Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106278
Name   oriT_pKP062-2 in_silico
Organism   Klebsiella pneumoniae strain KP062
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP089327 (115374..115422 [-], 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_pKP062-2
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTTTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4203 GenBank   WP_117098435
Name   traI_LUX41_RS27490_pKP062-2 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: 190192.94 Da        Isoelectric Point: 6.2880

>WP_117098435.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGLESVAQISGTREQSVLNGLIRDSLRNEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKARSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATALETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADIAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIQK
ALSEGKTLPAGQPATLYEALVKDYTGRAPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVAGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

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

(634-713)

AAA domain (AAA_30)

(970-1156)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   4228 GenBank   WP_020316650
Name   traD_LUX41_RS27485_pKP062-2 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 85197.99 Da        Isoelectric Point: 4.8865

>WP_020316650.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPAEVTV
SPAPVKATQTTKMPAEEPSVRATEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTEQELAQQ
SAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 117801..143325

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LUX41_RS27305 (LUX41_27260) 114254..114784 + 531 WP_015632491 antirestriction protein -
LUX41_RS27310 (LUX41_27265) 114822..115229 - 408 WP_020805750 transglycosylase SLT domain-containing protein -
LUX41_RS27315 (LUX41_27270) 115733..116125 + 393 WP_032419915 conjugal transfer relaxosome DNA-binding protein TraM -
LUX41_RS27320 (LUX41_27275) 116363..117064 + 702 WP_032419917 hypothetical protein -
LUX41_RS27325 (LUX41_27280) 117150..117350 + 201 WP_048289787 TraY domain-containing protein -
LUX41_RS27330 (LUX41_27285) 117419..117787 + 369 WP_020316649 type IV conjugative transfer system pilin TraA -
LUX41_RS27335 (LUX41_27290) 117801..118106 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
LUX41_RS27340 (LUX41_27295) 118126..118692 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
LUX41_RS27345 (LUX41_27300) 118679..119419 + 741 WP_020316652 type-F conjugative transfer system secretin TraK traK
LUX41_RS27350 (LUX41_27305) 119419..120843 + 1425 WP_020316642 F-type conjugal transfer pilus assembly protein TraB traB
LUX41_RS27355 (LUX41_27310) 120836..121432 + 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
LUX41_RS27360 (LUX41_27315) 121455..122024 + 570 WP_032419921 type IV conjugative transfer system lipoprotein TraV traV
LUX41_RS27365 (LUX41_27320) 122156..122566 + 411 WP_149999108 hypothetical protein -
LUX41_RS27370 (LUX41_27325) 122571..122861 + 291 WP_020316639 hypothetical protein -
LUX41_RS27375 (LUX41_27330) 122885..123103 + 219 WP_004171484 hypothetical protein -
LUX41_RS27380 (LUX41_27335) 123104..123421 + 318 WP_020316633 hypothetical protein -
LUX41_RS27385 (LUX41_27340) 123488..123892 + 405 WP_032419926 hypothetical protein -
LUX41_RS27390 (LUX41_27345) 123889..124179 + 291 WP_032419928 hypothetical protein -
LUX41_RS27395 (LUX41_27350) 124187..124585 + 399 WP_020316629 hypothetical protein -
LUX41_RS27400 (LUX41_27355) 124657..127296 + 2640 WP_020316635 type IV secretion system protein TraC virb4
LUX41_RS27405 (LUX41_27360) 127296..127685 + 390 WP_020316628 type-F conjugative transfer system protein TrbI -
LUX41_RS27410 (LUX41_27365) 127685..128311 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
LUX41_RS27415 (LUX41_27370) 128355..129314 + 960 WP_202386622 conjugal transfer pilus assembly protein TraU traU
LUX41_RS27420 (LUX41_27375) 129327..129965 + 639 WP_020316653 type-F conjugative transfer system pilin assembly protein TrbC trbC
LUX41_RS27425 (LUX41_27380) 130024..131979 + 1956 WP_020316657 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LUX41_RS27430 (LUX41_27385) 132012..132293 + 282 WP_032419932 hypothetical protein -
LUX41_RS27435 (LUX41_27390) 132283..132510 + 228 WP_012540032 conjugal transfer protein TrbE -
LUX41_RS27440 (LUX41_27395) 132521..132847 + 327 WP_020316638 hypothetical protein -
LUX41_RS27445 (LUX41_27400) 132868..133620 + 753 WP_020316647 type-F conjugative transfer system pilin assembly protein TraF traF
LUX41_RS27450 (LUX41_27405) 133631..133870 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
LUX41_RS27455 (LUX41_27410) 133842..134399 + 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LUX41_RS27460 (LUX41_27415) 134444..134887 + 444 WP_015065638 F-type conjugal transfer protein TrbF -
LUX41_RS27465 (LUX41_27420) 134865..136244 + 1380 WP_277738960 conjugal transfer pilus assembly protein TraH traH
LUX41_RS27470 (LUX41_27425) 136244..139066 + 2823 WP_277738961 conjugal transfer mating-pair stabilization protein TraG traG
LUX41_RS27475 (LUX41_27430) 139090..139692 + 603 WP_048263624 hypothetical protein -
LUX41_RS27480 (LUX41_27435) 139943..140674 + 732 WP_016831056 conjugal transfer complement resistance protein TraT -
LUX41_RS27485 (LUX41_27440) 141034..143325 + 2292 WP_020316650 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   6715 GenBank   NZ_CP089327
Plasmid name   pKP062-2 Incompatibility group   -
Plasmid size   153468 bp Coordinate of oriT [Strand]   115374..115422 [-]
Host baterium   Klebsiella pneumoniae strain KP062

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsH, arsC, arsB, nirD, ncrC, ncrB, ncrA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9