Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122146
Name   oriT_pn-96 in_silico
Organism   Klebsiella quasipneumoniae strain Kpn-96
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JANAVU010000002 (37787..37835 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pn-96
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13958 GenBank   WP_013023833
Name   traI_NLX98_RS26380_pn-96 insolico UniProt ID   D4HQM5
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190722.84 Da        Isoelectric Point: 6.3385

>WP_013023833.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKDAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDAFVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQLRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLTQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

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

(577-629)

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   16375 GenBank   WP_013023832
Name   traD_NLX98_RS26375_pn-96 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: 85974.10 Da        Isoelectric Point: 5.1149

>WP_013023832.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDYVEIGGNF

  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: 37229..67115

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NLX98_RS26160 (NLX98_26115) 33237..33593 + 357 WP_013023814 hypothetical protein -
NLX98_RS26165 (NLX98_26120) 33654..33866 + 213 WP_013023815 hypothetical protein -
NLX98_RS26170 (NLX98_26125) 33877..34101 + 225 WP_004152719 hypothetical protein -
NLX98_RS26175 (NLX98_26130) 34182..34502 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
NLX98_RS26180 (NLX98_26135) 34492..34770 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
NLX98_RS26185 (NLX98_26140) 34771..35184 + 414 WP_013023817 type II toxin-antitoxin system HigA family antitoxin -
NLX98_RS26190 (NLX98_26145) 36013..36834 + 822 WP_004152492 DUF932 domain-containing protein -
NLX98_RS26195 (NLX98_26150) 36867..37196 + 330 WP_011977736 DUF5983 family protein -
NLX98_RS26200 (NLX98_26155) 37229..37714 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
NLX98_RS26205 (NLX98_26160) 38146..38538 + 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
NLX98_RS26210 (NLX98_26165) 38768..39469 + 702 WP_004194113 hypothetical protein -
NLX98_RS26215 (NLX98_26170) 39555..39755 + 201 WP_004194116 TraY domain-containing protein -
NLX98_RS26220 (NLX98_26175) 39824..40192 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
NLX98_RS26225 (NLX98_26180) 40206..40511 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
NLX98_RS26230 (NLX98_26185) 40531..41097 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
NLX98_RS26235 (NLX98_26190) 41084..41824 + 741 WP_013023821 type-F conjugative transfer system secretin TraK traK
NLX98_RS26240 (NLX98_26195) 41824..43248 + 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
NLX98_RS26245 (NLX98_26200) 43362..43946 + 585 WP_013023822 type IV conjugative transfer system lipoprotein TraV traV
NLX98_RS26250 (NLX98_26205) 44078..44488 + 411 WP_009309869 hypothetical protein -
NLX98_RS26255 (NLX98_26210) 44594..44812 + 219 WP_015344987 hypothetical protein -
NLX98_RS26260 (NLX98_26215) 44813..45124 + 312 WP_015344986 hypothetical protein -
NLX98_RS26265 (NLX98_26220) 45191..45595 + 405 WP_004197817 hypothetical protein -
NLX98_RS26270 (NLX98_26225) 45859..46827 - 969 WP_077256550 IS5-like element IS903B family transposase -
NLX98_RS26275 (NLX98_26230) 47037..47435 + 399 WP_013609531 hypothetical protein -
NLX98_RS26280 (NLX98_26235) 47507..50146 + 2640 WP_013023824 type IV secretion system protein TraC virb4
NLX98_RS26285 (NLX98_26240) 50146..50535 + 390 WP_004197815 type-F conjugative transfer system protein TrbI -
NLX98_RS26290 (NLX98_26245) 50535..51161 + 627 WP_009309871 type-F conjugative transfer system protein TraW traW
NLX98_RS26295 (NLX98_26250) 51203..51592 + 390 WP_004194992 hypothetical protein -
NLX98_RS26300 (NLX98_26255) 51589..52578 + 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
NLX98_RS26305 (NLX98_26260) 52591..53229 + 639 WP_011977786 type-F conjugative transfer system pilin assembly protein TrbC trbC
NLX98_RS26310 (NLX98_26265) 53288..55243 + 1956 WP_013023827 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NLX98_RS26315 (NLX98_26270) 55275..55529 + 255 WP_004152674 conjugal transfer protein TrbE -
NLX98_RS26320 (NLX98_26275) 55507..55755 + 249 WP_004152675 hypothetical protein -
NLX98_RS26325 (NLX98_26280) 55768..56094 + 327 WP_004152676 hypothetical protein -
NLX98_RS26330 (NLX98_26285) 56115..56867 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
NLX98_RS26335 (NLX98_26290) 56878..57117 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
NLX98_RS26340 (NLX98_26295) 57089..57646 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NLX98_RS26345 (NLX98_26300) 57692..58135 + 444 WP_013023828 F-type conjugal transfer protein TrbF -
NLX98_RS26350 (NLX98_26305) 58113..59492 + 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
NLX98_RS26355 (NLX98_26310) 59492..62341 + 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
NLX98_RS26360 (NLX98_26315) 62344..62877 + 534 WP_014343486 conjugal transfer protein TraS -
NLX98_RS26365 (NLX98_26320) 63063..63794 + 732 WP_013023830 conjugal transfer complement resistance protein TraT -
NLX98_RS26370 (NLX98_26325) 63987..64676 + 690 WP_013023831 hypothetical protein -
NLX98_RS26375 (NLX98_26330) 64803..67115 + 2313 WP_013023832 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   22573 GenBank   NZ_JANAVU010000002
Plasmid name   pn-96 Incompatibility group   IncFII
Plasmid size   307284 bp Coordinate of oriT [Strand]   37787..37835 [-]
Host baterium   Klebsiella quasipneumoniae strain Kpn-96

Cargo genes

Drug resistance gene   blaCTX-M-15, blaTEM-1B, formA
Virulence gene   pla
Metal resistance gene   pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE, fecD, fecE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9