Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117571
Name   oriT_pWP3-S18-CRE-02_3 in_silico
Organism   Klebsiella quasipneumoniae strain WP3-S18-CRE-02
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP022008 (45548..45596 [-], 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_pWP3-S18-CRE-02_3
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11198 GenBank   WP_182949635
Name   traI_H7R71_RS28490_pWP3-S18-CRE-02_3 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: 190564.36 Da        Isoelectric Point: 6.2581

>WP_182949635.1 conjugative transfer relaxase/helicase TraI [Klebsiella quasipneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQIFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIAFGKIYQNTLRADVES
LGYRTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGNHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(11-283)


  Protein structure



No available structure.




Auxiliary protein

ID   6476 GenBank   WP_004197733
Name   WP_004197733_pWP3-S18-CRE-02_3 insolico UniProt ID   A0A0E3KB00
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14835.90 Da        Isoelectric Point: 4.6012

>WP_004197733.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
AlphaFold DB A0A0E3KB00


T4CP

ID   13082 GenBank   WP_227666872
Name   traD_H7R71_RS28485_pWP3-S18-CRE-02_3 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 85293.31 Da        Isoelectric Point: 5.1074

>WP_227666872.1 type IV conjugative transfer system coupling protein TraD [Klebsiella quasipneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGEQPEPVSQPA
PAVMTVTPAPVKSPPTTKRPAAEPSARTAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQVL
AQQSAEQGQAMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDLEIGGNF

  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: 44981..72905

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H7R71_RS28300 (WP3S18C02_P30470) 40270..41295 + 1026 WP_001101446 IS110 family transposase -
H7R71_RS28305 (WP3S18C02_P30480) 41590..42558 + 969 WP_072269292 IS5 family transposase -
H7R71_RS28310 (WP3S18C02_P30490) 42876..43901 - 1026 WP_001101446 IS110 family transposase -
H7R71_RS28315 43933..44421 - 489 WP_182949647 hypothetical protein -
H7R71_RS28320 (WP3S18C02_P30500) 44416..44958 + 543 WP_060415467 antirestriction protein -
H7R71_RS28325 (WP3S18C02_P30510) 44981..45403 - 423 WP_073972322 transglycosylase SLT domain-containing protein virB1
H7R71_RS28330 (WP3S18C02_P30520) 45908..46297 + 390 WP_004197733 conjugal transfer relaxosome DNA-binding protein TraM -
H7R71_RS28335 (WP3S18C02_P30530) 46536..47210 + 675 WP_004197737 hypothetical protein -
H7R71_RS28340 47402..47566 + 165 WP_032444506 TraY domain-containing protein -
H7R71_RS28345 (WP3S18C02_P30540) 47628..47996 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
H7R71_RS28350 (WP3S18C02_P30550) 48010..48315 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
H7R71_RS28355 (WP3S18C02_P30560) 48335..48901 + 567 WP_004194424 type IV conjugative transfer system protein TraE traE
H7R71_RS28360 (WP3S18C02_P30570) 48888..49628 + 741 WP_009309865 type-F conjugative transfer system secretin TraK traK
H7R71_RS28365 (WP3S18C02_P30580) 49628..51052 + 1425 WP_015065626 F-type conjugal transfer pilus assembly protein TraB traB
H7R71_RS28370 (WP3S18C02_P30590) 51166..51750 + 585 WP_009309868 type IV conjugative transfer system lipoprotein TraV traV
H7R71_RS28375 (WP3S18C02_P30600) 51882..52292 + 411 WP_009309869 hypothetical protein -
H7R71_RS28380 (WP3S18C02_P30610) 52398..52616 + 219 WP_004195468 hypothetical protein -
H7R71_RS28385 (WP3S18C02_P30620) 52617..52928 + 312 WP_004195465 hypothetical protein -
H7R71_RS28390 (WP3S18C02_P30630) 52995..53399 + 405 WP_004197817 hypothetical protein -
H7R71_RS28395 (WP3S18C02_P30640) 53777..54175 + 399 WP_023179972 hypothetical protein -
H7R71_RS28400 (WP3S18C02_P30650) 54247..56886 + 2640 WP_004197813 type IV secretion system protein TraC virb4
H7R71_RS28405 (WP3S18C02_P30660) 56886..57275 + 390 WP_004197815 type-F conjugative transfer system protein TrbI -
H7R71_RS28410 (WP3S18C02_P30670) 57275..57901 + 627 WP_009309871 type-F conjugative transfer system protein TraW traW
H7R71_RS28415 (WP3S18C02_P30680) 57943..58332 + 390 WP_004194992 hypothetical protein -
H7R71_RS28420 (WP3S18C02_P30690) 58329..59318 + 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
H7R71_RS28425 (WP3S18C02_P30700) 59331..59969 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
H7R71_RS28430 (WP3S18C02_P30710) 60028..61983 + 1956 WP_032426778 type-F conjugative transfer system mating-pair stabilization protein TraN traN
H7R71_RS28435 (WP3S18C02_P30720) 62015..62269 + 255 WP_004195500 conjugal transfer protein TrbE -
H7R71_RS28440 (WP3S18C02_P30730) 62247..62495 + 249 WP_004152675 hypothetical protein -
H7R71_RS28445 (WP3S18C02_P30740) 62508..62834 + 327 WP_004194451 hypothetical protein -
H7R71_RS28450 (WP3S18C02_P30750) 62855..63607 + 753 WP_042946327 type-F conjugative transfer system pilin assembly protein TraF traF
H7R71_RS28455 (WP3S18C02_P30760) 63618..63857 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
H7R71_RS28460 (WP3S18C02_P30770) 63829..64401 + 573 WP_009309876 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
H7R71_RS28465 (WP3S18C02_P30780) 64394..64822 + 429 WP_004152689 hypothetical protein -
H7R71_RS28470 (WP3S18C02_P30790) 64809..66179 + 1371 WP_009309877 conjugal transfer pilus assembly protein TraH traH
H7R71_RS28475 (WP3S18C02_P30800) 66179..69052 + 2874 WP_182949625 conjugal transfer mating-pair stabilization protein TraG traG
H7R71_RS28480 (WP3S18C02_P30820) 69787..70479 + 693 WP_182949627 hypothetical protein -
H7R71_RS28485 (WP3S18C02_P30830) 70605..72905 + 2301 WP_227666872 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18004 GenBank   NZ_AP022008
Plasmid name   pWP3-S18-CRE-02_3 Incompatibility group   IncFII
Plasmid size   104413 bp Coordinate of oriT [Strand]   45548..45596 [-]
Host baterium   Klebsiella quasipneumoniae strain WP3-S18-CRE-02

Cargo genes

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