Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120819
Name   oriT_p4_SCLZS62 in_silico
Organism   Raoultella planticola strain SCLZS62
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP082172 (5609..5657 [-], 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_p4_SCLZS62
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13129 GenBank   WP_064359958
Name   traI_K6028_RS27310_p4_SCLZS62 insolico UniProt ID   A0A7D6JMG2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 189724.34 Da        Isoelectric Point: 5.9228

>WP_064359958.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAETLELEGKVDKQVFTALLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALEQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKETIDPAEKMVEWMNT
LKETGFDIRGYREAADARAKELASAPAAPVKTDGPDIGDVVTNAIAGLSDRKVQFTYADLLARTVGQLEA
KPGVFERARGGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVTVTPDATVVRLAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQNGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGRQTTADIISEPDKGARYNRLAQEFAVSVREGQESVAQISGTREQGVLNGIIRDTLKNEGALGTKEM
AITALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVANGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQALSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDATRTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIATQKAGLHTPAEQVIHLSIPLLESEALTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTKVLEGKDAVPPLMDSVPGSLMADLTSGQRAATRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQAPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIQK
ALSEGEILPAGQPATLYEALVKDYADRTPEAQLQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVTGGRKQMASFESAYVGLSRMKLHVQVYTDSREGWVNAIQASPSKATAHDILAP
RNERAVKTADLLFGRAQPLNETAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKNAGIW
LSPLTDKDGRLEAIGGDGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMGRQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLSREKTLG
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)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   7323 GenBank   WP_020805752
Name   WP_020805752_p4_SCLZS62 insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   15410 GenBank   WP_064343540
Name   traD_K6028_RS27305_p4_SCLZS62 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 85378.44 Da        Isoelectric Point: 4.9296

>WP_064343540.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTVCVVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIQRRLDARVDGRLSALLEAREAEGSLARALFTPDEPVSESAEEKAGVQPEQTKPAEDS
VLPVPVKTSSKAAEGAGKTPDVPLSGAPVTRVKTVPLIRPEPAASVTGTAAAASTAAVSATAGGTEQELA
QQPVEADQDMLPAGMNEDGVIEDMQAYDAWLAGEQTQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 5051..33022

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
K6028_RS27105 (K6028_27105) 601..732 + 132 WP_222826737 DUF5431 family protein -
K6028_RS27110 (K6028_27110) 777..1925 + 1149 Protein_2 IS3 family transposase -
K6028_RS27115 (K6028_27115) 2011..2331 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
K6028_RS27120 (K6028_27120) 2321..2597 + 277 Protein_4 helix-turn-helix transcriptional regulator -
K6028_RS27125 (K6028_27125) 2598..3011 + 414 WP_023287139 type II toxin-antitoxin system HigA family antitoxin -
K6028_RS27130 (K6028_27130) 3836..4658 + 823 Protein_6 DUF932 domain-containing protein -
K6028_RS27135 (K6028_27135) 4691..5019 + 329 Protein_7 DUF5983 family protein -
K6028_RS27140 (K6028_27140) 5051..5536 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
K6028_RS27145 (K6028_27145) 5968..6360 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
K6028_RS27150 (K6028_27150) 6598..7062 + 465 WP_222826738 hypothetical protein -
K6028_RS27155 (K6028_27155) 7383..7583 + 201 WP_048289787 TraY domain-containing protein -
K6028_RS27160 (K6028_27160) 7652..8020 + 369 WP_064343525 type IV conjugative transfer system pilin TraA -
K6028_RS27165 (K6028_27165) 8034..8339 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
K6028_RS27170 (K6028_27170) 8355..8921 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
K6028_RS27175 (K6028_27175) 8908..9642 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
K6028_RS27180 (K6028_27180) 9642..11063 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
K6028_RS27185 (K6028_27185) 11056..11490 + 435 WP_020322358 conjugal transfer protein TraP -
K6028_RS27190 (K6028_27190) 11524..12108 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
K6028_RS27195 (K6028_27195) 12721..12909 + 189 WP_053390286 hypothetical protein -
K6028_RS33165 12993..13394 + 402 WP_064343532 hypothetical protein -
K6028_RS27205 (K6028_27205) 13391..13690 + 300 WP_053390308 hypothetical protein -
K6028_RS27210 (K6028_27210) 13778..14161 + 384 WP_042946290 hypothetical protein -
K6028_RS27215 (K6028_27215) 14254..16893 + 2640 WP_064343533 type IV secretion system protein TraC virb4
K6028_RS27220 (K6028_27220) 16893..17285 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
K6028_RS27225 (K6028_27225) 17282..17908 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
K6028_RS27230 (K6028_27230) 17952..18911 + 960 WP_327204683 conjugal transfer pilus assembly protein TraU traU
K6028_RS27235 (K6028_27235) 18924..19571 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
K6028_RS27240 (K6028_27240) 19568..19951 + 384 WP_053390297 hypothetical protein -
K6028_RS27245 (K6028_27245) 19948..21903 + 1956 WP_064359956 type-F conjugative transfer system mating-pair stabilization protein TraN traN
K6028_RS27250 (K6028_27250) 21935..22195 + 261 WP_053390216 hypothetical protein -
K6028_RS27255 (K6028_27255) 22188..22799 + 612 WP_053390217 hypothetical protein -
K6028_RS27260 (K6028_27260) 22789..23031 + 243 WP_053390218 conjugal transfer protein TrbE -
K6028_RS27265 (K6028_27265) 23077..23403 + 327 WP_053390219 hypothetical protein -
K6028_RS27270 (K6028_27270) 23424..24176 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
K6028_RS27275 (K6028_27275) 24187..24423 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
K6028_RS27280 (K6028_27280) 24398..24958 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
K6028_RS27285 (K6028_27285) 24945..26315 + 1371 WP_049078362 conjugal transfer pilus assembly protein TraH traH
K6028_RS27290 (K6028_27290) 26315..29158 + 2844 WP_049078361 conjugal transfer mating-pair stabilization protein TraG traG
K6028_RS27295 (K6028_27295) 29164..29679 + 516 WP_049078360 conjugal transfer protein TraS -
K6028_RS27300 (K6028_27300) 29742..30488 + 747 WP_049078359 hypothetical protein -
K6028_RS27305 (K6028_27305) 30728..33022 + 2295 WP_064343540 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21248 GenBank   NZ_CP082172
Plasmid name   p4_SCLZS62 Incompatibility group   IncFII
Plasmid size   125664 bp Coordinate of oriT [Strand]   5609..5657 [-]
Host baterium   Raoultella planticola strain SCLZS62

Cargo genes

Drug resistance gene   qnrS1
Virulence gene   -
Metal resistance gene   merR, merT, merP
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -