Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101398
Name   oriT_pKP29.8_CTXM-15 in_silico
Organism   Klebsiella pneumoniae strain Kp29
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_VXIY01000008 (109930..109979 [+], 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_pKP29.8_CTXM-15
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1280 GenBank   WP_031944111
Name   traI_F3Y16_RS23570_pKP29.8_CTXM-15 insolico UniProt ID   A0A078K2I2
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190771.89 Da        Isoelectric Point: 6.3093

>WP_031944111.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Gammaproteobacteria]
MMSIGSVKAAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDTAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTSFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGSWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(577-629)

TrwC relaxase (TrwC)

(10-284)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   891 GenBank   WP_267313141
Name   traD_F3Y16_RS23575_pKP29.8_CTXM-15 insolico UniProt ID   _
Length   670 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 670 a.a.        Molecular weight: 74294.23 Da        Isoelectric Point: 5.1077

>WP_267313141.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MPENPASYRVVRTKSYLFNKAICIVTFFIASWVLGRQGKQQSEDENTGGRQLSDKPKEVARQMKRDGMAS
DIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVRARGDMAIIYDRSCEFVKSYYDPSLDKILNP
LDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQGSGRTIFAEGAYLMREDKDRSYEKLVDTMLS
IKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKAIRYLQGIEKNGEPFTIRDWMRGVREDRPNG
WLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRVWIFADELPTLHKLPDLVEILPEARKFGGCY
VFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIAEFAAGEIGEKEILKASEQYSYGADPVRDGV
STGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLALKYKPRPKIAEGFIPRTLDARVDARLSALLE
AREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSQPAPADMTVSPAPVKAPPTTKRPAEEPSVRATE
PSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTEQELAQQSAEQGQDMLPAGMNEDGVIEDMQA
YDAWLADEQTQRDMQRREEVNINHSHRHDEQDEVEIGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(72-460)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 81051..110537

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
F3Y16_RS23575 (F3Y16_23585) 81051..83063 - 2013 WP_267313141 type IV conjugative transfer system coupling protein TraD virb4
F3Y16_RS23580 (F3Y16_23590) 83056..84024 - 969 WP_077256372 IS5 family transposase -
F3Y16_RS23585 (F3Y16_23595) 84057..84428 - 372 Protein_73 TraD N-terminal domain-containing protein -
F3Y16_RS23590 (F3Y16_23600) 84788..85519 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
F3Y16_RS23595 (F3Y16_23605) 85709..86236 - 528 WP_004153030 hypothetical protein -
F3Y16_RS23600 (F3Y16_23610) 86242..89091 - 2850 WP_004178054 conjugal transfer mating-pair stabilization protein TraG traG
F3Y16_RS23605 (F3Y16_23615) 89091..90461 - 1371 WP_004178055 conjugal transfer pilus assembly protein TraH traH
F3Y16_RS23610 (F3Y16_23620) 90448..90876 - 429 WP_004152689 hypothetical protein -
F3Y16_RS23615 (F3Y16_23625) 90869..91441 - 573 WP_004152688 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
F3Y16_RS23620 (F3Y16_23630) 91413..91652 - 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
F3Y16_RS23625 (F3Y16_23635) 91663..92415 - 753 WP_004152686 type-F conjugative transfer system pilin assembly protein TraF traF
F3Y16_RS23630 (F3Y16_23640) 92436..92762 - 327 WP_004152685 hypothetical protein -
F3Y16_RS28970 (F3Y16_23645) 92808..92993 - 186 WP_004152684 hypothetical protein -
F3Y16_RS23640 (F3Y16_23650) 92990..93226 - 237 WP_004152683 conjugal transfer protein TrbE -
F3Y16_RS23645 (F3Y16_23655) 93258..95213 - 1956 WP_004153093 type-F conjugative transfer system mating-pair stabilization protein TraN traN
F3Y16_RS23650 (F3Y16_23660) 95261..95899 - 639 WP_004152682 type-F conjugative transfer system pilin assembly protein TrbC trbC
F3Y16_RS23655 (F3Y16_23665) 95912..96871 - 960 WP_015065634 conjugal transfer pilus assembly protein TraU traU
F3Y16_RS23660 (F3Y16_23670) 96915..97541 - 627 WP_004152590 type-F conjugative transfer system protein TraW traW
F3Y16_RS23665 (F3Y16_23675) 97541..97930 - 390 WP_004152591 type-F conjugative transfer system protein TrbI -
F3Y16_RS23670 (F3Y16_23680) 97930..100569 - 2640 WP_004152592 type IV secretion system protein TraC virb4
F3Y16_RS23675 (F3Y16_23685) 100641..101039 - 399 WP_004153071 hypothetical protein -
F3Y16_RS23685 (F3Y16_23695) 101335..101739 - 405 WP_031944109 hypothetical protein -
F3Y16_RS23690 (F3Y16_23700) 101806..102123 - 318 WP_004152595 hypothetical protein -
F3Y16_RS23695 (F3Y16_23705) 102124..102342 - 219 WP_004171484 hypothetical protein -
F3Y16_RS23700 (F3Y16_23710) 102366..102656 - 291 WP_004152596 hypothetical protein -
F3Y16_RS23705 (F3Y16_23715) 102661..103071 - 411 WP_004152597 lipase chaperone -
F3Y16_RS23710 (F3Y16_23720) 103203..103772 - 570 WP_004152598 type IV conjugative transfer system lipoprotein TraV traV
F3Y16_RS23715 (F3Y16_23725) 103795..104391 - 597 WP_004152599 conjugal transfer pilus-stabilizing protein TraP -
F3Y16_RS23720 (F3Y16_23730) 104384..105808 - 1425 WP_004152600 F-type conjugal transfer pilus assembly protein TraB traB
F3Y16_RS23725 (F3Y16_23735) 105808..106548 - 741 WP_004152601 type-F conjugative transfer system secretin TraK traK
F3Y16_RS23730 (F3Y16_23740) 106535..107101 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
F3Y16_RS23735 (F3Y16_23745) 107121..107426 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
F3Y16_RS23740 (F3Y16_23750) 107440..107808 - 369 WP_004178060 type IV conjugative transfer system pilin TraA -
F3Y16_RS23745 (F3Y16_23755) 107862..108233 - 372 WP_004208838 TraY domain-containing protein -
F3Y16_RS23750 (F3Y16_23760) 108317..109012 - 696 WP_004178061 transcriptional regulator TraJ family protein -
F3Y16_RS23755 (F3Y16_23765) 109226..109618 - 393 WP_004178062 conjugal transfer relaxosome DNA-binding protein TraM -
F3Y16_RS23760 (F3Y16_23770) 110052..110537 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
F3Y16_RS23765 (F3Y16_23775) 110570..110899 - 330 WP_011977736 DUF5983 family protein -
F3Y16_RS23770 (F3Y16_23780) 110932..111753 - 822 WP_004178064 DUF932 domain-containing protein -
F3Y16_RS23790 (F3Y16_23800) 112587..113000 - 414 WP_004152722 helix-turn-helix domain-containing protein -
F3Y16_RS23795 (F3Y16_23805) 113001..113279 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
F3Y16_RS23800 (F3Y16_23810) 113269..113589 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
F3Y16_RS23805 (F3Y16_23815) 113670..113894 - 225 WP_004152719 hypothetical protein -
F3Y16_RS23810 (F3Y16_23820) 113905..114117 - 213 WP_004152718 hypothetical protein -
F3Y16_RS23815 (F3Y16_23825) 114178..114534 - 357 WP_004152717 hypothetical protein -
F3Y16_RS23825 (F3Y16_23835) 115170..115520 - 351 WP_004152758 hypothetical protein -

Host bacterium

ID   1842 GenBank   NZ_VXIY01000008
Plasmid name   pKP29.8_CTXM-15 Incompatibility group   IncFII
Plasmid size   237044 bp Coordinate of oriT [Strand]   109930..109979 [+]
Host baterium   Klebsiella pneumoniae strain Kp29

Cargo genes

Drug resistance gene   blaSCO-1, aac(3)-IIa, blaTEM-1B, blaCTX-M-15
Virulence gene   -
Metal resistance gene   merA, merC, merP, merT, merR, fecD, fecE, silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoE, arsH, arsC, arsB, arsA, arsD, arsR, merE, merD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9