Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119466
Name   oriT_Carbapenemase(IMP-4)_IncFI in_silico
Organism   Klebsiella quasipneumoniae
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050155 (91061..91110 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_Carbapenemase(IMP-4)_IncFI
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12293 GenBank   WP_022631527
Name   traI_HBA59_RS00745_Carbapenemase(IMP-4)_IncFI insolico UniProt ID   U5N3A2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190332.06 Da        Isoelectric Point: 6.2397

>WP_022631527.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQLELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   14428 GenBank   WP_015065541
Name   traD_HBA59_RS00740_Carbapenemase(IMP-4)_IncFI 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: 90503..119405

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HBA59_RS00525 86523..86879 + 357 WP_019706019 hypothetical protein -
HBA59_RS00530 86940..87152 + 213 WP_019706020 hypothetical protein -
HBA59_RS00535 87163..87387 + 225 WP_014343499 hypothetical protein -
HBA59_RS00540 87468..87788 + 321 WP_015065521 type II toxin-antitoxin system RelE/ParE family toxin -
HBA59_RS00545 87778..88056 + 279 WP_020801586 helix-turn-helix transcriptional regulator -
HBA59_RS00550 88057..88458 + 402 WP_015065522 type II toxin-antitoxin system HigA family antitoxin -
HBA59_RS00555 89287..90108 + 822 WP_004152492 DUF932 domain-containing protein -
HBA59_RS00560 90141..90470 + 330 WP_069335041 DUF5983 family protein -
HBA59_RS00565 90503..90988 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
HBA59_RS00570 91379..91795 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
HBA59_RS00575 91995..92714 + 720 WP_015065526 hypothetical protein -
HBA59_RS00580 92847..93050 + 204 WP_171486139 TraY domain-containing protein -
HBA59_RS00585 93115..93483 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HBA59_RS00590 93497..93802 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HBA59_RS00595 93822..94388 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
HBA59_RS00600 94375..95115 + 741 WP_164530159 type-F conjugative transfer system secretin TraK traK
HBA59_RS00605 95115..96539 + 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
HBA59_RS00610 96653..97237 + 585 WP_015065529 type IV conjugative transfer system lipoprotein TraV traV
HBA59_RS00615 97369..97779 + 411 WP_032329942 hypothetical protein -
HBA59_RS00620 97885..98103 + 219 WP_004152501 hypothetical protein -
HBA59_RS00625 98104..98415 + 312 WP_004152502 hypothetical protein -
HBA59_RS00630 98482..98886 + 405 WP_004152503 hypothetical protein -
HBA59_RS00635 98929..99318 + 390 WP_181370154 hypothetical protein -
HBA59_RS00640 99326..99724 + 399 WP_011977783 hypothetical protein -
HBA59_RS00645 99796..102435 + 2640 WP_004152505 type IV secretion system protein TraC virb4
HBA59_RS00650 102435..102824 + 390 WP_004152506 type-F conjugative transfer system protein TrbI -
HBA59_RS00655 102824..103450 + 627 WP_009309871 type-F conjugative transfer system protein TraW traW
HBA59_RS00660 103492..103881 + 390 WP_004194992 hypothetical protein -
HBA59_RS00665 103878..104867 + 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
HBA59_RS00670 104880..105518 + 639 WP_164530161 type-F conjugative transfer system pilin assembly protein TrbC trbC
HBA59_RS00675 105577..107532 + 1956 WP_013023827 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HBA59_RS00680 107564..107818 + 255 WP_004152674 conjugal transfer protein TrbE -
HBA59_RS00685 107796..108044 + 249 WP_004152675 hypothetical protein -
HBA59_RS00690 108057..108383 + 327 WP_004152676 hypothetical protein -
HBA59_RS00695 108404..109156 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
HBA59_RS00700 109167..109406 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HBA59_RS00705 109378..109935 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HBA59_RS00710 109981..110424 + 444 WP_004194305 F-type conjugal transfer protein TrbF -
HBA59_RS00715 110402..111781 + 1380 WP_164530163 conjugal transfer pilus assembly protein TraH traH
HBA59_RS00720 111781..114630 + 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
HBA59_RS00725 114633..115166 + 534 WP_014343486 conjugal transfer protein TraS -
HBA59_RS00730 115352..116083 + 732 WP_032329926 conjugal transfer complement resistance protein TraT -
HBA59_RS00735 116275..116964 + 690 WP_015065540 hypothetical protein -
HBA59_RS00740 117093..119405 + 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19896 GenBank   NZ_CP050155
Plasmid name   Carbapenemase(IMP-4)_IncFI Incompatibility group   IncFII
Plasmid size   130570 bp Coordinate of oriT [Strand]   91061..91110 [-]
Host baterium   Klebsiella quasipneumoniae

Cargo genes

Drug resistance gene   sul1, blaDHA-1, qnrB4, blaIMP-4, sul2, aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9