Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101890
Name   oriT_ZR-9|unnamed1 in_silico
Organism   Klebsiella huaxiensis strain ZR-9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAPQEX020000002 (53834..53882 [+], 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_ZR-9|unnamed1
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1550 GenBank   WP_130983534
Name   traI_OXR69_RS30200_ZR-9|unnamed1 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: 190629.30 Da        Isoelectric Point: 6.1046

>WP_130983534.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQIFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIAFGKIYQNTLRADVES
LGYRTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTSDASVVRQAPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGNHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPDSLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIQHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(11-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   627 GenBank   WP_032426796
Name   WP_032426796_ZR-9|unnamed1 insolico UniProt ID   _
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15036.10 Da        Isoelectric Point: 4.5326

>WP_032426796.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKEKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMRTFFPDEQEEADE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   1224 GenBank   WP_042946329
Name   traD_OXR69_RS30205_ZR-9|unnamed1 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: 85713.82 Da        Isoelectric Point: 5.3307

>WP_042946329.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASWPDDAGSHAGEQPEPVSQPA
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: 26125..51413

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OXR69_RS30205 (OXR69_030205) 26125..28434 - 2310 WP_042946329 type IV conjugative transfer system coupling protein TraD virb4
OXR69_RS30210 (OXR69_030210) 28563..29252 - 690 WP_023316411 hypothetical protein -
OXR69_RS30215 (OXR69_030215) 29445..29849 - 405 Protein_25 complement resistance protein TraT -
OXR69_RS30220 (OXR69_030220) 29859..30461 - 603 WP_013214035 conjugal transfer protein TraS -
OXR69_RS30225 (OXR69_030225) 30484..33306 - 2823 WP_032426775 conjugal transfer mating-pair stabilization protein TraG traG
OXR69_RS30230 (OXR69_030230) 33306..34685 - 1380 WP_072159474 conjugal transfer pilus assembly protein TraH traH
OXR69_RS30235 (OXR69_030235) 34663..35106 - 444 WP_023287131 F-type conjugal transfer protein TrbF -
OXR69_RS30240 (OXR69_030240) 35152..35709 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
OXR69_RS30245 (OXR69_030245) 35681..35920 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
OXR69_RS30250 (OXR69_030250) 35931..36683 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
OXR69_RS30255 (OXR69_030255) 36704..37030 - 327 WP_004144402 hypothetical protein -
OXR69_RS30260 (OXR69_030260) 37043..37291 - 249 WP_004152675 hypothetical protein -
OXR69_RS30265 (OXR69_030265) 37269..37523 - 255 WP_004195500 conjugal transfer protein TrbE -
OXR69_RS30270 (OXR69_030270) 37555..39510 - 1956 WP_032426778 type-F conjugative transfer system mating-pair stabilization protein TraN traN
OXR69_RS30275 (OXR69_030275) 39569..40207 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
OXR69_RS30280 (OXR69_030280) 40220..41209 - 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
OXR69_RS30285 (OXR69_030285) 41206..41595 - 390 WP_004194992 hypothetical protein -
OXR69_RS30290 (OXR69_030290) 41637..42263 - 627 WP_009309871 type-F conjugative transfer system protein TraW traW
OXR69_RS30295 (OXR69_030295) 42263..42652 - 390 WP_032426787 type-F conjugative transfer system protein TrbI -
OXR69_RS30300 (OXR69_030300) 42652..45291 - 2640 WP_032426788 type IV secretion system protein TraC virb4
OXR69_RS30305 (OXR69_030305) 45363..45761 - 399 WP_015065631 hypothetical protein -
OXR69_RS30310 (OXR69_030310) 45786..46190 - 405 WP_023320104 hypothetical protein -
OXR69_RS30315 (OXR69_030315) 46235..46573 - 339 WP_032426789 hypothetical protein -
OXR69_RS30320 (OXR69_030320) 46574..46792 - 219 WP_004171484 hypothetical protein -
OXR69_RS30325 (OXR69_030325) 46816..47106 - 291 WP_032426790 hypothetical protein -
OXR69_RS30330 (OXR69_030330) 47135..47533 - 399 WP_223294961 hypothetical protein -
OXR69_RS30335 (OXR69_030335) 47688..48257 - 570 WP_032426791 type IV conjugative transfer system lipoprotein TraV traV
OXR69_RS30340 (OXR69_030340) 48371..49795 - 1425 WP_032426793 F-type conjugal transfer pilus assembly protein TraB traB
OXR69_RS30345 (OXR69_030345) 49795..50535 - 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
OXR69_RS30350 (OXR69_030350) 50522..51088 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
OXR69_RS30355 (OXR69_030355) 51108..51413 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
OXR69_RS30360 (OXR69_030360) 51427..51795 - 369 WP_032426794 type IV conjugative transfer system pilin TraA -
OXR69_RS30365 (OXR69_030365) 51859..52023 - 165 WP_032426810 TraY domain-containing protein -
OXR69_RS30370 (OXR69_030370) 52199..52891 - 693 WP_032426795 conjugal transfer protein TrbJ -
OXR69_RS30375 (OXR69_030375) 53129..53521 - 393 WP_032426796 conjugal transfer relaxosome DNA-binding protein TraM -
OXR69_RS30380 (OXR69_030380) 54027..54449 + 423 WP_020315406 transglycosylase SLT domain-containing protein -
OXR69_RS30385 (OXR69_030385) 54472..55014 - 543 WP_032426797 antirestriction protein -
OXR69_RS30390 (OXR69_030390) 55207..55377 + 171 WP_164881277 hypothetical protein -
OXR69_RS30395 (OXR69_030395) 55663..55878 - 216 Protein_61 SAM-dependent DNA methyltransferase -
OXR69_RS30400 (OXR69_030400) 55976..56206 - 231 WP_020314756 hypothetical protein -

Host bacterium

ID   2334 GenBank   NZ_JAPQEX020000002
Plasmid name   ZR-9|unnamed1 Incompatibility group   -
Plasmid size   118459 bp Coordinate of oriT [Strand]   53834..53882 [+]
Host baterium   Klebsiella huaxiensis strain ZR-9

Cargo genes

Drug resistance gene   mph(E), msr(E)
Virulence gene   -
Metal resistance gene   merR2, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -