Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102589
Name   oriT_pKPN3 in_silico
Organism   Klebsiella pneumoniae subsp. pneumoniae strain INTEC_OZEC7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAGJVE010000023 (10111..10160 [-], 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_pKPN3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1936 GenBank   WP_015065542
Name   traI_J8647_RS25210_pKPN3 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   1565 GenBank   WP_015065541
Name   traD_J8647_RS25205_pKPN3 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: 9553..39567

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J8647_RS24980 (J8647_24975) 4942..5169 + 228 WP_004182050 hypothetical protein -
J8647_RS24985 (J8647_24980) 5261..5491 + 231 WP_001568051 hypothetical protein -
J8647_RS24990 (J8647_24985) 5543..6898 + 1356 WP_004182052 DUF3560 domain-containing protein -
J8647_RS24995 (J8647_24990) 6946..7509 + 564 WP_004182054 methyltransferase -
J8647_RS25000 (J8647_24995) 8337..9158 + 822 WP_004182076 DUF932 domain-containing protein -
J8647_RS25005 (J8647_25000) 9191..9520 + 330 WP_011977736 DUF5983 family protein -
J8647_RS25010 (J8647_25005) 9553..10038 - 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
J8647_RS25015 (J8647_25010) 10429..10845 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
J8647_RS25020 (J8647_25015) 11045..11764 + 720 WP_016831034 conjugal transfer protein TrbJ -
J8647_RS25025 (J8647_25020) 11897..12103 + 207 WP_171773970 TraY domain-containing protein -
J8647_RS25030 (J8647_25025) 12165..12533 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
J8647_RS25035 (J8647_25030) 12547..12852 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
J8647_RS25040 (J8647_25035) 12872..13438 + 567 WP_016831035 type IV conjugative transfer system protein TraE traE
J8647_RS25045 (J8647_25040) 13425..14165 + 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
J8647_RS25050 (J8647_25045) 14165..15589 + 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
J8647_RS25060 (J8647_25055) 15582..16178 + 597 Protein_20 conjugal transfer pilus-stabilizing protein TraP -
J8647_RS25065 (J8647_25060) 16201..16785 + 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
J8647_RS25070 (J8647_25065) 16917..17327 + 411 WP_016831039 hypothetical protein -
J8647_RS25075 (J8647_25070) 17332..17621 + 290 Protein_23 hypothetical protein -
J8647_RS25080 (J8647_25075) 17645..17863 + 219 WP_014386199 hypothetical protein -
J8647_RS25085 (J8647_25080) 17864..18175 + 312 WP_014386200 hypothetical protein -
J8647_RS25090 (J8647_25085) 18242..18646 + 405 WP_016831042 hypothetical protein -
J8647_RS25095 (J8647_25090) 18689..19078 + 390 WP_023158009 hypothetical protein -
J8647_RS25100 (J8647_25095) 19086..19484 + 399 WP_023158008 hypothetical protein -
J8647_RS25105 (J8647_25100) 19556..22195 + 2640 WP_023158007 type IV secretion system protein TraC virb4
J8647_RS25110 (J8647_25105) 22195..22584 + 390 WP_004167468 type-F conjugative transfer system protein TrbI -
J8647_RS25115 (J8647_25110) 22584..23219 + 636 WP_023158006 type-F conjugative transfer system protein TraW traW
J8647_RS25120 (J8647_25115) 23254..23655 + 402 WP_023158005 hypothetical protein -
J8647_RS25125 (J8647_25120) 23652..24641 + 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
J8647_RS25130 (J8647_25125) 24662..24838 + 177 WP_162866177 hypothetical protein -
J8647_RS25135 (J8647_25130) 24917..25564 + 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
J8647_RS25140 (J8647_25135) 25623..27578 + 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
J8647_RS25145 (J8647_25140) 27610..27864 + 255 WP_015065558 conjugal transfer protein TrbE -
J8647_RS25150 (J8647_25145) 27842..28090 + 249 WP_004152675 hypothetical protein -
J8647_RS25155 (J8647_25150) 28103..28429 + 327 WP_015065534 hypothetical protein -
J8647_RS25160 (J8647_25155) 28450..29202 + 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
J8647_RS25165 (J8647_25160) 29213..29452 + 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
J8647_RS25170 (J8647_25165) 29424..29981 + 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
J8647_RS25175 (J8647_25170) 30027..30470 + 444 WP_023158001 F-type conjugal transfer protein TrbF -
J8647_RS25180 (J8647_25175) 30448..31827 + 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
J8647_RS25185 (J8647_25180) 31827..34670 + 2844 WP_023157999 conjugal transfer mating-pair stabilization protein TraG traG
J8647_RS25190 (J8647_25185) 34681..35205 + 525 WP_015065538 hypothetical protein -
J8647_RS25195 (J8647_25190) 35514..36245 + 732 WP_032329926 conjugal transfer complement resistance protein TraT -
J8647_RS25200 (J8647_25195) 36437..37126 + 690 WP_015065540 hypothetical protein -
J8647_RS25205 (J8647_25200) 37255..39567 + 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3033 GenBank   NZ_JAGJVE010000023
Plasmid name   pKPN3 Incompatibility group   IncFII
Plasmid size   51920 bp Coordinate of oriT [Strand]   10111..10160 [-]
Host baterium   Klebsiella pneumoniae subsp. pneumoniae strain INTEC_OZEC7

Cargo genes

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