Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101263
Name   oriT_pMDR_448 in_silico
Organism   Klebsiella pneumoniae subsp. pneumoniae strain ENT448
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JADPQD010000002 (85369..85418 [-], 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_pMDR_448
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1224 GenBank   WP_004153029
Name   traI_IMZ27_RS26605_pMDR_448 insolico UniProt ID   A0A422WEA5
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190808.90 Da        Isoelectric Point: 6.2081

>WP_004153029.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1433-1555)

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

(577-629)

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

(635-714)

AAA domain (AAA_30)

(971-1157)

TrwC relaxase (TrwC)

(10-284)


  Protein structure



No available structure.




T4CP

ID   834 GenBank   WP_004152630
Name   traD_IMZ27_RS26600_pMDR_448 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: 84811..114019

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IMZ27_RS26390 (IMZ27_26390) 79967..80284 + 318 WP_014343505 hypothetical protein -
IMZ27_RS26395 (IMZ27_26395) 81125..81481 + 357 WP_014343501 hypothetical protein -
IMZ27_RS26400 (IMZ27_26400) 81542..81754 + 213 WP_014343500 hypothetical protein -
IMZ27_RS26405 (IMZ27_26405) 81765..81989 + 225 WP_014343499 hypothetical protein -
IMZ27_RS26410 (IMZ27_26410) 82070..82390 + 321 WP_014343498 type II toxin-antitoxin system RelE/ParE family toxin -
IMZ27_RS26415 (IMZ27_26415) 82380..82658 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
IMZ27_RS27680 82662..82766 + 105 Protein_110 transcriptional regulator -
IMZ27_RS26420 (IMZ27_26420) 83595..84416 + 822 WP_004152492 DUF932 domain-containing protein -
IMZ27_RS26425 (IMZ27_26425) 84449..84778 + 330 WP_013214015 DUF5983 family protein -
IMZ27_RS26430 (IMZ27_26430) 84811..85296 - 486 WP_014343495 transglycosylase SLT domain-containing protein virB1
IMZ27_RS26435 (IMZ27_26435) 85687..86103 + 417 WP_014343494 conjugal transfer relaxosome DNA-binding protein TraM -
IMZ27_RS26440 (IMZ27_26440) 86303..87040 + 738 WP_013214018 conjugal transfer protein TrbJ -
IMZ27_RS26445 (IMZ27_26445) 87155..87361 + 207 WP_171773970 TraY domain-containing protein -
IMZ27_RS26450 (IMZ27_26450) 87423..87791 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
IMZ27_RS26455 (IMZ27_26455) 87805..88110 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
IMZ27_RS26460 (IMZ27_26460) 88130..88696 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
IMZ27_RS26465 (IMZ27_26465) 88683..89423 + 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
IMZ27_RS26470 (IMZ27_26470) 89423..90847 + 1425 WP_013214020 F-type conjugal transfer pilus assembly protein TraB traB
IMZ27_RS26475 (IMZ27_26475) 90919..91503 + 585 WP_014343493 type IV conjugative transfer system lipoprotein TraV traV
IMZ27_RS26480 (IMZ27_26480) 91826..92044 + 219 WP_004195468 hypothetical protein -
IMZ27_RS26485 (IMZ27_26485) 92045..92356 + 312 WP_013214022 hypothetical protein -
IMZ27_RS26490 (IMZ27_26490) 92423..92827 + 405 WP_004197817 hypothetical protein -
IMZ27_RS26495 (IMZ27_26495) 93204..93602 + 399 WP_014343490 hypothetical protein -
IMZ27_RS26500 (IMZ27_26500) 93674..96313 + 2640 WP_013214024 type IV secretion system protein TraC virb4
IMZ27_RS26505 (IMZ27_26505) 96313..96702 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
IMZ27_RS26510 (IMZ27_26510) 96702..97337 + 636 WP_064162552 type-F conjugative transfer system protein TraW traW
IMZ27_RS26515 (IMZ27_26515) 97372..97773 + 402 WP_004194979 hypothetical protein -
IMZ27_RS26520 (IMZ27_26520) 97770..98759 + 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
IMZ27_RS26525 (IMZ27_26525) 98772..99410 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
IMZ27_RS26530 (IMZ27_26530) 99469..101424 + 1956 WP_085855703 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IMZ27_RS26535 (IMZ27_26535) 101456..101710 + 255 WP_004152674 conjugal transfer protein TrbE -
IMZ27_RS26540 (IMZ27_26540) 101688..101936 + 249 WP_004152675 hypothetical protein -
IMZ27_RS26545 (IMZ27_26545) 101949..102275 + 327 WP_004152676 hypothetical protein -
IMZ27_RS26550 (IMZ27_26550) 102296..103048 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
IMZ27_RS26555 (IMZ27_26555) 103059..103298 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
IMZ27_RS26560 (IMZ27_26560) 103270..103827 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IMZ27_RS26565 (IMZ27_26565) 103873..104316 + 444 WP_004152679 F-type conjugal transfer protein TrbF -
IMZ27_RS26570 (IMZ27_26570) 104294..105673 + 1380 WP_011977731 conjugal transfer pilus assembly protein TraH traH
IMZ27_RS26575 (IMZ27_26575) 105673..105855 + 183 Protein_142 conjugal transfer protein TraG N-terminal domain-containing protein -
IMZ27_RS26580 (IMZ27_26580) 105887..106963 - 1077 WP_000227969 IS110 family transposase -
IMZ27_RS26585 (IMZ27_26585) 107245..109896 + 2652 Protein_144 conjugal transfer mating-pair stabilization protein TraG -
IMZ27_RS26590 (IMZ27_26590) 109902..110429 + 528 WP_004153030 hypothetical protein -
IMZ27_RS26595 (IMZ27_26595) 110619..111350 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
IMZ27_RS26600 (IMZ27_26600) 111710..114019 + 2310 WP_004152630 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1707 GenBank   NZ_JADPQD010000002
Plasmid name   pMDR_448 Incompatibility group   IncR
Plasmid size   126629 bp Coordinate of oriT [Strand]   85369..85418 [-]
Host baterium   Klebsiella pneumoniae subsp. pneumoniae strain ENT448

Cargo genes

Drug resistance gene   qnrS1, blaTEM-1B, blaCTX-M-15, aac(3)-IIa, blaOXA-1, aac(6')-Ib-cr, catA1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9