (LB484_27850) 253411..253641 - 231 WP_001568051 hypothetical protein -
LB484_RS27855 (LB484_27855) 253733..253960 - 228 WP_004182050 hypothetical protein -

Host bacterium

ID   20436 GenBank   NZ_CP083791
Plasmid name   pINF352_1 Incompatibility group   IncFIB
Plasmid size   271926 bp Coordinate of oriT [Strand]   248742..248791 [+]
Host baterium   Klebsiella variicola strain INF352

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, blaCTX-M-15, dfrA14, qnrB1, tet(A), aac(6')-Ib-cr, blaOXA-1
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -