Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115859
Name   oriT_p4253-2 in_silico
Organism   Klebsiella variicola strain 4253
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP135070 (150760..150809 [+], 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_p4253-2
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10158 GenBank   WP_116995266
Name   traI_RJT51_RS29630_p4253-2 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: 190790.76 Da        Isoelectric Point: 6.0387

>WP_116995266.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKTLFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQTLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRTQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKD
TTITSLTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLHTPAEQAIHLSIPLLESQDLTFTRPQLLATALETGGDKVPMWSIEMTI
KKQIKSGQLLNVGVSPGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDIDRALATIEQVTPERVPRKEGAWVPGSSVVEFTPTQEEEIR
KALSKGESLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNNDRRALNGLIHEARRENGETGREEVTL
PVLVTSNIRDGELRKLSTWTAHKGAVALVDNVYHRIDNVDKDNQLITLTDSEGKERYISPREASAEGVTL
YRQEEITVSQGDRMRFSKSDPERGYVANSVWEVQSVSGDSVTLSDGKTTRTLTPKADEAQQHIDLAYAIT
AHGAQGASEPYAIALEGMVGARKLMASFESAYVGLSRMKQHVQVYTDRREGWIKAIQHSPEKATAHDILE
PLNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNIGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAITGGRVWAEQAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
VERVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRDRLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(971-1158)

TrwC relaxase (TrwC)

(10-284)

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

(636-714)

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

(577-629)

DNA helicase TraI (TraI_C)

(1433-1555)


  Protein structure



No available structure.




T4CP

ID   11866 GenBank   WP_227668502
Name   traD_RJT51_RS29635_p4253-2 insolico UniProt ID   _
Length   768 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 768 a.a.        Molecular weight: 85905.95 Da        Isoelectric Point: 5.0191

>WP_227668502.1 type IV conjugative transfer system coupling protein TraD [Klebsiella variicola]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSQPA
PAEVTVSPAPVKAPPTTKSPAAEPSARAAEPPVLRVTTVPLIKPKAAAAAAAAATASSVGTPAAGGTEQE
LAQQSAEQGQEMLPAGMNEDDVIEDMQAYDAWLADEQTQRDMQRREEVNINRSHRHDEQDDVEIGGNF

  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: 121763..148262

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RJT51_RS29635 (RJT51_29635) 121763..124069 - 2307 WP_227668502 type IV conjugative transfer system coupling protein TraD virb4
RJT51_RS29640 (RJT51_29640) 124143..124238 - 96 Protein_117 hypothetical protein -
RJT51_RS29645 (RJT51_29645) 124431..125162 - 732 WP_116995265 conjugal transfer complement resistance protein TraT -
RJT51_RS29650 (RJT51_29650) 125352..125879 - 528 WP_047665858 conjugal transfer protein TraS -
RJT51_RS29655 (RJT51_29655) 125885..128734 - 2850 WP_047665853 conjugal transfer mating-pair stabilization protein TraG traG
RJT51_RS29660 (RJT51_29660) 128734..130113 - 1380 WP_165451080 conjugal transfer pilus assembly protein TraH traH
RJT51_RS29665 (RJT51_29665) 130091..130534 - 444 WP_046622845 F-type conjugal transfer protein TrbF -
RJT51_RS29670 (RJT51_29670) 130580..131137 - 558 WP_116995264 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
RJT51_RS29675 (RJT51_29675) 131109..131348 - 240 WP_046622843 type-F conjugative transfer system pilin chaperone TraQ -
RJT51_RS29680 (RJT51_29680) 131450..131776 + 327 WP_052749784 hypothetical protein -
RJT51_RS29685 (RJT51_29685) 132125..132877 - 753 WP_046622841 type-F conjugative transfer system pilin assembly protein TraF traF
RJT51_RS29690 (RJT51_29690) 132898..133224 - 327 WP_042937346 hypothetical protein -
RJT51_RS29695 (RJT51_29695) 133235..133462 - 228 WP_046622840 conjugal transfer protein TrbE -
RJT51_RS29700 (RJT51_29700) 133494..135449 - 1956 WP_200589891 type-F conjugative transfer system mating-pair stabilization protein TraN traN
RJT51_RS29705 (RJT51_29705) 135508..136146 - 639 WP_046622838 type-F conjugative transfer system pilin assembly protein TrbC trbC
RJT51_RS29710 (RJT51_29710) 136159..137148 - 990 WP_046622837 conjugal transfer pilus assembly protein TraU traU
RJT51_RS29715 (RJT51_29715) 137145..137534 - 390 WP_032445235 hypothetical protein -
RJT51_RS29720 (RJT51_29720) 137576..138202 - 627 WP_046622836 type-F conjugative transfer system protein TraW traW
RJT51_RS29725 (RJT51_29725) 138202..138591 - 390 WP_046622835 type-F conjugative transfer system protein TrbI -
RJT51_RS29730 (RJT51_29730) 138591..141230 - 2640 WP_046622834 type IV secretion system protein TraC virb4
RJT51_RS29735 (RJT51_29735) 141302..141700 - 399 WP_004153071 hypothetical protein -
RJT51_RS29740 (RJT51_29740) 141708..141950 - 243 WP_071885119 hypothetical protein -
RJT51_RS29745 (RJT51_29745) 142142..142546 - 405 WP_046622833 hypothetical protein -
RJT51_RS29750 (RJT51_29750) 142613..142923 - 311 Protein_139 hypothetical protein -
RJT51_RS29755 (RJT51_29755) 142924..143142 - 219 WP_046622831 hypothetical protein -
RJT51_RS29760 (RJT51_29760) 143166..143456 - 291 WP_046622830 hypothetical protein -
RJT51_RS29765 (RJT51_29765) 143485..143883 - 399 WP_223170083 hypothetical protein -
RJT51_RS29770 (RJT51_29770) 144039..144608 - 570 WP_046622829 type IV conjugative transfer system lipoprotein TraV traV
RJT51_RS29775 (RJT51_29775) 144631..145227 - 597 WP_116995261 conjugal transfer pilus-stabilizing protein TraP -
RJT51_RS29780 (RJT51_29780) 145220..146644 - 1425 WP_116995260 F-type conjugal transfer pilus assembly protein TraB traB
RJT51_RS29785 (RJT51_29785) 146644..147384 - 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
RJT51_RS29790 (RJT51_29790) 147371..147937 - 567 WP_047665763 type IV conjugative transfer system protein TraE traE
RJT51_RS29795 (RJT51_29795) 147957..148262 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
RJT51_RS29800 (RJT51_29800) 148276..148644 - 369 WP_047665762 type IV conjugative transfer system pilin TraA -
RJT51_RS29805 (RJT51_29805) 148698..148868 - 171 WP_200589901 TraY domain-containing protein -
RJT51_RS29810 (RJT51_29810) 148959..149069 - 111 WP_200589888 TraY domain-containing protein -
RJT51_RS29815 (RJT51_29815) 149153..149848 - 696 WP_072194100 transcriptional regulator TraJ family protein -
RJT51_RS29820 (RJT51_29820) 150055..150447 - 393 WP_047665760 conjugal transfer relaxosome DNA-binding protein TraM -
RJT51_RS29825 (RJT51_29825) 150954..151361 + 408 WP_223170089 transglycosylase SLT domain-containing protein -
RJT51_RS29830 (RJT51_29830) 151399..151929 - 531 WP_023292160 antirestriction protein -

Host bacterium

ID   16292 GenBank   NZ_CP135070
Plasmid name   p4253-2 Incompatibility group   IncFIB
Plasmid size   175117 bp Coordinate of oriT [Strand]   150760..150809 [+]
Host baterium   Klebsiella variicola strain 4253

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -