Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121324
Name   oriT_p12084-FII in_silico
Organism   Klebsiella michiganensis strain 12084
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MZ398018 (153646..153695 [-], 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_p12084-FII
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13460 GenBank   WP_040224080
Name   traI_LO867_RS01005_p12084-FII insolico UniProt ID   A0A7W3BA55
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190352.82 Da        Isoelectric Point: 5.9133

>WP_040224080.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMNVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
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)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   15763 GenBank   WP_023329042
Name   traD_LO867_RS01000_p12084-FII 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: 85943.90 Da        Isoelectric Point: 5.0577

>WP_023329042.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEARESEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 153088..182332

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LO867_RS00775 148106..148456 + 351 WP_004182068 hypothetical protein -
LO867_RS00780 149092..149448 + 357 WP_004152717 hypothetical protein -
LO867_RS00785 149509..149721 + 213 WP_004182070 hypothetical protein -
LO867_RS00790 149732..149956 + 225 WP_020325128 hypothetical protein -
LO867_RS00795 150037..150357 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
LO867_RS00800 150347..150625 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
LO867_RS00805 150626..151039 + 414 WP_004182074 type II toxin-antitoxin system HigA family antitoxin -
LO867_RS00810 151872..152693 + 822 WP_004182076 DUF932 domain-containing protein -
LO867_RS00815 152726..153055 + 330 WP_011977736 DUF5983 family protein -
LO867_RS00820 153088..153573 - 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
LO867_RS00825 153964..154380 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
LO867_RS00830 154580..155299 + 720 WP_016831034 conjugal transfer protein TrbJ -
LO867_RS00835 155432..155638 + 207 WP_171773970 TraY domain-containing protein -
LO867_RS00840 155700..156068 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LO867_RS00845 156082..156387 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LO867_RS00850 156407..156973 + 567 WP_016831035 type IV conjugative transfer system protein TraE traE
LO867_RS00855 156960..157700 + 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
LO867_RS00860 157700..159124 + 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
LO867_RS00865 159117..159713 + 597 Protein_175 conjugal transfer pilus-stabilizing protein TraP -
LO867_RS00870 159736..160320 + 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
LO867_RS00875 160452..160862 + 411 WP_016831039 hypothetical protein -
LO867_RS00880 160867..161156 + 290 Protein_178 hypothetical protein -
LO867_RS00885 161180..161398 + 219 WP_014386199 hypothetical protein -
LO867_RS00890 161399..161710 + 312 WP_014386200 hypothetical protein -
LO867_RS00895 161777..162181 + 405 WP_016831042 hypothetical protein -
LO867_RS00900 162224..162613 + 390 WP_023158009 hypothetical protein -
LO867_RS00905 162621..163019 + 399 WP_023158008 hypothetical protein -
LO867_RS00910 163091..165730 + 2640 WP_023158007 type IV secretion system protein TraC virb4
LO867_RS00915 165730..166119 + 390 WP_004167468 type-F conjugative transfer system protein TrbI -
LO867_RS00920 166119..166754 + 636 WP_023158006 type-F conjugative transfer system protein TraW traW
LO867_RS00925 166789..167190 + 402 WP_023158005 hypothetical protein -
LO867_RS00930 167187..168176 + 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
LO867_RS00935 168452..169099 + 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
LO867_RS00940 169158..171113 + 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LO867_RS00945 171145..171399 + 255 WP_015065558 conjugal transfer protein TrbE -
LO867_RS00950 171377..171625 + 249 WP_004152675 hypothetical protein -
LO867_RS00955 171638..171964 + 327 WP_015065534 hypothetical protein -
LO867_RS00960 171985..172737 + 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
LO867_RS00965 172748..172987 + 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
LO867_RS00970 172959..173516 + 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LO867_RS00975 173562..174005 + 444 WP_023158001 F-type conjugal transfer protein TrbF -
LO867_RS00980 173983..175362 + 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
LO867_RS00985 175362..178211 + 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
LO867_RS00990 178217..178744 + 528 WP_029498351 conjugal transfer protein TraS -
LO867_RS00995 178934..179665 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
LO867_RS01000 180023..182332 + 2310 WP_023329042 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21751 GenBank   NZ_MZ398018
Plasmid name   p12084-FII Incompatibility group   IncFII
Plasmid size   193645 bp Coordinate of oriT [Strand]   153646..153695 [-]
Host baterium   Klebsiella michiganensis strain 12084

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merE, merD, merA, merF, merP, merT, merR2, arsC, arsB, arsR, arsD, arsA, arsH, pcoE, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9