Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101411
Name   oriT_NICU_3_P1|unnamed1 in_silico
Organism   Klebsiella pneumoniae strain NICU_3_P1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SPTY01000002 (211788..211837 [+], 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_NICU_3_P1|unnamed1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1287 GenBank   WP_029498346
Name   traI_E4W56_RS26495_NICU_3_P1|unnamed1 insolico UniProt ID   A0A2R4NEL5
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190742.66 Da        Isoelectric Point: 6.1403

>WP_029498346.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELLEAAGPDASLKSRDVAALDTRKSKEAIDPAENMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETAMVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLLEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRIWAEPAPVAPVPQTGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

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

(576-628)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(11-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   900 GenBank   WP_048255491
Name   traD_E4W56_RS26500_NICU_3_P1|unnamed1 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 84914.98 Da        Isoelectric Point: 5.0560

>WP_048255491.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYAAWLADEQTQRDMQRREEVNINHNHRHDEQDDVEIGGNI

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 182407..212395

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
E4W56_RS26500 (E4W56_26500) 182407..184689 - 2283 WP_048255491 type IV conjugative transfer system coupling protein TraD virb4
E4W56_RS26505 (E4W56_26505) 184816..185505 - 690 WP_014343485 hypothetical protein -
E4W56_RS26510 (E4W56_26510) 185698..186429 - 732 WP_013214036 conjugal transfer complement resistance protein TraT -
E4W56_RS26515 (E4W56_26515) 186680..187282 - 603 WP_013214035 conjugal transfer protein TraS -
E4W56_RS26520 (E4W56_26520) 187305..190127 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
E4W56_RS26525 (E4W56_26525) 190127..191506 - 1380 WP_074160414 conjugal transfer pilus assembly protein TraH traH
E4W56_RS26530 (E4W56_26530) 191484..191927 - 444 WP_013214032 F-type conjugal transfer protein TrbF -
E4W56_RS26535 (E4W56_26535) 191973..192530 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
E4W56_RS26540 (E4W56_26540) 192502..192741 - 240 WP_032442642 type-F conjugative transfer system pilin chaperone TraQ -
E4W56_RS26545 (E4W56_26545) 192752..193504 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
E4W56_RS26550 (E4W56_26550) 193525..193851 - 327 WP_013214030 hypothetical protein -
E4W56_RS26555 (E4W56_26555) 193864..194112 - 249 WP_013214029 hypothetical protein -
E4W56_RS26560 (E4W56_26560) 194090..194344 - 255 WP_004152674 conjugal transfer protein TrbE -
E4W56_RS26565 (E4W56_26565) 194376..196331 - 1956 WP_180813241 type-F conjugative transfer system mating-pair stabilization protein TraN traN
E4W56_RS26570 (E4W56_26570) 196390..197037 - 648 WP_032439622 type-F conjugative transfer system pilin assembly protein TrbC trbC
E4W56_RS26575 (E4W56_26575) 197313..198302 - 990 WP_032439620 conjugal transfer pilus assembly protein TraU traU
E4W56_RS26580 (E4W56_26580) 198299..198700 - 402 WP_016831047 hypothetical protein -
E4W56_RS26585 (E4W56_26585) 198735..199370 - 636 WP_020325113 type-F conjugative transfer system protein TraW traW
E4W56_RS26590 (E4W56_26590) 199370..199759 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
E4W56_RS26595 (E4W56_26595) 199759..202398 - 2640 WP_180813240 type IV secretion system protein TraC virb4
E4W56_RS26600 (E4W56_26600) 202470..202868 - 399 WP_072159473 hypothetical protein -
E4W56_RS26605 (E4W56_26605) 202876..203265 - 390 WP_065799586 hypothetical protein -
E4W56_RS26610 (E4W56_26610) 203308..203712 - 405 WP_016831042 hypothetical protein -
E4W56_RS26615 (E4W56_26615) 203779..204091 - 313 Protein_227 hypothetical protein -
E4W56_RS26620 (E4W56_26620) 204092..204310 - 219 WP_014386199 hypothetical protein -
E4W56_RS26625 (E4W56_26625) 204334..204624 - 291 WP_014386198 hypothetical protein -
E4W56_RS26630 (E4W56_26630) 204629..205039 - 411 WP_014386197 hypothetical protein -
E4W56_RS26635 (E4W56_26635) 205170..205754 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
E4W56_RS26640 (E4W56_26640) 205801..206373 - 573 WP_014386195 conjugal transfer pilus-stabilizing protein TraP -
E4W56_RS26645 (E4W56_26645) 206366..207790 - 1425 WP_014386194 F-type conjugal transfer pilus assembly protein TraB traB
E4W56_RS26650 (E4W56_26650) 207790..208530 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
E4W56_RS26655 (E4W56_26655) 208517..209083 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
E4W56_RS26660 (E4W56_26660) 209103..209408 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
E4W56_RS26665 (E4W56_26665) 209422..209790 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
E4W56_RS26670 (E4W56_26670) 209852..210058 - 207 WP_171773970 TraY domain-containing protein -
E4W56_RS26675 (E4W56_26675) 210191..210910 - 720 WP_014386192 conjugal transfer protein -
E4W56_RS26680 (E4W56_26680) 211103..211519 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
E4W56_RS26685 (E4W56_26685) 211910..212395 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
E4W56_RS26690 (E4W56_26690) 212428..212757 - 330 WP_014386191 DUF5983 family protein -
E4W56_RS26695 (E4W56_26695) 212790..213611 - 822 WP_004182076 DUF932 domain-containing protein -
E4W56_RS26700 (E4W56_26700) 214444..214857 - 414 WP_013023817 helix-turn-helix domain-containing protein -
E4W56_RS26705 (E4W56_26705) 214858..215136 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
E4W56_RS26710 (E4W56_26710) 215126..215446 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
E4W56_RS26715 (E4W56_26715) 215527..215751 - 225 WP_014386189 hypothetical protein -
E4W56_RS26720 (E4W56_26720) 215762..215974 - 213 WP_014386188 hypothetical protein -
E4W56_RS26725 (E4W56_26725) 216036..216362 - 327 WP_014386187 hypothetical protein -

Host bacterium

ID   1855 GenBank   NZ_SPTY01000002
Plasmid name   NICU_3_P1|unnamed1 Incompatibility group   IncFIB
Plasmid size   230532 bp Coordinate of oriT [Strand]   211788..211837 [+]
Host baterium   Klebsiella pneumoniae strain NICU_3_P1

Cargo genes

Drug resistance gene   blaCTX-M-14, aac(3)-IId, blaLAP-2, qnrS1, sul1, qacE, dfrA1, tet(A)
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsR, arsD, arsA, arsB, arsC, fecE, fecD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -