Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101450
Name   oriT_pCRE13_1 in_silico
Organism   Klebsiella pneumoniae strain S13_CRE13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAHBNN010000002 (244075..244124 [+], 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_pCRE13_1
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1307 GenBank   WP_268102403
Name   traI_KIN63_RS28325_pCRE13_1 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: 190806.82 Da        Isoelectric Point: 6.1567

>WP_268102403.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QTQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

DNA helicase TraI (TraI_C)

(1433-1555)

AAA domain (AAA_30)

(971-1157)

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

(577-629)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   922 GenBank   WP_004152630
Name   traD_KIN63_RS28330_pCRE13_1 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: 85951.02 Da        Isoelectric Point: 5.0632

>WP_004152630.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIPRRLDTRVDARLSALLEEREAEGSLARALFTPDAPASGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAAEPSVRATEPPVLRVTTVPLIKPKAAAAAAAASTASSAGIPAAAAGGTE
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: 216264..244682

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KIN63_RS28330 (KIN63_28260) 216264..218573 - 2310 WP_004152630 type IV conjugative transfer system coupling protein TraD virb4
KIN63_RS28335 (KIN63_28265) 218933..219664 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
KIN63_RS28340 (KIN63_28270) 219854..220381 - 528 WP_004153030 hypothetical protein -
KIN63_RS28345 (KIN63_28275) 220387..223236 - 2850 WP_124035974 conjugal transfer mating-pair stabilization protein TraG traG
KIN63_RS28350 (KIN63_28280) 223236..224606 - 1371 WP_004178055 conjugal transfer pilus assembly protein TraH traH
KIN63_RS28355 (KIN63_28285) 224593..225021 - 429 WP_004152689 hypothetical protein -
KIN63_RS28360 (KIN63_28290) 225014..225586 - 573 WP_004152688 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KIN63_RS28365 (KIN63_28295) 225558..225797 - 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
KIN63_RS28370 (KIN63_28300) 225808..226560 - 753 WP_004152686 type-F conjugative transfer system pilin assembly protein TraF traF
KIN63_RS28375 (KIN63_28305) 226581..226907 - 327 WP_004152685 hypothetical protein -
KIN63_RS30390 226953..227138 - 186 WP_004152684 hypothetical protein -
KIN63_RS28380 (KIN63_28310) 227135..227371 - 237 WP_004152683 conjugal transfer protein TrbE -
KIN63_RS28385 (KIN63_28315) 227403..229358 - 1956 WP_004153093 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KIN63_RS28390 (KIN63_28320) 229406..230044 - 639 WP_004152682 type-F conjugative transfer system pilin assembly protein TrbC trbC
KIN63_RS28395 (KIN63_28325) 230057..231016 - 960 WP_015065634 conjugal transfer pilus assembly protein TraU traU
KIN63_RS28400 (KIN63_28330) 231060..231686 - 627 WP_004152590 type-F conjugative transfer system protein TraW traW
KIN63_RS28405 (KIN63_28335) 231686..232075 - 390 WP_004152591 type-F conjugative transfer system protein TrbI -
KIN63_RS28410 (KIN63_28340) 232075..234714 - 2640 WP_004152592 type IV secretion system protein TraC virb4
KIN63_RS28415 (KIN63_28345) 234786..235184 - 399 WP_004153071 hypothetical protein -
KIN63_RS28420 (KIN63_28350) 235480..235884 - 405 WP_004152594 hypothetical protein -
KIN63_RS28425 (KIN63_28355) 235951..236268 - 318 WP_004152595 hypothetical protein -
KIN63_RS28430 (KIN63_28360) 236269..236487 - 219 WP_004171484 hypothetical protein -
KIN63_RS28435 (KIN63_28365) 236511..236801 - 291 WP_004152596 hypothetical protein -
KIN63_RS28440 (KIN63_28370) 236806..237216 - 411 WP_004152597 lipase chaperone -
KIN63_RS28445 (KIN63_28375) 237348..237917 - 570 WP_004152598 type IV conjugative transfer system lipoprotein TraV traV
KIN63_RS28450 (KIN63_28380) 237940..238536 - 597 WP_004152599 conjugal transfer pilus-stabilizing protein TraP -
KIN63_RS28455 (KIN63_28385) 238529..239953 - 1425 WP_268102405 F-type conjugal transfer pilus assembly protein TraB traB
KIN63_RS28460 (KIN63_28390) 239953..240693 - 741 WP_004152601 type-F conjugative transfer system secretin TraK traK
KIN63_RS28465 (KIN63_28395) 240680..241246 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
KIN63_RS28470 (KIN63_28400) 241266..241571 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
KIN63_RS28475 (KIN63_28405) 241585..241953 - 369 WP_004178060 type IV conjugative transfer system pilin TraA -
KIN63_RS28480 (KIN63_28410) 242007..242378 - 372 WP_004208838 TraY domain-containing protein -
KIN63_RS28485 (KIN63_28415) 242462..243157 - 696 WP_004178061 transcriptional regulator TraJ family protein -
KIN63_RS28490 (KIN63_28420) 243371..243763 - 393 WP_004178062 conjugal transfer relaxosome DNA-binding protein TraM -
KIN63_RS28495 (KIN63_28425) 244197..244682 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
KIN63_RS28500 (KIN63_28430) 244715..245044 - 330 WP_011977736 DUF5983 family protein -
KIN63_RS28505 (KIN63_28435) 245077..245898 - 822 WP_004178064 DUF932 domain-containing protein -
KIN63_RS28510 (KIN63_28440) 246732..247145 - 414 WP_004152722 helix-turn-helix domain-containing protein -
KIN63_RS28515 (KIN63_28445) 247146..247424 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
KIN63_RS28520 (KIN63_28450) 247414..247734 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
KIN63_RS28525 (KIN63_28455) 247815..248039 - 225 WP_004152719 hypothetical protein -
KIN63_RS28530 (KIN63_28460) 248050..248262 - 213 WP_004152718 hypothetical protein -
KIN63_RS28535 (KIN63_28465) 248323..248679 - 357 WP_004152717 hypothetical protein -
KIN63_RS28540 (KIN63_28470) 249315..249665 - 351 WP_004152758 hypothetical protein -

Host bacterium

ID   1894 GenBank   NZ_JAHBNN010000002
Plasmid name   pCRE13_1 Incompatibility group   IncFIB
Plasmid size   272849 bp Coordinate of oriT [Strand]   244075..244124 [+]
Host baterium   Klebsiella pneumoniae strain S13_CRE13

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1A, blaOXA-9, ant(3'')-Ia, aac(6')-Ib, blaKPC-3, dfrA14, mph(A), catA1
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, ncrA, ncrB, ncrC, ncrY, fecD, fecE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9