Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101400
Name   oriT_pKP33.4_OSEI in_silico
Organism   Klebsiella pneumoniae strain Kp33
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_VXIW01000004 (52555..52604 [+], 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_pKP33.4_OSEI
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1282 GenBank   WP_015065542
Name   traI_F3Y18_RS13340_pKP33.4_OSEI insolico UniProt ID   K7R3U7
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190318.03 Da        Isoelectric Point: 6.2890

>WP_015065542.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALAVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
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)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   893 GenBank   WP_015065541
Name   traD_F3Y18_RS13345_pKP33.4_OSEI 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: 86025.00 Da        Isoelectric Point: 5.0577

>WP_015065541.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
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: 23148..53162

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
F3Y18_RS13345 (F3Y18_13350) 23148..25460 - 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4
F3Y18_RS28725 25589..26278 - 690 WP_015065540 hypothetical protein -
F3Y18_RS13355 (F3Y18_13360) 26470..27201 - 732 WP_032329926 conjugal transfer complement resistance protein TraT -
F3Y18_RS13360 (F3Y18_13365) 27510..28034 - 525 WP_015065538 hypothetical protein -
F3Y18_RS13365 (F3Y18_13370) 28045..30888 - 2844 WP_023157999 conjugal transfer mating-pair stabilization protein TraG traG
F3Y18_RS13370 (F3Y18_13375) 30888..32267 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
F3Y18_RS13375 (F3Y18_13380) 32245..32688 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
F3Y18_RS13380 (F3Y18_13385) 32734..33291 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
F3Y18_RS13385 (F3Y18_13390) 33263..33502 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
F3Y18_RS13390 (F3Y18_13395) 33513..34265 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
F3Y18_RS13395 (F3Y18_13400) 34286..34612 - 327 WP_015065534 hypothetical protein -
F3Y18_RS13400 (F3Y18_13405) 34625..34873 - 249 WP_004152675 hypothetical protein -
F3Y18_RS13405 (F3Y18_13410) 34851..35105 - 255 WP_015065558 conjugal transfer protein TrbE -
F3Y18_RS13410 (F3Y18_13415) 35137..37092 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
F3Y18_RS13415 (F3Y18_13420) 37151..37798 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
F3Y18_RS28730 37877..38053 - 177 WP_162866177 hypothetical protein -
F3Y18_RS13420 (F3Y18_13425) 38074..39063 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
F3Y18_RS13425 (F3Y18_13430) 39060..39461 - 402 WP_023158005 hypothetical protein -
F3Y18_RS13430 (F3Y18_13435) 39496..40131 - 636 WP_023158006 type-F conjugative transfer system protein TraW traW
F3Y18_RS13435 (F3Y18_13440) 40131..40520 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
F3Y18_RS13440 (F3Y18_13445) 40520..43159 - 2640 WP_023158007 type IV secretion system protein TraC virb4
F3Y18_RS13445 (F3Y18_13450) 43231..43629 - 399 WP_023158008 hypothetical protein -
F3Y18_RS13450 (F3Y18_13455) 43637..44026 - 390 WP_023158009 hypothetical protein -
F3Y18_RS13455 (F3Y18_13460) 44069..44473 - 405 WP_016831042 hypothetical protein -
F3Y18_RS13460 (F3Y18_13465) 44540..44851 - 312 WP_014386200 hypothetical protein -
F3Y18_RS13465 (F3Y18_13470) 44852..45070 - 219 WP_014386199 hypothetical protein -
F3Y18_RS13470 (F3Y18_13475) 45094..45383 - 290 Protein_51 hypothetical protein -
F3Y18_RS13475 (F3Y18_13480) 45388..45798 - 411 WP_016831039 hypothetical protein -
F3Y18_RS13480 (F3Y18_13485) 45930..46514 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
F3Y18_RS13485 (F3Y18_13490) 46537..47133 - 597 Protein_54 conjugal transfer pilus-stabilizing protein TraP -
F3Y18_RS13490 (F3Y18_13495) 47126..48550 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
F3Y18_RS13495 (F3Y18_13500) 48550..49290 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
F3Y18_RS13500 (F3Y18_13505) 49277..49843 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
F3Y18_RS13505 (F3Y18_13510) 49863..50168 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
F3Y18_RS13510 (F3Y18_13515) 50182..50550 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
F3Y18_RS13515 (F3Y18_13520) 50612..50818 - 207 WP_171773970 TraY domain-containing protein -
F3Y18_RS13520 (F3Y18_13525) 50951..51670 - 720 WP_016831034 conjugal transfer protein TrbJ -
F3Y18_RS13525 (F3Y18_13530) 51870..52286 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
F3Y18_RS13530 (F3Y18_13535) 52677..53162 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
F3Y18_RS13535 (F3Y18_13540) 53195..53524 - 330 WP_011977736 DUF5983 family protein -
F3Y18_RS13540 (F3Y18_13545) 53557..54378 - 822 WP_004182076 DUF932 domain-containing protein -
F3Y18_RS13555 (F3Y18_13560) 55206..55769 - 564 WP_004182054 methyltransferase -
F3Y18_RS13560 (F3Y18_13565) 55817..57172 - 1356 WP_004182052 DUF3560 domain-containing protein -
F3Y18_RS13565 (F3Y18_13570) 57224..57454 - 231 WP_001568051 hypothetical protein -
F3Y18_RS13570 (F3Y18_13575) 57546..57773 - 228 WP_004182050 hypothetical protein -

Host bacterium

ID   1844 GenBank   NZ_VXIW01000004
Plasmid name   pKP33.4_OSEI Incompatibility group   IncFII
Plasmid size   181384 bp Coordinate of oriT [Strand]   52555..52604 [+]
Host baterium   Klebsiella pneumoniae strain Kp33

Cargo genes

Drug resistance gene   tet(A), aac(6')-Ib-cr, blaOXA-1, sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, blaCTX-M-15, dfrA14, qnrB1
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
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -