Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107877
Name   oriT_pJBIWA001_1 in_silico
Organism   Raoultella planticola strain JBIWA001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP074183 (93519..93568 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pJBIWA001_1
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5288 GenBank   WP_223526237
Name   traI_KGP19_RS27425_pJBIWA001_1 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190316.25 Da        Isoelectric Point: 6.2703

>WP_223526237.1 conjugative transfer relaxase/helicase TraI [Raoultella planticola]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAANARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKARSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTQAQEKAIQ
KALSEGETLPAGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDIQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASEGLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

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

(577-629)

TrwC relaxase (TrwC)

(10-284)

DNA helicase TraI (TraI_C)

(1433-1555)

AAA domain (AAA_30)

(971-1157)


  Protein structure



No available structure.




T4CP

ID   5542 GenBank   WP_032072078
Name   traD_KGP19_RS27420_pJBIWA001_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: 85822.78 Da        Isoelectric Point: 4.9615

>WP_032072078.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
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: 92961..121957

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KGP19_RS27210 (KGP19_27120) 88063..88413 + 351 WP_004153414 hypothetical protein -
KGP19_RS27215 (KGP19_27125) 89043..89396 + 354 WP_023179962 hypothetical protein -
KGP19_RS27220 (KGP19_27130) 89453..89800 + 348 WP_004152749 hypothetical protein -
KGP19_RS27225 (KGP19_27135) 89895..90041 + 147 WP_004152750 hypothetical protein -
KGP19_RS27230 (KGP19_27140) 90092..90925 + 834 WP_004152751 N-6 DNA methylase -
KGP19_RS27235 (KGP19_27145) 91745..92566 + 822 WP_004152492 DUF932 domain-containing protein -
KGP19_RS27240 (KGP19_27150) 92599..92928 + 330 WP_011977736 DUF5983 family protein -
KGP19_RS27245 (KGP19_27155) 92961..93446 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
KGP19_RS27250 (KGP19_27160) 93868..94266 + 399 WP_004152493 conjugal transfer relaxosome DNA-binding protein TraM -
KGP19_RS27255 (KGP19_27165) 94440..95126 + 687 WP_004152494 transcriptional regulator TraJ family protein -
KGP19_RS27260 (KGP19_27170) 95205..95591 + 387 WP_004152495 TraY domain-containing protein -
KGP19_RS27265 (KGP19_27175) 95645..96013 + 369 WP_004152496 type IV conjugative transfer system pilin TraA -
KGP19_RS27270 (KGP19_27180) 96027..96332 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
KGP19_RS27275 (KGP19_27185) 96352..96918 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
KGP19_RS27280 (KGP19_27190) 96905..97645 + 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
KGP19_RS27285 (KGP19_27195) 97645..99069 + 1425 WP_223526234 F-type conjugal transfer pilus assembly protein TraB traB
KGP19_RS27290 (KGP19_27200) 99183..99767 + 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
KGP19_RS27295 (KGP19_27205) 99899..100309 + 411 WP_032329942 hypothetical protein -
KGP19_RS27300 (KGP19_27210) 100415..100633 + 219 WP_004152501 hypothetical protein -
KGP19_RS27305 (KGP19_27215) 100634..100945 + 312 WP_004152502 hypothetical protein -
KGP19_RS27310 (KGP19_27220) 101012..101416 + 405 WP_004152503 hypothetical protein -
KGP19_RS27315 (KGP19_27225) 101459..101848 + 390 WP_223526235 hypothetical protein -
KGP19_RS27320 (KGP19_27230) 101856..102254 + 399 WP_011977783 hypothetical protein -
KGP19_RS27325 (KGP19_27235) 102326..104965 + 2640 WP_004152505 type IV secretion system protein TraC virb4
KGP19_RS27330 (KGP19_27240) 104965..105354 + 390 WP_004152506 type-F conjugative transfer system protein TrbI -
KGP19_RS27335 (KGP19_27245) 105354..105980 + 627 WP_032420974 type-F conjugative transfer system protein TraW traW
KGP19_RS27340 (KGP19_27250) 106022..106411 + 390 WP_004152508 hypothetical protein -
KGP19_RS27345 (KGP19_27255) 106408..107397 + 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
KGP19_RS27350 (KGP19_27260) 107410..108048 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
KGP19_RS27355 (KGP19_27265) 108107..110062 + 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KGP19_RS27360 (KGP19_27270) 110094..110348 + 255 WP_223526236 conjugal transfer protein TrbE -
KGP19_RS27365 (KGP19_27275) 110326..110574 + 249 WP_004152675 hypothetical protein -
KGP19_RS27370 (KGP19_27280) 110587..110913 + 327 WP_125064279 hypothetical protein -
KGP19_RS27375 (KGP19_27285) 110934..111686 + 753 WP_074015674 type-F conjugative transfer system pilin assembly protein TraF traF
KGP19_RS27380 (KGP19_27290) 111697..111936 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
KGP19_RS27385 (KGP19_27295) 111908..112465 + 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KGP19_RS27390 (KGP19_27300) 112510..112953 + 444 WP_015065638 F-type conjugal transfer protein TrbF -
KGP19_RS27395 (KGP19_27305) 112931..114310 + 1380 WP_004165169 conjugal transfer pilus assembly protein TraH traH
KGP19_RS27400 (KGP19_27310) 114310..117159 + 2850 WP_004152624 conjugal transfer mating-pair stabilization protein TraG traG
KGP19_RS27405 (KGP19_27315) 117172..117720 + 549 WP_004152623 conjugal transfer entry exclusion protein TraS -
KGP19_RS27410 (KGP19_27320) 117904..118635 + 732 WP_004152622 conjugal transfer complement resistance protein TraT -
KGP19_RS27415 (KGP19_27325) 118827..119516 + 690 WP_022644928 hypothetical protein -
KGP19_RS27420 (KGP19_27330) 119645..121957 + 2313 WP_032072078 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   8312 GenBank   NZ_CP074183
Plasmid name   pJBIWA001_1 Incompatibility group   IncFIB
Plasmid size   136413 bp Coordinate of oriT [Strand]   93519..93568 [-]
Host baterium   Raoultella planticola strain JBIWA001

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9