Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106011
Name   oriT_pKpn14-2 in_silico
Organism   Klebsiella pneumoniae strain Kpn-14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047702 (159620..159669 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKpn14-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4043 GenBank   WP_040224080
Name   traI_GVI79_RS28565_pKpn14-2 insolico UniProt ID   A0A7W3BA55
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190352.82 Da        Isoelectric Point: 5.9133

>WP_040224080.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMNVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
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)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   4055 GenBank   WP_023329042
Name   traD_GVI79_RS28570_pKpn14-2 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: 85943.90 Da        Isoelectric Point: 5.0577

>WP_023329042.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEARESEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 130983..160227

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GVI79_RS28570 (GVI79_28205) 130983..133292 - 2310 WP_023329042 type IV conjugative transfer system coupling protein TraD virb4
GVI79_RS28575 (GVI79_28210) 133650..134381 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
GVI79_RS28580 (GVI79_28215) 134571..135098 - 528 WP_029498351 conjugal transfer protein TraS -
GVI79_RS28585 (GVI79_28220) 135104..137953 - 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
GVI79_RS28590 (GVI79_28225) 137953..139332 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
GVI79_RS28595 (GVI79_28230) 139310..139753 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
GVI79_RS28600 (GVI79_28235) 139799..140356 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GVI79_RS28605 (GVI79_28240) 140328..140567 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
GVI79_RS28610 (GVI79_28245) 140578..141330 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
GVI79_RS28615 (GVI79_28250) 141351..141677 - 327 WP_015065534 hypothetical protein -
GVI79_RS28620 (GVI79_28255) 141690..141938 - 249 WP_004152675 hypothetical protein -
GVI79_RS28625 (GVI79_28260) 141916..142170 - 255 WP_015065558 conjugal transfer protein TrbE -
GVI79_RS28630 (GVI79_28265) 142202..144157 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GVI79_RS28635 (GVI79_28270) 144216..144863 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
GVI79_RS28640 144942..145118 - 177 WP_162866177 hypothetical protein -
GVI79_RS28645 (GVI79_28275) 145139..146128 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
GVI79_RS28650 (GVI79_28280) 146125..146526 - 402 WP_023158005 hypothetical protein -
GVI79_RS28655 (GVI79_28285) 146561..147196 - 636 WP_023158006 type-F conjugative transfer system protein TraW traW
GVI79_RS28660 (GVI79_28290) 147196..147585 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
GVI79_RS28665 (GVI79_28295) 147585..150224 - 2640 WP_023158007 type IV secretion system protein TraC virb4
GVI79_RS28670 (GVI79_28300) 150296..150694 - 399 WP_023158008 hypothetical protein -
GVI79_RS28675 (GVI79_28305) 150702..151091 - 390 WP_023158009 hypothetical protein -
GVI79_RS28680 (GVI79_28310) 151134..151538 - 405 WP_016831042 hypothetical protein -
GVI79_RS28685 (GVI79_28315) 151605..151916 - 312 WP_014386200 hypothetical protein -
GVI79_RS28690 (GVI79_28320) 151917..152135 - 219 WP_014386199 hypothetical protein -
GVI79_RS28695 (GVI79_28325) 152159..152448 - 290 Protein_154 hypothetical protein -
GVI79_RS28700 (GVI79_28330) 152453..152863 - 411 WP_016831039 hypothetical protein -
GVI79_RS28705 (GVI79_28335) 152995..153579 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
GVI79_RS28710 (GVI79_28340) 153602..154198 - 597 Protein_157 conjugal transfer pilus-stabilizing protein TraP -
GVI79_RS28715 (GVI79_28345) 154191..155615 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
GVI79_RS28720 (GVI79_28350) 155615..156355 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
GVI79_RS28725 (GVI79_28355) 156342..156908 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
GVI79_RS28730 (GVI79_28360) 156928..157233 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
GVI79_RS28735 (GVI79_28365) 157247..157615 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
GVI79_RS28740 (GVI79_28370) 157677..157883 - 207 WP_171773970 TraY domain-containing protein -
GVI79_RS28745 (GVI79_28375) 158016..158735 - 720 WP_016831034 conjugal transfer protein TrbJ -
GVI79_RS28750 (GVI79_28380) 158935..159351 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
GVI79_RS28755 (GVI79_28385) 159742..160227 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
GVI79_RS28760 (GVI79_28390) 160260..160589 - 330 WP_011977736 DUF5983 family protein -
GVI79_RS28765 (GVI79_28395) 160622..161443 - 822 WP_004182076 DUF932 domain-containing protein -
GVI79_RS28770 (GVI79_28400) 162276..162689 - 414 WP_004182074 helix-turn-helix domain-containing protein -
GVI79_RS28775 (GVI79_28405) 162690..162968 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
GVI79_RS28780 (GVI79_28410) 162958..163278 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
GVI79_RS28785 (GVI79_28415) 163359..163583 - 225 WP_020325128 hypothetical protein -
GVI79_RS28790 (GVI79_28420) 163594..163806 - 213 WP_004182070 hypothetical protein -
GVI79_RS28795 (GVI79_28425) 163867..164223 - 357 WP_004152717 hypothetical protein -
GVI79_RS28800 (GVI79_28430) 164859..165209 - 351 WP_004182068 hypothetical protein -

Host bacterium

ID   6448 GenBank   NZ_CP047702
Plasmid name   pKpn14-2 Incompatibility group   IncFIB
Plasmid size   192765 bp Coordinate of oriT [Strand]   159620..159669 [+]
Host baterium   Klebsiella pneumoniae strain Kpn-14

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, arsH, arsC, arsB, arsA, arsD, arsR, merR2, merT, merP, merF, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9